# Date 2008-01-16 Time 01:37:06 PST -0800 (1200476226.14 s)
#phil __OFF__

Command line arguments: "../491.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9855
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 491

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 45.7567, 87.2539, 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: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.7567, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.95316
Completeness in resolution range: 0.937587
Completeness with d_max=infinity: 0.934813

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9790
                             d_min =   1.9532

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.7567, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.95316
Completeness in resolution range: 0.937587
Completeness with d_max=infinity: 0.934813

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9794 -  4.1803 [2193/2218]  1973   220  10.0%
  bin  2:  4.1803 -  3.3300 [2107/2127]  1898   209   9.9%
  bin  3:  3.3300 -  2.9126 [2083/2102]  1876   207   9.9%
  bin  4:  2.9126 -  2.6479 [2056/2086]  1845   211  10.3%
  bin  5:  2.6479 -  2.4590 [2063/2082]  1864   199   9.6%
  bin  6:  2.4590 -  2.3146 [2042/2067]  1835   207  10.1%
  bin  7:  2.3146 -  2.1990 [2004/2032]  1800   204  10.2%
  bin  8:  2.1990 -  2.1036 [2043/2079]  1832   211  10.3%
  bin  9:  2.1036 -  2.0228 [2018/2060]  1827   191   9.5%
  bin 10:  2.0228 -  1.9532 [ 980/2040]   880   100  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_491/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: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 27
        2.22 -     2.89: 1353
        2.89 -     3.56: 4538
        3.56 -     4.23: 9306
        4.23 -     4.90: 13364
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.546 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.726 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28583 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_491/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_491/model_refine_001.geo

CPU time processing inputs: 7.92


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 45.75675 87.2539 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 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4964   r_free= 0.4907   ksol= 0.00   Bsol= 0.00   scale= 0.784    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.300754                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.6630 0.99   1423  157 0.4272 0.4258      6.6442      6.6877|
|  2:  4.6630 -  3.7198 0.99   1375  154 0.4322 0.4122      6.8495      6.8025|
|  3:  3.7198 -  3.2551 0.99   1344  149 0.4594 0.3998      6.7023      6.6536|
|  4:  3.2551 -  2.9600 0.99   1341  150 0.4859 0.4705      6.5538      6.5202|
|  5:  2.9600 -  2.7492 0.99   1320  149 0.5318 0.5315      6.3759      6.4085|
|  6:  2.7492 -  2.5880 0.99   1324  145 0.5265 0.5508      6.2861      6.2177|
|  7:  2.5880 -  2.4590 0.99   1329  142 0.5196 0.5340      6.2505      6.2025|
|  8:  2.4590 -  2.3524 0.98   1303  152 0.5447 0.5023      6.1869      6.1802|
|  9:  2.3524 -  2.2621 0.98   1291  142 0.5354 0.5503      6.1279      6.1921|
| 10:  2.2621 -  2.1843 1.00   1314  148 0.5369 0.5547      6.0954      6.1067|
| 11:  2.1843 -  2.1162 0.98   1303  145 0.5124 0.5128      6.0396      6.0226|
| 12:  2.1162 -  2.0559 0.98   1289  137 0.5235 0.5709      5.9454      5.9866|
| 13:  2.0559 -  2.0019 0.96   1259  144 0.5577 0.5423      5.8894      5.8055|
| 14:  2.0019 -  1.9532 0.31    415   45 0.5430 0.4772      5.8726      5.8568|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9794 -  4.6630  1423   157  0.64  39.73   0.78     0.69      92305.98|
|  2:  4.6630 -  3.7198  1375   154  0.67  37.90   0.85     0.76     122045.07|
|  3:  3.7198 -  3.2551  1344   149  0.56  47.03   0.84     0.70     126170.48|
|  4:  3.2551 -  2.9600  1341   150  0.46  55.01   0.78     0.56     112995.44|
|  5:  2.9600 -  2.7492  1320   149  0.33  64.79   0.72     0.42      92801.90|
|  6:  2.7492 -  2.5880  1324   145  0.29  68.48   0.71     0.34      82930.11|
|  7:  2.5880 -  2.4590  1329   142  0.22  73.84   0.75     0.26      77407.76|
|  8:  2.4590 -  2.3524  1303   152  0.20  74.73   0.72     0.25      70165.52|
|  9:  2.3524 -  2.2621  1291   142  0.21  74.46   0.73     0.26      63632.53|
| 10:  2.2621 -  2.1843  1314   148  0.26  70.60   0.74     0.31      53572.28|
| 11:  2.1843 -  2.1162  1303   145  0.27  69.78   0.78     0.34      51444.92|
| 12:  2.1162 -  2.0559  1289   137  0.26  71.00   0.76     0.34      46235.03|
| 13:  2.0559 -  2.0019  1259   144  0.24  72.14   0.71     0.32      41329.42|
| 14:  2.0019 -  1.9532   415    45  0.28  69.61   0.73     0.32      32887.54|
|alpha:            min =        0.25 max =            0.76 mean =         0.43|
|beta:             min =    32887.54 max =       126170.48 mean =     78940.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           90.00 mean =        62.87|
|phase err.(test): min =        0.00 max =           89.98 mean =        63.14|
|-----------------------------------------------------------------------------|

