# Date 2008-01-16 Time 02:51:11 PST -0800 (1200480671.22 s)
#phil __OFF__

Command line arguments: "../1000.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12547
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1000

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.2261, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 1.9738
Completeness in resolution range: 0.9258
Completeness with d_max=infinity: 0.923139

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2591
                             d_min =   1.9738

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 1.9738
Completeness in resolution range: 0.9258
Completeness with d_max=infinity: 0.923139

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2595 -  4.2252 [2219/2245]  1997   222  10.0%
  bin  2:  4.2252 -  3.3655 [2144/2164]  1931   213   9.9%
  bin  3:  3.3655 -  2.9435 [2099/2118]  1889   210  10.0%
  bin  4:  2.9435 -  2.6760 [2086/2116]  1871   215  10.3%
  bin  5:  2.6760 -  2.4850 [2090/2109]  1886   204   9.8%
  bin  6:  2.4850 -  2.3391 [2072/2097]  1862   210  10.1%
  bin  7:  2.3391 -  2.2223 [2048/2076]  1840   208  10.2%
  bin  8:  2.2223 -  2.1258 [2038/2074]  1832   206  10.1%
  bin  9:  2.1258 -  2.0442 [2043/2091]  1855   188   9.2%
  bin 10:  2.0442 -  1.9738 [ 750/2069]   667    83  11.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1000/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 29
        2.42 -     3.04: 2176
        3.04 -     3.66: 4657
        3.66 -     4.28: 8927
        4.28 -     4.90: 12206
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.045 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.064 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.064 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.089 3.040 -x,y-1/2,-z+1/2
  ... (remaining 27990 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_1000/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1000/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.22605 88.54975 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: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5080   r_free= 0.4988   ksol= 0.00   Bsol= 0.00   scale= 0.764    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.307397                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.7133 0.99   1440  158 0.4315 0.4020      6.6601      6.6173|
|  2:  4.7133 -  3.7595 0.99   1389  157 0.4420 0.4496      6.8612      6.8731|
|  3:  3.7595 -  3.2897 0.99   1365  150 0.4774 0.4472      6.7027      6.6747|
|  4:  3.2897 -  2.9914 0.99   1345  156 0.5095 0.4777      6.5588      6.4974|
|  5:  2.9914 -  2.7784 0.99   1350  147 0.5398 0.5199      6.3817      6.4021|
|  6:  2.7784 -  2.6154 0.99   1345  148 0.5384 0.5504      6.2788      6.2248|
|  7:  2.6154 -  2.4850 0.99   1340  148 0.5497 0.4820      6.2516      6.1812|
|  8:  2.4850 -  2.3773 0.98   1318  150 0.5577 0.5600      6.1843      6.1763|
|  9:  2.3773 -  2.2861 0.98   1319  145 0.5372 0.5579      6.1361      6.2096|
| 10:  2.2861 -  2.2074 1.00   1341  144 0.5381 0.5632      6.0857      6.0934|
| 11:  2.2074 -  2.1386 0.98   1319  148 0.5277 0.5427       6.031      6.0518|
| 12:  2.1386 -  2.0776 0.98   1308  141 0.5421 0.5296      5.9376      5.9428|
| 13:  2.0776 -  2.0230 0.88   1173  134 0.5476 0.5267      5.8961      5.8082|
| 14:  2.0230 -  1.9738 0.21    278   33 0.5307 0.4142      5.8562      5.8311|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2595 -  4.7133  1440   158  0.67  36.54   0.77     0.72      81099.81|
|  2:  4.7133 -  3.7595  1389   157  0.67  37.58   0.84     0.75     122952.28|
|  3:  3.7595 -  3.2897  1365   150  0.54  48.56   0.81     0.68     130464.69|
|  4:  3.2897 -  2.9914  1345   156  0.45  56.12   0.74     0.55     116427.78|
|  5:  2.9914 -  2.7784  1350   147  0.36  62.86   0.70     0.45      90898.73|
|  6:  2.7784 -  2.6154  1345   148  0.31  66.55   0.69     0.37      79322.83|
|  7:  2.6154 -  2.4850  1340   148  0.27  69.74   0.71     0.32      72848.15|
|  8:  2.4850 -  2.3773  1318   150  0.22  73.56   0.70     0.27      67602.11|
|  9:  2.3773 -  2.2861  1319   145  0.18  76.24   0.71     0.22      65952.00|
| 10:  2.2861 -  2.2074  1341   144  0.17  77.35   0.72     0.21      58387.43|
| 11:  2.2074 -  2.1386  1319   148  0.16  78.35   0.76     0.21      56447.56|