============================== 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 = 21.278888             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.934   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.850510              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.836   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       36 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      175 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      721 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1510 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2671 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3979 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5127 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6613 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7810 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.281 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.416 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.596)------------------------------------------|
|    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 = 11.596)------------------------------------------|
|    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 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5007   r_free= 0.4893   ksol= 0.00   Bsol= 0.00   scale= 0.755    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.301627                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4879   r_free= 0.4774   ksol= 0.37   Bsol= 20.00   scale= 0.967   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.91,9.29,8.26,0.00,0.00,0.00); trace/3= 7.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.297044                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.186748             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.254   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.698032              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.061   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4879      final r-factor (work) = 0.4243          |
| start r-factor (free) = 0.4774      final r-factor (free) = 0.4488          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.2302 = 16.19 * 0.50 * 6.2951 + 1.00 * 53.2813                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.6893 = 16.19 * 0.50 * 6.2451 + 1.00 * 0.1456                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4243      final r-factor (work) = 0.3860          |
| start r-factor (free) = 0.4488      final r-factor (free) = 0.4500          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6188 = 1.70 * 1.00 * 6.2451 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5348 = 1.70 * 1.00 * 6.1926 + 1.00 * 0.0196                              |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.596)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.79   14.49    None  None   None       |
|    all(noH): 2823   0      0.00    62.79   14.49    None  None   None       |
|    Sol.    : 438    0      0.00    61.37   21.32    None  None   None       |
|    Mac.    : 2385   0      0.00    62.79   13.23    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.279:  649   |   5:    31.395 -  37.674:  117        |
|      1:     6.279 -  12.558:  755   |   6:    37.674 -  43.953:   57        |
|      2:    12.558 -  18.837:  603   |   7:    43.953 -  50.232:   21        |
|      3:    18.837 -  25.116:  385   |   8:    50.232 -  56.511:   12        |
|      4:    25.116 -  31.395:  216   |   9:    56.511 -  62.790:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3860 r_free = 0.4500             target_work(ml) = 6.188         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3856 r_free = 0.4505             target_work(ml) = 6.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3856   r_free= 0.4505   ksol= 0.37   Bsol= 20.00   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.91,9.29,8.26,0.00,0.00,0.00); trace/3= 7.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.187613                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3843   r_free= 0.4471   ksol= 0.36   Bsol= 37.83   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.03,5.63,4.83,0.00,0.00,0.00); trace/3= 4.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.189117                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.275131             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.057  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.857398              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.635  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3843      final r-factor (work) = 0.3343          |
| start r-factor (free) = 0.4471      final r-factor (free) = 0.4175          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.1318 = 12.28 * 0.50 * 6.1891 + 1.00 * 0.1456                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.7307 = 12.28 * 0.50 * 6.1316 + 1.00 * 0.0978                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3343      final r-factor (work) = 0.3221          |
| start r-factor (free) = 0.4175      final r-factor (free) = 0.4095          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2847 = 0.86 * 1.00 * 6.1316 + 1.00 * 0.0275                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2644 = 0.86 * 1.00 * 6.0800 + 1.00 * 0.0514                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.596)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.03   14.42    None  None   None       |
|    all(noH): 2823   0      0.00    91.03   14.42    None  None   None       |
|    Sol.    : 438    0      0.00    61.48   23.14    None  None   None       |
|    Mac.    : 2385   0      0.00    91.03   12.81    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 -   9.103: 1024   |   5:    45.517 -  54.621:   23        |
|      1:     9.103 -  18.207:  965   |   6:    54.621 -  63.724:    7        |
|      2:    18.207 -  27.310:  510   |   7:    63.724 -  72.827:    0        |
|      3:    27.310 -  36.414:  221   |   8:    72.827 -  81.931:    0        |
|      4:    36.414 -  45.517:   72   |   9:    81.931 -  91.034:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3221 r_free = 0.4095             target_work(ml) = 6.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3220 r_free = 0.4095             target_work(ml) = 6.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3220   r_free= 0.4095   ksol= 0.36   Bsol= 37.83   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.03,5.63,4.83,0.00,0.00,0.00); trace/3= 4.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.070499                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3229   r_free= 0.4066   ksol= 0.34   Bsol= 37.83   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.44,3.69,3.85,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.070151                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.736469              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.383  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.056514              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.889   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3229      final r-factor (work) = 0.2774          |
| start r-factor (free) = 0.4066      final r-factor (free) = 0.3513          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.6168 = 7.74 * 0.50 * 6.0801 + 1.00 * 0.0975                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.3598 = 7.74 * 0.50 * 6.0166 + 1.00 * 0.0863                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2774      final r-factor (work) = 0.2523          |
| start r-factor (free) = 0.3513      final r-factor (free) = 0.3435          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.4084 = 2.06 * 1.00 * 6.0166 + 1.00 * 0.0352                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1592 = 2.06 * 1.00 * 5.9021 + 1.00 * 0.0214                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.596)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.27   16.21    None  None   None       |
|    all(noH): 2823   0      0.00    83.27   16.21    None  None   None       |
|    Sol.    : 438    0      0.00    83.27   34.26    None  None   None       |
|    Mac.    : 2385   0      0.00    76.17   12.90    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 -   8.327: 1041   |   5:    41.635 -  49.962:  106        |
|      1:     8.327 -  16.654:  747   |   6:    49.962 -  58.289:   58        |
|      2:    16.654 -  24.981:  427   |   7:    58.289 -  66.616:   28        |
|      3:    24.981 -  33.308:  257   |   8:    66.616 -  74.943:   15        |
|      4:    33.308 -  41.635:  138   |   9:    74.943 -  83.270:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2523 r_free = 0.3435             target_work(ml) = 5.884         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2519 r_free = 0.3432             target_work(ml) = 5.883         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2519   r_free= 0.3432   ksol= 0.34   Bsol= 37.83   scale= 1.060   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.44,3.69,3.85,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.882893                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2511   r_free= 0.3428   ksol= 0.32   Bsol= 42.05   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,2.09,2.87,0.00,0.00,0.00); trace/3= 2.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.880891                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.153583              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.884   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.490345              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.467  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2511      final r-factor (work) = 0.2173          |
| start r-factor (free) = 0.3428      final r-factor (free) = 0.2973          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3405 = 4.15 * 0.50 * 5.9005 + 1.00 * 0.0863                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1570 = 4.15 * 0.50 * 5.8241 + 1.00 * 0.0616                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2173      final r-factor (work) = 0.2017          |
| start r-factor (free) = 0.2973      final r-factor (free) = 0.2750          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7010 = 1.49 * 1.00 * 5.8241 + 1.00 * 0.0211                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5428 = 1.49 * 1.00 * 5.7198 + 1.00 * 0.0184                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.596)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.01   15.93    None  None   None       |
|    all(noH): 2823   0      0.00    93.01   15.93    None  None   None       |
|    Sol.    : 438    0      1.77    93.01   39.65    None  None   None       |
|    Mac.    : 2385   0      0.00    87.41   11.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.301: 1332   |   5:    46.507 -  55.808:   97        |
|      1:     9.301 -  18.603:  688   |   6:    55.808 -  65.110:   55        |
|      2:    18.603 -  27.904:  282   |   7:    65.110 -  74.411:   34        |
|      3:    27.904 -  37.206:  182   |   8:    74.411 -  83.713:    6        |
|      4:    37.206 -  46.507:  142   |   9:    83.713 -  93.014:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2017 r_free = 0.2750             target_work(ml) = 5.679         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2014 r_free = 0.2750             target_work(ml) = 5.678         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2014   r_free= 0.2750   ksol= 0.32   Bsol= 42.05   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,2.09,2.87,0.00,0.00,0.00); trace/3= 2.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.677954                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2016   r_free= 0.2750   ksol= 0.33   Bsol= 51.25   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.26,1.37,2.84,0.00,0.00,0.00); trace/3= 1.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.678655                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.147650              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.262  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.527283              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.578  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2016      final r-factor (work) = 0.1612          |
| start r-factor (free) = 0.2750      final r-factor (free) = 0.2258          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7829 = 5.15 * 0.50 * 5.7196 + 1.00 * 0.0616                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4542 = 5.15 * 0.50 * 5.5892 + 1.00 * 0.0687                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1612      final r-factor (work) = 0.1463          |
| start r-factor (free) = 0.2258      final r-factor (free) = 0.2080          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 30.9113 = 5.53 * 1.00 * 5.5892 + 1.00 * 0.0184                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 30.1035 = 5.53 * 1.00 * 5.4431 + 1.00 * 0.0178                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.596)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.52  15.79    None  None   None       |
|    all(noH): 2823   0      0.00    101.52  15.79    None  None   None       |
|    Sol.    : 438    0      2.98    101.52  44.74    None  None   None       |
|    Mac.    : 2385   0      0.00    100.60  10.47    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 -  10.152: 1595   |   5:    50.760 -  60.912:   96        |
|      1:    10.152 -  20.304:  615   |   6:    60.912 -  71.064:   71        |
|      2:    20.304 -  30.456:  182   |   7:    71.064 -  81.216:   30        |
|      3:    30.456 -  40.608:  112   |   8:    81.216 -  91.368:   18        |
|      4:    40.608 -  50.760:   98   |   9:    91.368 - 101.520:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1463 r_free = 0.2080             target_work(ml) = 5.395         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1462 r_free = 0.2080             target_work(ml) = 5.395         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1462   r_free= 0.2080   ksol= 0.33   Bsol= 51.25   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.26,1.37,2.84,0.00,0.00,0.00); trace/3= 1.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.394880                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.6630 0.99   1423  157 0.1015 0.1441      5.4568      5.6989|
|  2:  4.6630 -  3.7198 0.99   1375  154 0.0980 0.1469       5.591      5.8891|
|  3:  3.7198 -  3.2551 0.99   1344  149 0.1350 0.1911      5.6877      6.0063|
|  4:  3.2551 -  2.9600 0.99   1341  150 0.1630 0.2186      5.7001      5.8669|
|  5:  2.9600 -  2.7492 0.99   1320  149 0.1710 0.2289        5.57      5.8309|
|  6:  2.7492 -  2.5880 0.99   1324  145 0.1627 0.2659       5.447      5.7225|
|  7:  2.5880 -  2.4590 0.99   1329  142 0.1672 0.2116       5.413      5.5698|
|  8:  2.4590 -  2.3524 0.98   1303  152 0.1665 0.2279       5.365      5.6077|
|  9:  2.3524 -  2.2621 0.98   1291  142 0.1648 0.2536      5.3139      5.5963|
| 10:  2.2621 -  2.1843 1.00   1314  148 0.1476 0.2307      5.2127      5.4404|
| 11:  2.1843 -  2.1162 0.98   1303  145 0.1547 0.2516      5.2167      5.5888|
| 12:  2.1162 -  2.0559 0.98   1289  137 0.1655 0.2520      5.1714      5.4812|
| 13:  2.0559 -  2.0019 0.96   1259  144 0.1601 0.1992      5.0744      5.2013|
| 14:  2.0019 -  1.9532 0.31    415   45 0.1528 0.2360      4.9651      5.2336|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9794 -  4.6630  1423   157  0.92  11.32   0.97     0.95       9810.06|
|  2:  4.6630 -  3.7198  1375   154  0.93  10.95   1.05     1.03      13419.11|
|  3:  3.7198 -  3.2551  1344   149  0.89  16.23   1.07     1.06      17095.01|
|  4:  3.2551 -  2.9600  1341   150  0.86  20.06   1.04     1.00      18200.59|
|  5:  2.9600 -  2.7492  1320   149  0.85  21.64   1.02     0.99      14546.35|
|  6:  2.7492 -  2.5880  1324   145  0.84  22.82   1.00     0.94      12079.75|
|  7:  2.5880 -  2.4590  1329   142  0.84  22.31   1.02     0.98      11012.02|
|  8:  2.4590 -  2.3524  1303   152  0.83  23.38   1.01     0.97      10487.14|
|  9:  2.3524 -  2.2621  1291   142  0.84  22.59   1.00     0.94       9266.48|
| 10:  2.2621 -  2.1843  1314   148  0.84  22.61   1.02     0.96       8006.18|
| 11:  2.1843 -  2.1162  1303   145  0.83  23.52   1.02     0.93       8015.96|
| 12:  2.1162 -  2.0559  1289   137  0.83  23.76   1.03     1.01       7681.16|
| 13:  2.0559 -  2.0019  1259   144  0.83  24.06   1.01     0.96       6216.37|
| 14:  2.0019 -  1.9532   415    45  0.87  19.67   1.01     0.96       4459.88|
|alpha:            min =        0.93 max =            1.06 mean =         0.98|
|beta:             min =     4459.88 max =        18200.59 mean =     11105.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.96 mean =        20.27|
|phase err.(test): min =        0.00 max =           88.81 mean =        19.18|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1466   r_free= 0.2078   ksol= 0.32   Bsol= 52.89   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-0.64,1.14,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.393729                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1466   r_free= 0.2078   ksol= 0.32   Bsol= 52.89   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-0.64,1.14,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.393729                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.6630 0.99   1423  157 0.1020 0.1400      5.4393       5.685|
|  2:  4.6630 -  3.7198 0.99   1375  154 0.0995 0.1465      5.5909        5.89|
|  3:  3.7198 -  3.2551 0.99   1344  149 0.1355 0.1902      5.6913      6.0057|
|  4:  3.2551 -  2.9600 0.99   1341  150 0.1632 0.2192      5.7014        5.87|
|  5:  2.9600 -  2.7492 0.99   1320  149 0.1710 0.2281        5.57      5.8279|
|  6:  2.7492 -  2.5880 0.99   1324  145 0.1623 0.2666      5.4461      5.7236|
|  7:  2.5880 -  2.4590 0.99   1329  142 0.1672 0.2116      5.4132      5.5705|
|  8:  2.4590 -  2.3524 0.98   1303  152 0.1660 0.2282      5.3647      5.6075|
|  9:  2.3524 -  2.2621 0.98   1291  142 0.1647 0.2524      5.3141      5.5943|
| 10:  2.2621 -  2.1843 1.00   1314  148 0.1473 0.2316      5.2124      5.4438|
| 11:  2.1843 -  2.1162 0.98   1303  145 0.1545 0.2522      5.2169      5.5915|
| 12:  2.1162 -  2.0559 0.98   1289  137 0.1654 0.2522      5.1719      5.4815|
| 13:  2.0559 -  2.0019 0.96   1259  144 0.1602 0.1984      5.0739      5.1996|
| 14:  2.0019 -  1.9532 0.31    415   45 0.1531 0.2365      4.9639      5.2323|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9794 -  4.6630  1423   157  0.93  10.91   0.97     0.95       9120.44|
|  2:  4.6630 -  3.7198  1375   154  0.93  10.75   1.04     1.03      13079.10|
|  3:  3.7198 -  3.2551  1344   149  0.89  16.22   1.07     1.06      17169.00|
|  4:  3.2551 -  2.9600  1341   150  0.86  20.09   1.04     0.99      18268.83|
|  5:  2.9600 -  2.7492  1320   149  0.85  21.65   1.02     0.98      14539.33|
|  6:  2.7492 -  2.5880  1324   145  0.84  22.82   0.99     0.93      12072.97|
|  7:  2.5880 -  2.4590  1329   142  0.84  22.32   1.01     0.97      11026.99|
|  8:  2.4590 -  2.3524  1303   152  0.83  23.39   1.00     0.96      10501.52|
|  9:  2.3524 -  2.2621  1291   142  0.84  22.59   1.00     0.94       9272.32|
| 10:  2.2621 -  2.1843  1314   148  0.84  22.62   1.01     0.95       8021.85|
| 11:  2.1843 -  2.1162  1303   145  0.83  23.56   1.01     0.92       8042.65|
| 12:  2.1162 -  2.0559  1289   137  0.83  23.80   1.02     0.99       7702.52|
| 13:  2.0559 -  2.0019  1259   144  0.83  24.05   1.00     0.95       6212.21|
| 14:  2.0019 -  1.9532   415    45  0.87  19.57   0.99     0.95       4433.10|
|alpha:            min =        0.92 max =            1.06 mean =         0.97|
|beta:             min =     4433.10 max =        18268.83 mean =     11039.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.92 mean =        20.23|
|phase err.(test): min =        0.00 max =           89.91 mean =        19.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.596)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.64    103.16  17.43    None  None   None       |
|    all(noH): 2823   0      1.64    103.16  17.43    None  None   None       |
|    Sol.    : 438    0      4.62    103.16  46.39    None  None   None       |
|    Mac.    : 2385   0      1.64    102.24  12.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.641 -  11.793: 1595   |   5:    52.401 -  62.553:   96        |
|      1:    11.793 -  21.945:  615   |   6:    62.553 -  72.705:   71        |
|      2:    21.945 -  32.097:  182   |   7:    72.705 -  82.857:   30        |
|      3:    32.097 -  42.249:  112   |   8:    82.857 -  93.009:   18        |
|      4:    42.249 -  52.401:   98   |   9:    93.009 - 103.161:    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)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.290 - 5.688
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 338 from: 341
   mapped sites are within: 0.729 - 5.688