| 12:  2.1386 -  2.0776  1308   141  0.20  74.99   0.71     0.26      47668.15|
| 13:  2.0776 -  2.0230  1173   134  0.24  71.88   0.69     0.32      41000.53|
| 14:  2.0230 -  1.9738   278    33  0.37  62.51   0.71     0.40      30681.29|
|alpha:            min =        0.21 max =            0.75 mean =         0.42|
|beta:             min =    30681.29 max =       130464.69 mean =     79244.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.46|
|phase err.(test): min =        0.00 max =           89.96 mean =        63.53|
|-----------------------------------------------------------------------------|

============================== 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 = 21.966746             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.982   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.997936              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.594   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       29 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1499 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2597 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3892 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4999 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6515 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7631 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.190 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.824 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.119)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.119)------------------------------------------|
|    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: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5123   r_free= 0.5016   ksol= 0.00   Bsol= 0.00   scale= 0.736    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.308075                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5007   r_free= 0.4873   ksol= 0.33   Bsol= 20.00   scale= 0.945   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.61,7.12,10.31,0.00,0.00,0.00); trace/3= 8.01                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.304266                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.295517             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.727   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.632952              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.021   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5007      final r-factor (work) = 0.4332          |
| start r-factor (free) = 0.4873      final r-factor (free) = 0.4573          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 111.8186 = 18.30 * 0.50 * 6.2998 + 1.00 * 54.1900                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.2847 = 18.30 * 0.50 * 6.2442 + 1.00 * 0.1639                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4332      final r-factor (work) = 0.3917          |
| start r-factor (free) = 0.4573      final r-factor (free) = 0.4486          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2110 = 1.63 * 1.00 * 6.2442 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1237 = 1.63 * 1.00 * 6.1863 + 1.00 * 0.0219                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.119)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.76   17.01    None  None   None       |
|    all(noH): 2823   0      0.00    85.76   17.01    None  None   None       |
|    Sol.    : 438    0      0.00    85.76   27.09    None  None   None       |
|    Mac.    : 2385   0      0.00    78.35   15.16    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 -   8.576:  904   |   5:    42.880 -  51.457:   85        |
|      1:     8.576 -  17.152:  772   |   6:    51.457 -  60.033:   46        |
|      2:    17.152 -  25.728:  530   |   7:    60.033 -  68.609:   26        |
|      3:    25.728 -  34.304:  299   |   8:    68.609 -  77.185:    7        |