peak=    7.569 closest distance to " CB  VAL A 230 " =    1.444
peak=    7.403 closest distance to " O   HOH Z 268 " =    1.253
peak=    7.285 closest distance to " O   HOH Z 390 " =    1.227
peak=    7.159 closest distance to " CB  VAL A 296 " =    1.422
peak=    6.521 closest distance to " O   HOH Z 130 " =    2.096
peak=    6.473 closest distance to " CG  LEU A   5 " =    1.494
peak=    6.076 closest distance to " CD1AILE A 234 " =    1.040
peak=    5.680 closest distance to " CG  ARG A 138 " =    1.177
peak=    5.650 closest distance to " O   HOH Z 105 " =    1.294
peak=    5.606 closest distance to " NH1 ARG A 138 " =    1.001
peak=    5.564 closest distance to " O   HOH Z 415 " =    1.341
peak=    5.545 closest distance to " NE2 GLN A  11 " =    1.240
peak=    5.489 closest distance to " O   HOH Z 127 " =    1.203
peak=    5.373 closest distance to " OD1 ASP A  27 " =    1.040
peak=    5.341 closest distance to " O   HOH Z 385 " =    1.809
peak=    5.340 closest distance to " O   HOH Z 422 " =    1.248
peak=    5.314 closest distance to " O   HOH Z 350 " =    1.648
peak=    5.206 closest distance to " O   HOH Z 139 " =    1.693
peak=    5.181 closest distance to " O   HOH Z 124 " =    1.670
peak=    5.162 closest distance to " O   HOH Z 375 " =    1.189
peak=    5.143 closest distance to " O   HOH Z  77 " =    1.176
peak=    5.129 closest distance to " O   HOH Z  65 " =    2.051
peak=    5.060 closest distance to " NH2 ARG A  56 " =    2.171
peak=    5.032 closest distance to " O   HOH Z 418 " =    1.592
peak=    4.957 closest distance to " O   HOH Z  66 " =    1.365
peak=    4.931 closest distance to " CD  ARG A 138 " =    0.876
peak=    4.913 closest distance to " O   HOH Z 359 " =    1.439
peak=    4.890 closest distance to " O   HOH Z 403 " =    1.637
peak=    4.842 closest distance to " O   VAL A  72 " =    0.978
peak=    4.824 closest distance to " O   HOH Z  63 " =    1.731
peak=    4.792 closest distance to " O   HOH Z  69 " =    2.374
peak=    4.729 closest distance to " NZ BLYS A 290 " =    1.074
peak=    4.722 closest distance to " CG2 ILE A 120 " =    0.924
peak=    4.719 closest distance to " O   HOH Z 142 " =    2.012
peak=    4.715 closest distance to " O   HOH Z 245 " =    1.066
peak=    4.710 closest distance to " O   HOH Z 293 " =    1.487
peak=    4.690 closest distance to " O   HOH Z 232 " =    2.173
peak=    4.676 closest distance to " O   HOH Z  46 " =    1.237
peak=    4.619 closest distance to " O   HOH Z 425 " =    1.537
peak=    4.608 closest distance to " O   HOH Z  59 " =    1.693
peak=    4.603 closest distance to " O   HOH Z 417 " =    2.078
peak=    4.560 closest distance to " O   HOH Z 287 " =    1.625
peak=    4.557 closest distance to " O   HOH Z 427 " =    2.128
peak=    4.533 closest distance to " O   HOH Z  24 " =    1.884
peak=    4.510 closest distance to " O   HOH Z 428 " =    1.657
peak=    4.478 closest distance to " O   HOH Z 428 " =    1.279
peak=    4.477 closest distance to " O   HOH Z 410 " =    1.464
peak=    4.452 closest distance to " O   HOH Z  43 " =    1.495
peak=    4.425 closest distance to " CB  ARG A 275 " =    1.274
peak=    4.416 closest distance to " O   HOH Z 225 " =    1.997
peak=    4.386 closest distance to " CG  LEU A 228 " =    1.107
peak=    4.383 closest distance to " CB  PRO A  54 " =    1.222
peak=    4.351 closest distance to " CB  VAL A 230 " =    1.196
peak=    4.350 closest distance to " O   HOH Z  15 " =    0.941
peak=    4.345 closest distance to " O   HOH Z  21 " =    1.294
peak=    4.342 closest distance to " O   PRO A 198 " =    1.321
peak=    4.334 closest distance to " O   HOH Z   9 " =    2.099
peak=    4.308 closest distance to " CA  ILE A 234 " =    1.131
peak=    4.302 closest distance to " O   HOH Z 214 " =    1.311
peak=    4.279 closest distance to " O   HOH Z 331 " =    1.258
peak=    4.232 closest distance to " O   HOH Z   7 " =    1.851
peak=    4.231 closest distance to " O   HOH Z 422 " =    2.362
peak=    4.173 closest distance to " O   HOH Z 360 " =    1.131
peak=    4.158 closest distance to " N   ARG A 275 " =    0.827
peak=    4.139 closest distance to " O   HOH Z 416 " =    1.420
peak=    4.108 closest distance to " O   HOH Z 427 " =    1.043
peak=    4.093 closest distance to " OG ASER A 258 " =    2.897
peak=    4.087 closest distance to " CB  LYS A 290 " =    0.973
peak=    4.070 closest distance to " CG2 ILE A 234 " =    0.769
peak=    4.066 closest distance to " O   HOH Z 298 " =    1.777
peak=    4.056 closest distance to " O   HOH Z 112 " =    1.354
peak=    4.029 closest distance to " O   HOH Z 103 " =    0.974
peak=    4.009 closest distance to " CD1 LEU A   5 " =    1.279
peak=    4.005 closest distance to " CE2 PHE A  16 " =    1.052
peak=    3.996 closest distance to " CB  ASN A  39 " =    0.810
peak=    3.990 closest distance to " O  BHOH Z  74 " =    1.165
peak=    3.988 closest distance to " O   HOH Z  53 " =    2.252
peak=    3.986 closest distance to " CB  TRP A 266 " =    1.038
peak=    3.981 closest distance to " CG  LEU A   5 " =    1.133
peak=    3.977 closest distance to " O   HOH Z  51 " =    1.955
peak=    3.972 closest distance to " O   HOH Z 366 " =    3.055
peak=    3.968 closest distance to " O   HOH Z 347 " =    0.839
peak=    3.935 closest distance to " O   HOH Z 258 " =    1.230
peak=    3.934 closest distance to " OE1 GLU A   2 " =    1.922
peak=    3.928 closest distance to " N   TYR A  15 " =    1.128
peak=    3.923 closest distance to " O   HOH Z 414 " =    1.583
peak=    3.920 closest distance to " CB  SER A   3 " =    1.478
peak=    3.914 closest distance to " O   HOH Z 352 " =    1.537
peak=    3.912 closest distance to " CE  MET A  93 " =    1.460
peak=    3.911 closest distance to " CB  SER A  63 " =    1.355
peak=    3.901 closest distance to " OD2 ASP A 253 " =    0.993
peak=    3.891 closest distance to " O   ARG A 275 " =    1.446
peak=    3.883 closest distance to " O   HOH Z 371 " =    2.365
peak=    3.883 closest distance to " CD2 LEU A 297 " =    0.973
peak=    3.874 closest distance to " O   HOH Z 361 " =    1.654
peak=    3.867 closest distance to " N   GLN A 278 " =    1.314
peak=    3.856 closest distance to " CG1BVAL A 121 " =    2.317
peak=    3.826 closest distance to " CG  LEU A 167 " =    1.314
peak=    3.826 closest distance to " O   HOH Z 419 " =    2.125
peak=    3.817 closest distance to " O   HOH Z 233 " =    1.578
peak=    3.815 closest distance to " O   HOH Z 119 " =    1.491
peak=    3.813 closest distance to " O   HOH Z 279 " =    2.576
peak=    3.804 closest distance to " OG  SER A 276 " =    0.943
peak=    3.781 closest distance to " CG2 THR A 279 " =    1.087
peak=    3.775 closest distance to " NZ  LYS A 119 " =    2.652
peak=    3.774 closest distance to " CA  ARG A  36 " =    1.044
peak=    3.765 closest distance to " O   HOH Z  52 " =    1.070
peak=    3.762 closest distance to " OG  SER A  32 " =    0.997
peak=    3.756 closest distance to " O   HOH Z 358 " =    1.434
peak=    3.756 closest distance to " NH2 ARG A 269 " =    0.729
peak=    3.752 closest distance to " O   HOH Z 392 " =    1.575
peak=    3.749 closest distance to " O   HOH Z 222 " =    1.633
peak=    3.741 closest distance to " CB  ALA A  10 " =    1.112
peak=    3.741 closest distance to " CG2AVAL A  72 " =    0.900
peak=    3.739 closest distance to " CE AMET A  47 " =    1.528
peak=    3.737 closest distance to " CB  SER A 216 " =    1.044
peak=    3.734 closest distance to " O   HOH Z 371 " =    2.368
peak=    3.730 closest distance to " NE2 GLN A  73 " =    1.425
peak=    3.723 closest distance to " O   HOH Z 342 " =    1.114
peak=    3.710 closest distance to " NH1AARG A 275 " =    1.144
peak=    3.710 closest distance to " O   HOH Z 126 " =    1.762
peak=    3.708 closest distance to " O   HOH Z   7 " =    3.246
peak=    3.699 closest distance to " O   HOH Z 257 " =    2.258
peak=    3.694 closest distance to " CB  LEU A 300 " =    0.956
peak=    3.680 closest distance to " CG  ASP A 140 " =    0.911
peak=    3.672 closest distance to " N   ARG A 156 " =    1.330
peak=    3.672 closest distance to " NH2BARG A 145 " =    1.519
peak=    3.669 closest distance to " CD2 LEU A 228 " =    1.321
peak=    3.667 closest distance to " CE3 TRP A 274 " =    1.386
peak=    3.667 closest distance to " O   HOH Z 389 " =    1.495
peak=    3.662 closest distance to " O   HOH Z 371 " =    3.094
peak=    3.658 closest distance to " O   HOH Z 133 " =    1.533
peak=    3.657 closest distance to " O   HOH Z 125 " =    1.882
peak=    3.655 closest distance to " O   HOH Z  78 " =    1.906
peak=    3.653 closest distance to " O   HOH Z  39 " =    1.620
peak=    3.652 closest distance to " O   HOH Z 158 " =    2.466
peak=    3.652 closest distance to " CG  ARG A 156 " =    1.165
peak=    3.650 closest distance to " NH2AARG A 145 " =    2.213
peak=    3.649 closest distance to " O   HOH Z 381 " =    1.042
peak=    3.645 closest distance to " CG  PRO A  54 " =    1.347
peak=    3.635 closest distance to " O   ASP A 124 " =    1.052
peak=    3.634 closest distance to " CB  ARG A 138 " =    0.929
peak=    3.626 closest distance to " CB  ALA A 242 " =    1.562
peak=    3.624 closest distance to " O   HOH Z 425 " =    2.219
peak=    3.623 closest distance to " CB  ASN A 110 " =    1.033
peak=    3.619 closest distance to " O   HOH Z 272 " =    1.853
peak=    3.611 closest distance to " O   HOH Z 353 " =    2.038
peak=    3.605 closest distance to " O   HOH Z   1 " =    1.907
peak=    3.604 closest distance to " CB  ALA A 114 " =    1.542
peak=    3.592 closest distance to " OD2 ASP A 286 " =    2.144
peak=    3.591 closest distance to " CB  ASN A 215 " =    1.460
peak=    3.585 closest distance to " OD1 ASP A  50 " =    0.819
peak=    3.581 closest distance to " CG2 THR A 221 " =    1.316
peak=    3.578 closest distance to " O   HOH Z 193 " =    1.952
peak=    3.571 closest distance to " O   HOH Z  92 " =    1.328
peak=    3.570 closest distance to " O   HOH Z 220 " =    1.445
peak=    3.568 closest distance to " O   HOH Z 330 " =    1.048
peak=    3.566 closest distance to " O   HOH Z  88 " =    3.450
peak=    3.563 closest distance to " O   HOH Z 411 " =    3.278
peak=    3.557 closest distance to " CG  PRO A 243 " =    1.080
peak=    3.556 closest distance to " C   GLN A  73 " =    1.007
peak=    3.551 closest distance to " O   HOH Z  61 " =    1.939
peak=    3.549 closest distance to " O   HOH Z  68 " =    1.941
peak=    3.549 closest distance to " CB  GLN A 183 " =    1.171
peak=    3.543 closest distance to " O   HOH Z 123 " =    1.176
peak=    3.542 closest distance to " O   HOH Z 356 " =    1.835
peak=    3.541 closest distance to " CB  SER A 276 " =    1.176
peak=    3.535 closest distance to " NE1 TRP A 274 " =    1.151
peak=    3.532 closest distance to " O   HOH Z  30 " =    1.249
peak=    3.528 closest distance to " CA  PHE A 283 " =    1.316
peak=    3.526 closest distance to " CB  GLN A 223 " =    1.688
peak=    3.521 closest distance to " NE2 GLN A  58 " =    5.688
peak=    3.520 closest distance to " CB  ASP A 124 " =    1.043
peak=    3.501 closest distance to " CG1 ILE A  33 " =    1.359
peak=    3.499 closest distance to " CD2 LEU A 167 " =    1.418
peak=    3.499 closest distance to " CG2 THR A 178 " =    1.312
peak=    3.497 closest distance to " CB  PHE A 204 " =    1.215
peak=    3.493 closest distance to " O   HOH Z  11 " =    1.147
peak=    3.490 closest distance to " CB  TRP A 179 " =    1.388
peak=    3.489 closest distance to " NE AARG A 275 " =    1.823
peak=    3.486 closest distance to " N   TRP A  85 " =    1.020
peak=    3.479 closest distance to " NZ  LYS A 119 " =    2.391
peak=    3.476 closest distance to " CD1 PHE A 283 " =    0.966
peak=    3.472 closest distance to " O   HOH Z 211 " =    1.373
peak=    3.471 closest distance to " CA  ASP A 124 " =    0.792
peak=    3.471 closest distance to " O   HOH Z 303 " =    2.049
peak=    3.469 closest distance to " O   HOH Z 143 " =    1.585
peak=    3.464 closest distance to " N   CYS A 260 " =    1.139
peak=    3.457 closest distance to " CD  GLN A 240 " =    1.619
peak=    3.454 closest distance to " OD1 ASN A  45 " =    1.179
peak=    3.454 closest distance to " CB  ASN A 148 " =    1.417
peak=    3.450 closest distance to " O   HOH Z 405 " =    1.979
peak=    3.447 closest distance to " CB  ALA A 114 " =    1.158
peak=    3.446 closest distance to " O   HOH Z 191 " =    2.186
peak=    3.441 closest distance to " O   HOH Z 232 " =    2.004
peak=    3.441 closest distance to " CG  LYS A  76 " =    1.794
peak=    3.436 closest distance to " CB  SER A  62 " =    1.219
peak=    3.435 closest distance to " O   THR A 220 " =    1.812
peak=    3.432 closest distance to " O   HOH Z 153 " =    3.510
peak=    3.430 closest distance to " CG  GLN A  58 " =    1.128
peak=    3.429 closest distance to " O   HOH Z 400 " =    0.749
peak=    3.426 closest distance to " O   HOH Z  95 " =    1.412
peak=    3.425 closest distance to " O   HOH Z 278 " =    0.958
peak=    3.422 closest distance to " CB  ARG A  79 " =    0.920
peak=    3.419 closest distance to " CB  VAL A 202 " =    1.686
peak=    3.403 closest distance to " O   HOH Z 362 " =    1.667
peak=    3.402 closest distance to " O   HOH Z 303 " =    1.181
peak=    3.402 closest distance to " CG BARG A 102 " =    1.916
peak=    3.402 closest distance to " O   HOH Z 118 " =    2.360
peak=    3.394 closest distance to " NH1AARG A 145 " =    1.337
peak=    3.387 closest distance to " O   HOH Z 215 " =    1.466
peak=    3.385 closest distance to " C   VAL A 153 " =    0.994
peak=    3.383 closest distance to " O   HOH Z  47 " =    1.603
peak=    3.381 closest distance to " N   GLU A   2 " =    1.414
peak=    3.379 closest distance to " CB  ALA A 248 " =    1.561
peak=    3.377 closest distance to " NH2 ARG A 138 " =    1.272
peak=    3.376 closest distance to " O   HOH Z  49 " =    1.142
peak=    3.371 closest distance to " CE  LYS A  48 " =    1.050
peak=    3.367 closest distance to " CA  GLN A  55 " =    1.018
peak=    3.366 closest distance to " CE1 PHE A  38 " =    1.180
peak=    3.364 closest distance to " CD  ARG A  66 " =    2.348
peak=    3.363 closest distance to " CA  TYR A  30 " =    1.008
peak=    3.362 closest distance to " CA  GLY A 287 " =    1.296
peak=    3.355 closest distance to " CA  ARG A  56 " =    2.019
peak=    3.347 closest distance to " O   HOH Z 426 " =    1.209
peak=    3.347 closest distance to " N   PHE A 130 " =    1.331
peak=    3.345 closest distance to " SD  MET A 105 " =    0.986
peak=    3.344 closest distance to " O   HOH Z 219 " =    1.889
peak=    3.335 closest distance to " O   HOH Z 201 " =    1.646
peak=    3.334 closest distance to " O   ASN A 301 " =    2.079
peak=    3.334 closest distance to " O   ASP A 286 " =    2.325
peak=    3.332 closest distance to " O   HOH Z 404 " =    1.161
peak=    3.328 closest distance to " O   HOH Z 146 " =    1.751
peak=    3.319 closest distance to " O   SER A  87 " =    2.646
peak=    3.319 closest distance to " O   HOH Z 364 " =    1.221
peak=    3.318 closest distance to " O   HOH Z  97 " =    1.854
peak=    3.315 closest distance to " CG1AVAL A 121 " =    0.960
peak=    3.314 closest distance to " OD1 ASP A 286 " =    1.153
peak=    3.312 closest distance to " O   HOH Z 412 " =    2.671
peak=    3.311 closest distance to " O   HOH Z 123 " =    1.299
peak=    3.311 closest distance to " O   HOH Z 423 " =    2.120
peak=    3.305 closest distance to " CD  GLN A  77 " =    1.247
peak=    3.303 closest distance to " O   HOH Z  76 " =    1.251
peak=    3.303 closest distance to " CE1 TYR A  68 " =    1.243
peak=    3.301 closest distance to " ND2 ASN A 249 " =    0.850
peak=    3.300 closest distance to " C   ASN A 301 " =    0.993
peak=    3.300 closest distance to " CB  ASN A  74 " =    1.242
peak=    3.296 closest distance to " ND2 ASN A 110 " =    1.703
peak=    3.295 closest distance to " O   HOH Z 430 " =    1.736
peak=    3.295 closest distance to " N   TYR A 116 " =    1.625
peak=    3.291 closest distance to " CA  LEU A 282 " =    1.038
peak=    3.291 closest distance to " CG  PRO A 213 " =    1.220
peak=    3.290 closest distance to " CD  ARG A 139 " =    1.372
peak=    3.289 closest distance to " O   HOH Z 368 " =    3.135
peak=    3.286 closest distance to " CG2BVAL A  72 " =    1.459
peak=    3.282 closest distance to " CG1 VAL A 197 " =    1.174
peak=    3.282 closest distance to " N   VAL A 296 " =    1.769
peak=    3.282 closest distance to " O   HOH Z  49 " =    2.743
peak=    3.279 closest distance to " CB  PRO A  90 " =    1.242
peak=    3.277 closest distance to " O   HOH Z 158 " =    1.151
peak=    3.276 closest distance to " CG BASN A 224 " =    0.973
peak=    3.274 closest distance to " O   HOH Z 106 " =    4.082
peak=    3.270 closest distance to " N   SER A  97 " =    0.815
peak=    3.260 closest distance to " O   HOH Z  61 " =    1.569
peak=    3.259 closest distance to " CG1 VAL A 153 " =    0.982
peak=    3.257 closest distance to " O   HOH Z 323 " =    1.728
peak=    3.256 closest distance to " CB  TRP A  85 " =    1.642
peak=    3.252 closest distance to " O   ASN A  74 " =    1.603
peak=    3.250 closest distance to " OG1 THR A 157 " =    1.092
peak=    3.248 closest distance to " O   HOH Z   3 " =    1.639
peak=    3.246 closest distance to " O   HOH Z 248 " =    1.964
peak=    3.245 closest distance to " O   HOH Z 355 " =    1.779
peak=    3.241 closest distance to " NH2AARG A 145 " =    1.051
peak=    3.241 closest distance to " CE1 PHE A 130 " =    1.141
peak=    3.235 closest distance to " O   HOH Z 357 " =    2.524
peak=    3.230 closest distance to " CG  GLN A 205 " =    1.249
peak=    3.230 closest distance to " CB  PHE A  16 " =    1.123
peak=    3.223 closest distance to " CA  ASN A 284 " =    1.036
peak=    3.223 closest distance to " O   HOH Z 147 " =    1.173
peak=    3.219 closest distance to " NZ  LYS A 117 " =    1.016
peak=    3.218 closest distance to " CG  PRO A 198 " =    1.314
peak=    3.216 closest distance to " O   HOH Z  26 " =    1.717
peak=    3.212 closest distance to " O   HOH Z  57 " =    1.150
peak=    3.212 closest distance to " O   HOH Z  91 " =    1.043
peak=    3.209 closest distance to " CA  GLY A 136 " =    1.028
peak=    3.207 closest distance to " O   HOH Z 116 " =    2.028
peak=    3.207 closest distance to " CG  ARG A 159 " =    0.932
peak=    3.202 closest distance to " NZ  LYS A  48 " =    2.383
peak=    3.201 closest distance to " CZ3 TRP A 123 " =    1.715
peak=    3.196 closest distance to " CZ  PHE A  16 " =    0.937
peak=    3.195 closest distance to " O   HOH Z 313 " =    1.649
peak=    3.191 closest distance to " N   ALA A   1 " =    2.796
peak=    3.191 closest distance to " O   HOH Z  42 " =    1.608
peak=    3.188 closest distance to " O   HOH Z 131 " =    2.295
peak=    3.187 closest distance to " O   HOH Z  27 " =    1.055
peak=    3.184 closest distance to " CA  ARG A 159 " =    1.307
peak=    3.183 closest distance to " CA  ASN A 127 " =    1.253
peak=    3.183 closest distance to " CE1 PHE A  38 " =    0.752
peak=    3.180 closest distance to " CB  GLU A 277 " =    1.070
peak=    3.174 closest distance to " OG BSER A 258 " =    0.999
peak=    3.170 closest distance to " CA  ALA A 160 " =    0.995
peak=    3.168 closest distance to " O   HOH Z 368 " =    1.724
peak=    3.167 closest distance to " CA  ASN A 209 " =    1.401
peak=    3.166 closest distance to " CA  ALA A 299 " =    0.909
peak=    3.163 closest distance to " CG2 ILE A  20 " =    1.285
peak=    3.161 closest distance to " O   HOH Z  78 " =    2.462
peak=    3.156 closest distance to " CD2 LEU A 101 " =    1.195
peak=    3.151 closest distance to " O   ASN A  69 " =    1.435
peak=    3.150 closest distance to " N   GLN A  73 " =    1.548
peak=    3.149 closest distance to " CH2 TRP A 266 " =    1.209
peak=    3.148 closest distance to " O   ASN A 142 " =    1.113
peak=    3.148 closest distance to " O   HOH Z 238 " =    1.106
peak=    3.147 closest distance to " OG ASER A 134 " =    1.458
peak=    3.147 closest distance to " CA  GLN A  11 " =    1.364
peak=    3.146 closest distance to " N   PHE A  38 " =    1.068
peak=    3.145 closest distance to " CB  VAL A 265 " =    1.292
peak=    3.144 closest distance to " CE AMET A  47 " =    1.627
peak=    3.135 closest distance to " NZ  LYS A 289 " =    1.125
peak=    3.134 closest distance to " O   ALA A  10 " =    1.185
peak=    3.129 closest distance to " NZ  LYS A 117 " =    3.401
peak=    3.126 closest distance to " CD1 LEU A 228 " =    1.677
peak=    3.124 closest distance to " O   HOH Z 148 " =    1.795
peak=    3.122 closest distance to " O   HOH Z  28 " =    1.553
peak=    3.122 closest distance to " O   HOH Z  88 " =    3.646
peak=    3.113 closest distance to " O   GLY A 302 " =    2.289
peak=    3.107 closest distance to " O   HOH Z 132 " =    1.044
peak=    3.106 closest distance to " O   ARG A  14 " =    0.993
peak=    3.096 closest distance to " O   HOH Z 172 " =    1.587
peak=    3.096 closest distance to " N   ALA A   1 " =    1.442
peak=    3.093 closest distance to " CG  GLN A  89 " =    1.597
peak=    3.090 closest distance to " O   HOH Z 274 " =    2.246
peak=    3.085 closest distance to " O   HOH Z 145 " =    2.116
peak=    3.083 closest distance to " O   HOH Z 223 " =    1.142
peak=    3.082 closest distance to " CA  THR A  42 " =    1.218
peak=    3.079 closest distance to " N   LYS A  76 " =    1.403
peak=    3.062 closest distance to " O   HOH Z 207 " =    2.420
peak=    3.045 closest distance to " O   SER A 271 " =    1.205
peak=    3.041 closest distance to " O   HOH Z 392 " =    2.026