|      4:    34.304 -  42.880:  149   |   9:    77.185 -  85.761:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3917 r_free = 0.4486             target_work(ml) = 6.175         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3910 r_free = 0.4492             target_work(ml) = 6.175         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3910   r_free= 0.4492   ksol= 0.33   Bsol= 20.00   scale= 1.109   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.61,7.12,10.31,0.00,0.00,0.00); trace/3= 8.01                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.174818                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3892   r_free= 0.4473   ksol= 0.35   Bsol= 62.67   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.99,3.90,6.91,0.00,0.00,0.00); trace/3= 4.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.176757                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.361090             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.123  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.599036              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.855  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3892      final r-factor (work) = 0.3144          |
| start r-factor (free) = 0.4473      final r-factor (free) = 0.3791          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.3764 = 12.36 * 0.50 * 6.1827 + 1.00 * 0.1639                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.7763 = 12.36 * 0.50 * 6.0947 + 1.00 * 0.1076                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3144      final r-factor (work) = 0.2903          |
| start r-factor (free) = 0.3791      final r-factor (free) = 0.3581          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6736 = 0.60 * 1.00 * 6.0947 + 1.00 * 0.0226                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6025 = 0.60 * 1.00 * 5.9811 + 1.00 * 0.0196                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.119)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.70   15.71    None  None   None       |
|    all(noH): 2823   0      0.00    85.70   15.71    None  None   None       |
|    Sol.    : 438    0      0.00    85.70   32.88    None  None   None       |
|    Mac.    : 2385   0      0.00    65.96   12.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.570:  974   |   5:    42.849 -  51.419:   71        |
|      1:     8.570 -  17.140:  906   |   6:    51.419 -  59.988:   37        |
|      2:    17.140 -  25.709:  449   |   7:    59.988 -  68.558:   27        |
|      3:    25.709 -  34.279:  223   |   8:    68.558 -  77.128:    3        |
|      4:    34.279 -  42.849:  129   |   9:    77.128 -  85.697:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2903 r_free = 0.3581             target_work(ml) = 5.959         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2902 r_free = 0.3575             target_work(ml) = 5.958         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2902   r_free= 0.3575   ksol= 0.35   Bsol= 62.67   scale= 1.073   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.99,3.90,6.91,0.00,0.00,0.00); trace/3= 4.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.958256                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2882   r_free= 0.3568   ksol= 0.33   Bsol= 62.67   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,1.37,4.20,0.00,0.00,0.00); trace/3= 2.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.958915                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.482467              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.932  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.973325              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.586  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2882      final r-factor (work) = 0.2276          |
| start r-factor (free) = 0.3568      final r-factor (free) = 0.2910          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5147 = 4.48 * 0.50 * 5.9820 + 1.00 * 0.1076                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2311 = 4.48 * 0.50 * 5.8715 + 1.00 * 0.0716                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2276      final r-factor (work) = 0.2057          |
| start r-factor (free) = 0.2910      final r-factor (free) = 0.2741          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7307 = 0.97 * 1.00 * 5.8715 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5837 = 0.97 * 1.00 * 5.7200 + 1.00 * 0.0164                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.119)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.82   16.31    None  None   None       |
|    all(noH): 2823   0      0.00    98.82   16.31    None  None   None       |
|    Sol.    : 438    0      0.00    98.82   41.68    None  None   None       |
|    Mac.    : 2385   0      0.00    80.47   11.65    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 -   9.882: 1335   |   5:    49.410 -  59.292:   96        |
|      1:     9.882 -  19.764:  762   |   6:    59.292 -  69.174:   53        |
|      2:    19.764 -  29.646:  283   |   7:    69.174 -  79.056:   31        |
|      3:    29.646 -  39.528:  143   |   8:    79.056 -  88.938:    9        |
|      4:    39.528 -  49.410:  109   |   9:    88.938 -  98.820:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2057 r_free = 0.2741             target_work(ml) = 5.692         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2056 r_free = 0.2739             target_work(ml) = 5.691         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2056   r_free= 0.2739   ksol= 0.33   Bsol= 62.67   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,1.37,4.20,0.00,0.00,0.00); trace/3= 2.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.691398                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2057   r_free= 0.2743   ksol= 0.33   Bsol= 71.26   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.87,0.57,3.11,0.00,0.00,0.00); trace/3= 1.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.692399                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.076898              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.970  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.297327              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.149  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2057      final r-factor (work) = 0.1638          |
| start r-factor (free) = 0.2743      final r-factor (free) = 0.2261          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7355 = 4.08 * 0.50 * 5.7219 + 1.00 * 0.0716                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4949 = 4.08 * 0.50 * 5.6033 + 1.00 * 0.0730                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1638      final r-factor (work) = 0.1555          |
| start r-factor (free) = 0.2261      final r-factor (free) = 0.2099          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6822 = 0.30 * 1.00 * 5.6033 + 1.00 * 0.0162                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6393 = 0.30 * 1.00 * 5.4743 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.119)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.39   15.48    None  None   None       |
|    all(noH): 2823   0      0.00    97.39   15.48    None  None   None       |
|    Sol.    : 438    0      3.02    97.39   41.11    None  None   None       |
|    Mac.    : 2385   0      0.00    77.53   10.77    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 -   9.739: 1450   |   5:    48.696 -  58.435:   94        |
|      1:     9.739 -  19.478:  756   |   6:    58.435 -  68.174:   56        |
|      2:    19.478 -  29.217:  194   |   7:    68.174 -  77.913:   21        |
|      3:    29.217 -  38.957:  125   |   8:    77.913 -  87.652:    8        |
|      4:    38.957 -  48.696:  117   |   9:    87.652 -  97.391:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1555 r_free = 0.2099             target_work(ml) = 5.434         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1554 r_free = 0.2097             target_work(ml) = 5.433         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1554   r_free= 0.2097   ksol= 0.33   Bsol= 71.26   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.87,0.57,3.11,0.00,0.00,0.00); trace/3= 1.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.433064                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1556   r_free= 0.2096   ksol= 0.32   Bsol= 65.98   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.39,0.05,2.34,0.00,0.00,0.00); trace/3= 0.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.433114                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.007727              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.583  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.750120              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.954  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1556      final r-factor (work) = 0.1348          |