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.726 - 5.576
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 214
   mapped sites are within: 0.726 - 5.576

peak=   -5.516 closest distance to " CD  ARG A 138 " =    1.142
peak=   -4.689 closest distance to " OE1 GLU A 277 " =    2.203
peak=   -4.371 closest distance to " OG BSER A 134 " =    1.587
peak=   -4.266 closest distance to " O   PRO A 198 " =    1.198
peak=   -4.227 closest distance to " N   VAL A  72 " =    2.113
peak=   -4.222 closest distance to " O   ASP A 191 " =    1.912
peak=   -4.192 closest distance to " CA  GLY A  35 " =    1.979
peak=   -4.142 closest distance to " CA  GLY A 133 " =    1.958
peak=   -4.133 closest distance to " OG  SER A  97 " =    2.221
peak=   -4.128 closest distance to " CE BLYS A 290 " =    2.050
peak=   -4.084 closest distance to " CG2 VAL A 230 " =    0.930
peak=   -4.044 closest distance to " O   HOH Z 242 " =    1.496
peak=   -4.022 closest distance to " O   ALA A  84 " =    1.541
peak=   -4.005 closest distance to " OD1 ASP A  27 " =    0.758
peak=   -3.995 closest distance to " O   HOH Z 300 " =    1.017
peak=   -3.933 closest distance to " O   HOH Z 415 " =    0.960
peak=   -3.933 closest distance to " OD2 ASP A 253 " =    0.885
peak=   -3.905 closest distance to " OG BSER A  12 " =    1.207
peak=   -3.895 closest distance to " O   HOH Z 131 " =    3.799
peak=   -3.891 closest distance to " CD  ARG A  14 " =    2.969
peak=   -3.853 closest distance to " CA  GLY A 203 " =    2.528
peak=   -3.846 closest distance to " CG2AVAL A  41 " =    2.719
peak=   -3.823 closest distance to " O   HOH Z 352 " =    1.618
peak=   -3.813 closest distance to " C   GLU A   2 " =    1.856
peak=   -3.811 closest distance to " O   HOH Z 313 " =    0.863
peak=   -3.796 closest distance to " O   HOH Z  24 " =    1.221
peak=   -3.786 closest distance to " CB  VAL A 230 " =    0.864
peak=   -3.768 closest distance to " O   HOH Z  52 " =    2.152
peak=   -3.757 closest distance to " O   ARG A 145 " =    1.342
peak=   -3.709 closest distance to " CA  GLN A  55 " =    1.201
peak=   -3.708 closest distance to " N   ASN A 127 " =    1.406
peak=   -3.695 closest distance to " CB  PHE A 208 " =    2.026
peak=   -3.695 closest distance to " CA  TYR A  68 " =    1.119
peak=   -3.694 closest distance to " O   HOH Z 390 " =    2.612
peak=   -3.678 closest distance to " CE2 TYR A  30 " =    2.482
peak=   -3.674 closest distance to " N   ARG A 275 " =    0.726
peak=   -3.664 closest distance to " O   ALA A  10 " =    1.597
peak=   -3.657 closest distance to " O   HOH Z 286 " =    1.554
peak=   -3.657 closest distance to " O   HOH Z 207 " =    2.131
peak=   -3.648 closest distance to " N   GLN A  11 " =    0.956
peak=   -3.635 closest distance to " CG  TRP A 266 " =    1.663
peak=   -3.630 closest distance to " CD1 TRP A 179 " =    1.256
peak=   -3.630 closest distance to " CD  LYS A 166 " =    2.512
peak=   -3.627 closest distance to " C   ASN A 285 " =    2.077
peak=   -3.621 closest distance to " CD2 TYR A 293 " =    1.753
peak=   -3.617 closest distance to " O   HOH Z 385 " =    1.106
peak=   -3.599 closest distance to " N   GLU A 277 " =    1.342
peak=   -3.583 closest distance to " CB  PHE A 130 " =    1.005
peak=   -3.581 closest distance to " CB  ASP A  27 " =    2.426
peak=   -3.581 closest distance to " CG  PRO A 163 " =    2.474
peak=   -3.577 closest distance to " O   HOH Z 128 " =    2.378
peak=   -3.573 closest distance to " CG2 ILE A 120 " =    1.306
peak=   -3.573 closest distance to " CE2 PHE A 218 " =    2.504
peak=   -3.561 closest distance to " N   THR A 157 " =    1.527
peak=   -3.549 closest distance to " N   LYS A 290 " =    1.008
peak=   -3.544 closest distance to " O   HOH Z 422 " =    3.512
peak=   -3.541 closest distance to " O   HOH Z 435 " =    2.405
peak=   -3.535 closest distance to " CG  MET A 105 " =    0.850
peak=   -3.531 closest distance to " N   PRO A 163 " =    1.418
peak=   -3.526 closest distance to " N   VAL A 125 " =    1.102
peak=   -3.516 closest distance to " O   GLN A  11 " =    1.587
peak=   -3.514 closest distance to " C   HIS A 108 " =    1.302
peak=   -3.511 closest distance to " NE2 GLN A  11 " =    1.384
peak=   -3.488 closest distance to " O   HOH Z 113 " =    1.630
peak=   -3.487 closest distance to " O   HOH Z 189 " =    3.611
peak=   -3.486 closest distance to " O   HOH Z 174 " =    2.846
peak=   -3.486 closest distance to " O   ALA A  51 " =    1.311
peak=   -3.478 closest distance to " C   ILE A 239 " =    1.762
peak=   -3.473 closest distance to " CD2 TYR A 116 " =    2.248
peak=   -3.461 closest distance to " NH2 ARG A  24 " =    0.978
peak=   -3.459 closest distance to " O   ASN A 301 " =    1.293
peak=   -3.459 closest distance to " O   HOH Z  67 " =    3.014
peak=   -3.457 closest distance to " O   HOH Z 216 " =    1.763
peak=   -3.457 closest distance to " O   HOH Z 359 " =    1.840
peak=   -3.451 closest distance to " O   ILE A  49 " =    1.505
peak=   -3.449 closest distance to " O   ARG A 275 " =    0.781
peak=   -3.449 closest distance to " OG  SER A 245 " =    1.723
peak=   -3.447 closest distance to " CE3 TRP A 274 " =    2.069
peak=   -3.444 closest distance to " O   HOH Z 389 " =    2.427
peak=   -3.441 closest distance to " O   SER A 245 " =    1.386
peak=   -3.439 closest distance to " CG BLYS A 290 " =    0.913
peak=   -3.437 closest distance to " N   ALA A 244 " =    1.072
peak=   -3.431 closest distance to " CA  GLY A  57 " =    2.154
peak=   -3.421 closest distance to " OE2 GLU A 152 " =    1.035
peak=   -3.418 closest distance to " O   HOH Z 205 " =    1.221
peak=   -3.409 closest distance to " CB  ALA A   7 " =    1.976
peak=   -3.405 closest distance to " O   SER A  22 " =    2.596
peak=   -3.405 closest distance to " CG  PRO A 243 " =    1.745
peak=   -3.403 closest distance to " C   PHE A 155 " =    0.734
peak=   -3.400 closest distance to " O   HOH Z 359 " =    3.453
peak=   -3.398 closest distance to " O   HOH Z 197 " =    1.988
peak=   -3.398 closest distance to " O   HOH Z 428 " =    1.366
peak=   -3.397 closest distance to " CB  ALA A  10 " =    1.995
peak=   -3.391 closest distance to " O   HOH Z  54 " =    0.915
peak=   -3.389 closest distance to " O   ARG A 156 " =    0.848
peak=   -3.387 closest distance to " CA  GLY A  57 " =    2.130
peak=   -3.384 closest distance to " OD2 ASP A 272 " =    1.474
peak=   -3.382 closest distance to " NE2 GLN A 223 " =    1.542
peak=   -3.377 closest distance to " O   HOH Z 189 " =    1.213
peak=   -3.375 closest distance to " O   HOH Z 103 " =    0.800
peak=   -3.373 closest distance to " O   CYS A 260 " =    1.380
peak=   -3.371 closest distance to " CB  PRO A 243 " =    2.599
peak=   -3.370 closest distance to " CG  GLN A  73 " =    1.405
peak=   -3.366 closest distance to " O   HOH Z 402 " =    1.157
peak=   -3.362 closest distance to " O   HOH Z 111 " =    2.021