| start r-factor (free) = 0.2096      final r-factor (free) = 0.1865          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0451 = 4.01 * 0.50 * 5.4755 + 1.00 * 0.0730                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8577 = 4.01 * 0.50 * 5.3783 + 1.00 * 0.0803                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1348      final r-factor (work) = 0.1293          |
| start r-factor (free) = 0.1865      final r-factor (free) = 0.1822          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0458 = 0.75 * 1.00 * 5.3783 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9848 = 0.75 * 1.00 * 5.2947 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.119)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.84  15.63    None  None   None       |
|    all(noH): 2823   0      0.00    101.84  15.63    None  None   None       |
|    Sol.    : 438    0      3.53    101.84  43.04    None  None   None       |
|    Mac.    : 2385   0      0.00    84.84   10.59    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 -  10.184: 1542   |   5:    50.919 -  61.103:   85        |
|      1:    10.184 -  20.368:  714   |   6:    61.103 -  71.287:   60        |
|      2:    20.368 -  30.552:  164   |   7:    71.287 -  81.471:   28        |
|      3:    30.552 -  40.736:  121   |   8:    81.471 -  91.655:   12        |
|      4:    40.736 -  50.919:   95   |   9:    91.655 - 101.839:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1293 r_free = 0.1822             target_work(ml) = 5.283         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1292 r_free = 0.1822             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1292   r_free= 0.1822   ksol= 0.32   Bsol= 65.98   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.39,0.05,2.34,0.00,0.00,0.00); trace/3= 0.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.282214                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.7133 0.99   1440  158 0.0984 0.1397      5.4149      5.6166|
|  2:  4.7133 -  3.7595 0.99   1389  157 0.0903 0.1195       5.489      5.6792|
|  3:  3.7595 -  3.2897 0.99   1365  150 0.1210 0.1731      5.5739      5.9174|
|  4:  3.2897 -  2.9914 0.99   1345  156 0.1467 0.1971      5.5887      5.7523|
|  5:  2.9914 -  2.7784 0.99   1350  147 0.1593 0.2077      5.4876      5.7244|
|  6:  2.7784 -  2.6154 0.99   1345  148 0.1528 0.2350      5.3802      5.6349|
|  7:  2.6154 -  2.4850 0.99   1340  148 0.1480 0.1854      5.3238      5.4742|
|  8:  2.4850 -  2.3773 0.98   1318  150 0.1427 0.2024      5.2256      5.4658|
|  9:  2.3773 -  2.2861 0.98   1319  145 0.1457 0.2239      5.1933      5.4681|
| 10:  2.2861 -  2.2074 1.00   1341  144 0.1341 0.1804      5.0781      5.2531|
| 11:  2.2074 -  2.1386 0.98   1319  148 0.1322 0.2068      5.0715      5.4637|
| 12:  2.1386 -  2.0776 0.98   1308  141 0.1327 0.2063      4.9842      5.2336|
| 13:  2.0776 -  2.0230 0.88   1173  134 0.1224 0.1835      4.8783      5.0727|
| 14:  2.0230 -  1.9738 0.21    278   33 0.1084 0.1802      4.7551      5.0823|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2595 -  4.7133  1440   158  0.93   9.87   0.97     0.94       8254.31|
|  2:  4.7133 -  3.7595  1389   157  0.95   8.88   1.01     1.00      10300.95|
|  3:  3.7595 -  3.2897  1365   150  0.92  13.06   1.04     1.04      12489.17|
|  4:  3.2897 -  2.9914  1345   156  0.89  16.84   1.01     0.99      13621.09|
|  5:  2.9914 -  2.7784  1350   147  0.87  19.49   1.00     0.97      11700.17|
|  6:  2.7784 -  2.6154  1345   148  0.86  20.53   0.98     0.94      10175.00|
|  7:  2.6154 -  2.4850  1340   148  0.87  19.30   0.99     0.94       8983.31|
|  8:  2.4850 -  2.3773  1318   150  0.87  19.33   0.99     0.96       7477.37|
|  9:  2.3773 -  2.2861  1319   145  0.87  19.20   1.00     0.94       6808.42|
| 10:  2.2861 -  2.2074  1341   144  0.88  18.60   1.01     0.97       5712.98|
| 11:  2.2074 -  2.1386  1319   148  0.87  19.28   0.99     0.93       5805.45|
| 12:  2.1386 -  2.0776  1308   141  0.88  18.64   1.00     0.99       5043.00|
| 13:  2.0776 -  2.0230  1173   134  0.87  19.82   0.99     0.96       4345.11|
| 14:  2.0230 -  1.9738   278    33  0.91  15.74   0.98     0.95       3262.46|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3262.46 max =        13621.09 mean =      8498.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.84 mean =        17.02|
|phase err.(test): min =        0.00 max =           89.15 mean =        16.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1292   r_free= 0.1822   ksol= 0.32   Bsol= 64.92   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.88,1.34,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.282216                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1292   r_free= 0.1822   ksol= 0.32   Bsol= 64.92   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.88,1.34,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.282216                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.7133 0.99   1440  158 0.0983 0.1397      5.4142      5.6173|
|  2:  4.7133 -  3.7595 0.99   1389  157 0.0902 0.1195      5.4888       5.679|
|  3:  3.7595 -  3.2897 0.99   1365  150 0.1210 0.1730      5.5739      5.9174|
|  4:  3.2897 -  2.9914 0.99   1345  156 0.1467 0.1973       5.589      5.7527|
|  5:  2.9914 -  2.7784 0.99   1350  147 0.1593 0.2077      5.4878      5.7249|
|  6:  2.7784 -  2.6154 0.99   1345  148 0.1529 0.2352      5.3807      5.6356|
|  7:  2.6154 -  2.4850 0.99   1340  148 0.1480 0.1854      5.3242      5.4746|
|  8:  2.4850 -  2.3773 0.98   1318  150 0.1427 0.2027      5.2259      5.4666|
|  9:  2.3773 -  2.2861 0.98   1319  145 0.1457 0.2240      5.1932      5.4682|
| 10:  2.2861 -  2.2074 1.00   1341  144 0.1342 0.1801      5.0781      5.2523|
| 11:  2.2074 -  2.1386 0.98   1319  148 0.1323 0.2063       5.071      5.4625|
| 12:  2.1386 -  2.0776 0.98   1308  141 0.1327 0.2065      4.9841      5.2338|
| 13:  2.0776 -  2.0230 0.88   1173  134 0.1224 0.1835      4.8783      5.0727|
| 14:  2.0230 -  1.9738 0.21    278   33 0.1083 0.1800      4.7548      5.0811|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2595 -  4.7133  1440   158  0.93   9.88   0.97     0.94       8266.34|
|  2:  4.7133 -  3.7595  1389   157  0.95   8.88   1.01     1.00      10307.60|
|  3:  3.7595 -  3.2897  1365   150  0.92  13.06   1.03     1.04      12491.82|
|  4:  3.2897 -  2.9914  1345   156  0.89  16.84   1.01     0.98      13623.75|
|  5:  2.9914 -  2.7784  1350   147  0.87  19.49   0.99     0.97      11714.95|
|  6:  2.7784 -  2.6154  1345   148  0.86  20.53   0.97     0.94      10184.54|
|  7:  2.6154 -  2.4850  1340   148  0.87  19.31   0.99     0.94       8993.33|
|  8:  2.4850 -  2.3773  1318   150  0.87  19.34   0.99     0.96       7485.78|
|  9:  2.3773 -  2.2861  1319   145  0.87  19.21   0.99     0.94       6817.09|
| 10:  2.2861 -  2.2074  1341   144  0.88  18.59   1.00     0.97       5709.86|
| 11:  2.2074 -  2.1386  1319   148  0.87  19.26   0.99     0.93       5796.88|
| 12:  2.1386 -  2.0776  1308   141  0.88  18.62   0.99     0.99       5036.23|
| 13:  2.0776 -  2.0230  1173   134  0.87  19.82   0.99     0.96       4343.00|
| 14:  2.0230 -  1.9738   278    33  0.91  15.73   0.98     0.95       3260.53|
|alpha:            min =        0.93 max =            1.04 mean =         0.96|
|beta:             min =     3260.53 max =        13623.75 mean =      8503.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.85 mean =        17.01|
|phase err.(test): min =        0.00 max =           89.29 mean =        16.35|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.119)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.85    102.69  16.48    None  None   None       |
|    all(noH): 2823   0      0.85    102.69  16.48    None  None   None       |
|    Sol.    : 438    0      4.38    102.69  43.90    None  None   None       |
|    Mac.    : 2385   0      0.85    85.69   11.45    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:     0.855 -  11.039: 1542   |   5:    51.774 -  61.958:   85        |
|      1:    11.039 -  21.223:  714   |   6:    61.958 -  72.142:   60        |
|      2:    21.223 -  31.407:  164   |   7:    72.142 -  82.326:   28        |
|      3:    31.407 -  41.590:  121   |   8:    82.326 -  92.510:   12        |
|      4:    41.590 -  51.774:   95   |   9:    92.510 - 102.694:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.408 - 5.220
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 324 from: 329
   mapped sites are within: 0.739 - 5.220

peak=    9.538 closest distance to " CB  VAL A 230 " =    1.429