peak=   -3.361 closest distance to " O   HOH Z 148 " =    2.719
peak=   -3.357 closest distance to " CG2 ILE A  20 " =    2.651
peak=   -3.355 closest distance to " O   GLU A 277 " =    1.944
peak=   -3.349 closest distance to " CG  ASP A  50 " =    0.859
peak=   -3.349 closest distance to " CG2 VAL A 197 " =    2.383
peak=   -3.348 closest distance to " CG  LEU A 228 " =    0.904
peak=   -3.339 closest distance to " O   VAL A  72 " =    0.803
peak=   -3.335 closest distance to " OG  SER A 276 " =    0.893
peak=   -3.331 closest distance to " CD2 LEU A 167 " =    1.848
peak=   -3.328 closest distance to " CD1 LEU A 297 " =    2.270
peak=   -3.323 closest distance to " O   HOH Z 268 " =    1.030
peak=   -3.322 closest distance to " CG1 VAL A 125 " =    2.157
peak=   -3.322 closest distance to " O   SER A 271 " =    1.655
peak=   -3.319 closest distance to " O   HOH Z 404 " =    1.441
peak=   -3.316 closest distance to " O   HOH Z 100 " =    1.718
peak=   -3.314 closest distance to " O   TRP A  92 " =    1.671
peak=   -3.314 closest distance to " O   HOH Z 414 " =    2.042
peak=   -3.310 closest distance to " OG  SER A  87 " =    1.448
peak=   -3.309 closest distance to " O   HOH Z 426 " =    1.605
peak=   -3.309 closest distance to " CD  ARG A 139 " =    1.616
peak=   -3.307 closest distance to " O   HOH Z 377 " =    1.536
peak=   -3.306 closest distance to " O   VAL A  72 " =    1.055
peak=   -3.300 closest distance to " OG  SER A  63 " =    1.591
peak=   -3.300 closest distance to " O   LEU A 101 " =    1.242
peak=   -3.299 closest distance to " CG  PRO A  54 " =    1.766
peak=   -3.299 closest distance to " CA  MET A 113 " =    1.152
peak=   -3.286 closest distance to " O   ILE A 106 " =    2.215
peak=   -3.285 closest distance to " O   HOH Z 276 " =    1.536
peak=   -3.282 closest distance to " O   LEU A 222 " =    1.585
peak=   -3.281 closest distance to " CG  LEU A   5 " =    1.002
peak=   -3.281 closest distance to " O   HOH Z 191 " =    5.576
peak=   -3.281 closest distance to " O   HOH Z 126 " =    1.789
peak=   -3.278 closest distance to " O   HOH Z 409 " =    1.851
peak=   -3.275 closest distance to " CA  GLY A  98 " =    1.779
peak=   -3.271 closest distance to " CB  ASN A 301 " =    1.721
peak=   -3.271 closest distance to " CZ3 TRP A 123 " =    1.772
peak=   -3.270 closest distance to " CG  PHE A  59 " =    1.345
peak=   -3.269 closest distance to " O   GLU A  44 " =    1.781
peak=   -3.264 closest distance to " NH2AARG A 275 " =    5.153
peak=   -3.263 closest distance to " O   HOH Z 385 " =    1.993
peak=   -3.263 closest distance to " O   HOH Z 314 " =    1.378
peak=   -3.263 closest distance to " O   LYS A  76 " =    1.199
peak=   -3.256 closest distance to " CA  ASN A 110 " =    1.038
peak=   -3.253 closest distance to " N   ARG A 138 " =    1.695
peak=   -3.248 closest distance to " NH1 ARG A  36 " =    0.920
peak=   -3.247 closest distance to " O   HOH Z 234 " =    4.737
peak=   -3.246 closest distance to " O   GLN A 240 " =    1.652
peak=   -3.246 closest distance to " O   HOH Z 328 " =    0.988
peak=   -3.246 closest distance to " OG  SER A   3 " =    1.397
peak=   -3.243 closest distance to " O   HOH Z 298 " =    2.843
peak=   -3.240 closest distance to " CB  ALA A   9 " =    2.440
peak=   -3.239 closest distance to " O   HOH Z 185 " =    2.101
peak=   -3.235 closest distance to " N   VAL A 189 " =    1.637
peak=   -3.234 closest distance to " C   ASP A 124 " =    1.962
peak=   -3.233 closest distance to " O   HOH Z  28 " =    1.097
peak=   -3.231 closest distance to " O   PHE A 218 " =    1.630
peak=   -3.229 closest distance to " CG  ASN A 284 " =    1.263
peak=   -3.227 closest distance to " O   HOH Z  82 " =    1.520
peak=   -3.225 closest distance to " CG  ASP A 140 " =    1.135
peak=   -3.224 closest distance to " CG2 VAL A  78 " =    2.462
peak=   -3.222 closest distance to " CB  CYS A 201 " =    1.819
peak=   -3.219 closest distance to " CB  ALA A  43 " =    2.473
peak=   -3.216 closest distance to " CZ  TYR A 169 " =    1.803
peak=   -3.206 closest distance to " NE1 TRP A 177 " =    1.727
peak=   -3.199 closest distance to " O   HOH Z 414 " =    1.866
peak=   -3.195 closest distance to " O   PHE A 155 " =    1.975
peak=   -3.194 closest distance to " N   ALA A   1 " =    1.091
peak=   -3.191 closest distance to " CA  HIS A  86 " =    2.104
peak=   -3.186 closest distance to " CD  GLU A  44 " =    1.328
peak=   -3.184 closest distance to " CD2 LEU A 237 " =    2.150
peak=   -3.183 closest distance to " CB  ASN A  39 " =    2.348
peak=   -3.182 closest distance to " CE BMET A  47 " =    1.251
peak=   -3.178 closest distance to " O   HOH Z 337 " =    1.745
peak=   -3.177 closest distance to " CD  GLN A  77 " =    1.133
peak=   -3.175 closest distance to " N   ALA A  43 " =    2.675
peak=   -3.168 closest distance to " O   HOH Z 416 " =    0.848
peak=   -3.168 closest distance to " CZ  ARG A  36 " =    1.805
peak=   -3.167 closest distance to " O   HOH Z  54 " =    1.287
peak=   -3.164 closest distance to " O   HOH Z  39 " =    0.883
peak=   -3.154 closest distance to " O   TRP A 179 " =    1.782
peak=   -3.151 closest distance to " OG1 THR A 178 " =    1.168
peak=   -3.147 closest distance to " C   GLN A 205 " =    1.889
peak=   -3.145 closest distance to " O   HOH Z 434 " =    4.100
peak=   -3.144 closest distance to " O   HOH Z 325 " =    1.706
peak=   -3.141 closest distance to " CA  GLY A 136 " =    1.516
peak=   -3.135 closest distance to " O   HOH Z 392 " =    3.035
peak=   -3.128 closest distance to " CG1 ILE A 263 " =    1.890
peak=   -3.119 closest distance to " ND2 ASN A 252 " =    2.275
peak=   -3.117 closest distance to " NH2 ARG A  79 " =    2.204
peak=   -3.115 closest distance to " O   HOH Z 359 " =    1.570
peak=   -3.113 closest distance to " OG  SER A  87 " =    1.892
peak=   -3.112 closest distance to " CB  ALA A 114 " =    2.418
peak=   -3.104 closest distance to " O   LYS A  76 " =    1.444
peak=   -3.102 closest distance to " CZ3 TRP A 266 " =    1.641
peak=   -3.092 closest distance to " NE2 GLN A 194 " =    1.985
peak=   -3.091 closest distance to " CB  SER A 276 " =    1.623
peak=   -3.091 closest distance to " NH2 ARG A  66 " =    5.300
peak=   -3.086 closest distance to " O   THR A  52 " =    1.055
peak=   -3.082 closest distance to " O   HOH Z 412 " =    5.306
peak=   -3.077 closest distance to " O   HOH Z  30 " =    0.836
peak=   -3.076 closest distance to " O   HOH Z 298 " =    0.908
peak=   -3.072 closest distance to " O   HOH Z  24 " =    1.525
peak=   -3.067 closest distance to " O   LEU A 261 " =    1.222
peak=   -3.063 closest distance to " CB  ASN A 249 " =    1.457
peak=   -3.059 closest distance to " CB  ASN A  45 " =    2.053
peak=   -3.038 closest distance to " O   HOH Z  97 " =    1.174
peak=   -3.023 closest distance to " O   HOH Z 135 " =    1.596
peak=   -3.012 closest distance to " CG1BVAL A  41 " =    1.993

================= 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    :  0.4964 0.4907   6.300754e+00   6.288719e+00
   1_bss:  0.4879 0.4774   6.297044e+00   6.281313e+00
   1_xyz:  0.4243 0.4488   6.229613e+00   6.255172e+00
   1_adp:  0.3860 0.4500   6.187928e+00   6.254115e+00
   1_occ:  0.3856 0.4505   6.187613e+00   6.254842e+00
   2_bss:  0.3843 0.4471   6.189117e+00   6.254027e+00
   2_xyz:  0.3343 0.4175   6.089805e+00   6.208567e+00
   2_adp:  0.3221 0.4095   6.070477e+00   6.197044e+00
   2_occ:  0.3220 0.4095   6.070499e+00   6.197172e+00
   3_bss:  0.3229 0.4066   6.070151e+00   6.195501e+00
   3_xyz:  0.2774 0.3513   5.939624e+00   6.092090e+00
   3_adp:  0.2523 0.3435   5.883544e+00   6.066876e+00
   3_occ:  0.2519 0.3432   5.882893e+00   6.066662e+00
   4_bss:  0.2511 0.3428   5.880891e+00   6.066088e+00
   4_xyz:  0.2173 0.2973   5.746785e+00   5.955260e+00
   4_adp:  0.2017 0.2750   5.678668e+00   5.892519e+00
   4_occ:  0.2014 0.2750   5.677954e+00   5.892321e+00
   5_bss:  0.2016 0.2750   5.678655e+00   5.892019e+00
   5_xyz:  0.1612 0.2258   5.481536e+00   5.726128e+00
   5_adp:  0.1463 0.2080   5.395398e+00   5.648285e+00
   5_occ:  0.1462 0.2080   5.394880e+00   5.647850e+00
   5_bss:  0.1466 0.2078   5.393729e+00   5.647039e+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:  0.373  20.000   5.907   9.286   8.262   0.000   0.000   0.000
   1_xyz:  0.373  20.000   5.907   9.286   8.262   0.000   0.000   0.000
   1_adp:  0.373  20.000   5.907   9.286   8.262   0.000   0.000   0.000
   1_occ:  0.373  20.000   5.907   9.286   8.262   0.000   0.000   0.000
   2_bss:  0.364  37.826   3.029   5.629   4.831   0.000   0.000   0.000
   2_xyz:  0.364  37.826   3.029   5.629   4.831   0.000   0.000   0.000
   2_adp:  0.364  37.826   3.029   5.629   4.831   0.000   0.000   0.000
   2_occ:  0.364  37.826   3.029   5.629   4.831   0.000   0.000   0.000
   3_bss:  0.344  37.826   2.441   3.690   3.850   0.000   0.000   0.000
   3_xyz:  0.344  37.826   2.441   3.690   3.850   0.000   0.000   0.000
   3_adp:  0.344  37.826   2.441   3.690   3.850   0.000   0.000   0.000
   3_occ:  0.344  37.826   2.441   3.690   3.850   0.000   0.000   0.000
   4_bss:  0.315  42.053   1.443   2.089   2.874   0.000   0.000   0.000
   4_xyz:  0.315  42.053   1.443   2.089   2.874   0.000   0.000   0.000
   4_adp:  0.315  42.053   1.443   2.089   2.874   0.000   0.000   0.000
   4_occ:  0.315  42.053   1.443   2.089   2.874   0.000   0.000   0.000
   5_bss:  0.331  51.252   1.261   1.367   2.838   0.000   0.000   0.000
   5_xyz:  0.331  51.252   1.261   1.367   2.838   0.000   0.000   0.000
   5_adp:  0.331  51.252   1.261   1.367   2.838   0.000   0.000   0.000
   5_occ:  0.331  51.252   1.261   1.367   2.838   0.000   0.000   0.000
   5_bss:  0.320  52.893  -0.505  -0.640   1.145   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.895 0.3559  0.4290    78944.917
   1_bss:  61.970 0.3671  0.5532    76541.975
   1_xyz:  55.052 0.4557  0.6740    65001.713
   1_adp:  55.020 0.4557  0.7317    64726.302
   1_occ:  55.125 0.4543  0.7285    65001.440
   2_bss:  54.825 0.4581  0.6585    64427.425
   2_xyz:  48.503 0.5374  0.7732    52749.783
   2_adp:  46.824 0.5587  0.8117    50535.049
   2_occ:  46.830 0.5586  0.8115    50560.632
   3_bss:  46.593 0.5613  0.7820    49962.798
   3_xyz:  37.809 0.6679  0.9157    35016.430
   3_adp:  36.075 0.6883  0.9303    32354.603
   3_occ:  36.078 0.6882  0.9298    32308.719
   4_bss:  35.987 0.6892  0.8923    32180.616
   4_xyz:  30.837 0.7467  0.9427    23260.180
   4_adp:  27.527 0.7840  0.9540    19530.724
   4_occ:  27.503 0.7843  0.9537    19480.680
   5_bss:  27.498 0.7844  0.9434    19502.627
   5_xyz:  22.402 0.8370  0.9810    13207.788
   5_adp:  20.177 0.8594  0.9787    11130.153
   5_occ:  20.162 0.8596  0.9783    11106.555
   5_bss:  20.120 0.8598  0.9717    11040.581
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3281e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3281e+01
   1_xyz:   1.696  0.013  0.105 18.441  0.006  4.104   1.4561e-01
   1_adp:   1.696  0.013  0.105 18.441  0.006  4.104   1.4561e-01
   1_occ:   1.696  0.013  0.105 18.441  0.006  4.104   1.4561e-01
   2_bss:   1.696  0.013  0.105 18.441  0.006  4.104   1.4561e-01
   2_xyz:   1.211  0.008  0.080 16.623  0.005  4.121   9.7823e-02
   2_adp:   1.211  0.008  0.080 16.623  0.005  4.121   9.7823e-02
   2_occ:   1.211  0.008  0.080 16.623  0.005  4.121   9.7823e-02
   3_bss:   1.211  0.008  0.080 16.623  0.005  4.121   9.7823e-02
   3_xyz:   1.189  0.009  0.087 15.998  0.005  4.119   8.6324e-02
   3_adp:   1.189  0.009  0.087 15.998  0.005  4.119   8.6324e-02
   3_occ:   1.189  0.009  0.087 15.998  0.005  4.119   8.6324e-02
   4_bss:   1.189  0.009  0.087 15.998  0.005  4.119   8.6324e-02
   4_xyz:   0.975  0.007  0.069 15.676  0.004  4.107   6.1591e-02
   4_adp:   0.975  0.007  0.069 15.676  0.004  4.107   6.1591e-02
   4_occ:   0.975  0.007  0.069 15.676  0.004  4.107   6.1591e-02
   5_bss:   0.975  0.007  0.069 15.676  0.004  4.107   6.1591e-02
   5_xyz:   1.058  0.008  0.075 15.643  0.004  4.114   6.8650e-02
   5_adp:   1.058  0.008  0.075 15.643  0.004  4.114   6.8650e-02
   5_occ:   1.058  0.008  0.075 15.643  0.004  4.114   6.8650e-02
   5_bss:   1.058  0.008  0.075 15.643  0.004  4.114   6.8650e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9029e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9029e+00
   1_xyz:  13.161  0.188  0.411 86.955  0.033  2.103   9.7214e-02
   1_adp:  13.161  0.188  0.411 86.955  0.033  2.103   9.7214e-02
   1_occ:  13.161  0.188  0.411 86.955  0.033  2.103   9.7214e-02
   2_bss:  13.161  0.188  0.411 86.955  0.033  2.103   9.7214e-02
   2_xyz:   7.685  0.062  0.315 81.142  0.046  1.926   5.9653e-02
   2_adp:   7.685  0.062  0.315 81.142  0.046  1.926   5.9653e-02
   2_occ:   7.685  0.062  0.315 81.142  0.046  1.926   5.9653e-02
   3_bss:   7.685  0.062  0.315 81.142  0.046  1.926   5.9653e-02
   3_xyz:   7.372  0.118  0.326 81.990  0.027  2.149   8.4412e-02
   3_adp:   7.372  0.118  0.326 81.990  0.027  2.149   8.4412e-02
   3_occ:   7.372  0.118  0.326 81.990  0.027  2.149   8.4412e-02
   4_bss:   7.372  0.118  0.326 81.990  0.027  2.149   8.4412e-02
   4_xyz:   7.155  0.075  0.246 88.742  0.028  2.310   4.5318e-02
   4_adp:   7.155  0.075  0.246 88.742  0.028  2.310   4.5318e-02
   4_occ:   7.155  0.075  0.246 88.742  0.028  2.310   4.5318e-02
   5_bss:   7.155  0.075  0.246 88.742  0.028  2.310   4.5318e-02
   5_xyz:   6.889  0.059  0.239 88.106  0.031  2.327   5.2752e-02
   5_adp:   6.889  0.059  0.239 88.106  0.031  2.327   5.2752e-02
   5_occ:   6.889  0.059  0.239 88.106  0.031  2.327   5.2752e-02
   5_bss:   6.889  0.059  0.239 88.106  0.031  2.327   5.2752e-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:  62.79   0.00  14.49  62.79   0.00  13.23  61.37   0.00  21.32
   1_occ:  62.79   0.00  14.49  62.79   0.00  13.23  61.37   0.00  21.32
   2_bss:  62.79   0.00  14.49  62.79   0.00  13.23  61.37   0.00  21.32
   2_xyz:  62.79   0.00  14.49  62.79   0.00  13.23  61.37   0.00  21.32
   2_adp:  91.03   0.00  14.42  91.03   0.00  12.81  61.48   0.00  23.14
   2_occ:  91.03   0.00  14.42  91.03   0.00  12.81  61.48   0.00  23.14
   3_bss:  91.03   0.00  14.42  91.03   0.00  12.81  61.48   0.00  23.14
   3_xyz:  91.03   0.00  14.42  91.03   0.00  12.81  61.48   0.00  23.14
   3_adp:  83.27   0.00  16.21  76.17   0.00  12.90  83.27   0.00  34.26
   3_occ:  83.27   0.00  16.21  76.17   0.00  12.90  83.27   0.00  34.26
   4_bss:  83.27   0.00  16.21  76.17   0.00  12.90  83.27   0.00  34.26
   4_xyz:  83.27   0.00  16.21  76.17   0.00  12.90  83.27   0.00  34.26
   4_adp:  93.01   0.00  15.93  87.41   0.00  11.57  93.01   1.77  39.65
   4_occ:  93.01   0.00  15.93  87.41   0.00  11.57  93.01   1.77  39.65
   5_bss:  93.01   0.00  15.93  87.41   0.00  11.57  93.01   1.77  39.65
   5_xyz:  93.01   0.00  15.93  87.41   0.00  11.57  93.01   1.77  39.65
   5_adp: 101.52   0.00  15.79 100.60   0.00  10.47 101.52   2.98  44.74
   5_occ: 101.52   0.00  15.79 100.60   0.00  10.47 101.52   2.98  44.74
   5_bss: 103.16   1.64  17.43 102.24   1.64  12.11 103.16   4.62  46.39
------------------------------------------------------------------------
 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:    1.286    0.009    0.409
   1_adp:    1.286    0.009    0.409
   1_occ:    1.286    0.009    0.409
   2_bss:    1.286    0.009    0.409
   2_xyz:    1.649    0.011    0.567
   2_adp:    1.649    0.011    0.567
   2_occ:    1.649    0.011    0.567
   3_bss:    1.649    0.011    0.567
   3_xyz:    1.586    0.048    0.678
   3_adp:    1.586    0.048    0.678
   3_occ:    1.586    0.048    0.678
   4_bss:    1.586    0.048    0.678
   4_xyz:    1.799    0.070    0.767
   4_adp:    1.799    0.070    0.767
   4_occ:    1.799    0.070    0.767
   5_bss:    1.799    0.070    0.767
   5_xyz:    1.934    0.044    0.857
   5_adp:    1.934    0.044    0.857
   5_occ:    1.934    0.044    0.857
   5_bss:    1.934    0.044    0.857
------------------------------------------------------------------------

CPU time actual refinement: 286.78


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_491/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_491/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_491/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_491/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_491/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 286.65 
  Macro-tasks:
    bulk solvent and scale       = 35.66  
    individual site refinement   = 119.36 
    weights calculation          = 27.73  
    collect and process          = 5.42   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 188.30 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 88.11  
    alpha_beta                      = 7.10   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 97.42  
    fmodel                         = 6.28   
    r_factors                      = 0.18   
    phase_errors                   = 8.11   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 210.87 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.045 micro seconds
Total CPU time: 4.97 minutes
from_scatterers_fft:    641 calls, 87.85 s
gradients_fft:          586 calls, 86.00 s

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

# Date 2008-01-16 Time 01:42:03 PST -0800 (1200476523.68 s)
Start R-work = 0.4964, R-free = 0.4907 (no bulk solvent and anisotropic scale)
Final R-work = 0.1613, R-free = 0.2207 (no bulk solvent and anisotropic scale)

Start R-work = 0.4879, R-free = 0.4774
Final R-work = 0.1466, R-free = 0.2078