peak=    7.724 closest distance to " O   HOH Z 103 " =    1.157
peak=    6.885 closest distance to " CG2 VAL A 296 " =    1.242
peak=    6.651 closest distance to " CD2 LEU A   5 " =    1.327
peak=    6.384 closest distance to " O   HOH Z  70 " =    1.177
peak=    5.983 closest distance to " CG  ARG A 138 " =    1.164
peak=    5.685 closest distance to " O   HOH Z 222 " =    1.510
peak=    5.588 closest distance to " O   HOH Z 130 " =    1.136
peak=    5.440 closest distance to " NE2 GLN A  11 " =    1.125
peak=    5.375 closest distance to " O   HOH Z   7 " =    1.765
peak=    5.177 closest distance to " CG  PRO A  54 " =    1.424
peak=    5.007 closest distance to " O   HOH Z 143 " =    2.079
peak=    4.929 closest distance to " CB  VAL A 230 " =    1.287
peak=    4.889 closest distance to " O   HOH Z 127 " =    1.299
peak=    4.886 closest distance to " O   HOH Z  63 " =    1.428
peak=    4.841 closest distance to " CB  ASN A 148 " =    1.418
peak=    4.818 closest distance to " O   HOH Z 427 " =    2.496
peak=    4.800 closest distance to " CG  LEU A 228 " =    1.141
peak=    4.762 closest distance to " CB  SER A  63 " =    1.288
peak=    4.738 closest distance to " O   HOH Z 232 " =    2.168
peak=    4.727 closest distance to " NH1 ARG A 138 " =    1.107
peak=    4.695 closest distance to " CD1AILE A 234 " =    1.036
peak=    4.626 closest distance to " O   HOH Z 246 " =    1.185
peak=    4.617 closest distance to " O   HOH Z  65 " =    1.430
peak=    4.615 closest distance to " O   HOH Z 425 " =    1.740
peak=    4.606 closest distance to " CB  GLN A 223 " =    1.587
peak=    4.573 closest distance to " O   HOH Z 369 " =    2.104
peak=    4.500 closest distance to " CB  PRO A  54 " =    1.055
peak=    4.468 closest distance to " O   HOH Z 255 " =    1.067
peak=    4.451 closest distance to " O   HOH Z 186 " =    1.355
peak=    4.402 closest distance to " O   HOH Z 287 " =    2.130
peak=    4.357 closest distance to " NH2AARG A 190 " =    1.838
peak=    4.265 closest distance to " O   HOH Z  69 " =    1.210
peak=    4.218 closest distance to " O   SER A  87 " =    2.474
peak=    4.211 closest distance to " CZ3 TRP A 266 " =    1.150
peak=    4.207 closest distance to " O   HOH Z 126 " =    2.007
peak=    4.203 closest distance to " CA  ALA A  51 " =    1.037
peak=    4.175 closest distance to " CG  LEU A 167 " =    1.254
peak=    4.172 closest distance to " CG BARG A 275 " =    1.386
peak=    4.164 closest distance to " O   HOH Z 207 " =    1.203
peak=    4.141 closest distance to " CD2 LEU A 228 " =    1.280
peak=    4.119 closest distance to " CB  ASN A 142 " =    0.900
peak=    4.104 closest distance to " CD  ARG A 159 " =    0.788
peak=    4.098 closest distance to " O   HOH Z 406 " =    1.583
peak=    4.094 closest distance to " O   HOH Z 411 " =    3.218
peak=    4.078 closest distance to " O   HOH Z 148 " =    1.513
peak=    4.074 closest distance to " ND1 HIS A  86 " =    1.803
peak=    4.073 closest distance to " O   HOH Z  49 " =    1.117
peak=    4.070 closest distance to " O   HOH Z   9 " =    2.426
peak=    4.064 closest distance to " O   HOH Z 298 " =    2.006
peak=    4.063 closest distance to " O   HOH Z 389 " =    1.440
peak=    4.044 closest distance to " CB  SER A 216 " =    1.098
peak=    4.035 closest distance to " CE  LYS A  76 " =    0.926
peak=    4.028 closest distance to " CG1 VAL A 296 " =    1.233
peak=    4.019 closest distance to " O   HOH Z 423 " =    1.874
peak=    4.005 closest distance to " CB  GLN A 183 " =    1.216
peak=    3.983 closest distance to " CB  ASP A 124 " =    0.866
peak=    3.955 closest distance to " CD1 LEU A   5 " =    1.389
peak=    3.933 closest distance to " O   HOH Z 427 " =    1.230
peak=    3.908 closest distance to " O   HOH Z 362 " =    2.293
peak=    3.903 closest distance to " O   HOH Z  39 " =    1.119
peak=    3.882 closest distance to " CE3 TRP A 274 " =    1.363
peak=    3.882 closest distance to " CG  LYS A  76 " =    1.722
peak=    3.882 closest distance to " O   HOH Z 183 " =    1.315
peak=    3.872 closest distance to " CG  LEU A   5 " =    1.211
peak=    3.871 closest distance to " CZ  PHE A 218 " =    1.122
peak=    3.870 closest distance to " CG2 ILE A 234 " =    0.985
peak=    3.859 closest distance to " CB  VAL A 202 " =    1.538
peak=    3.858 closest distance to " CB  LEU A 237 " =    0.858
peak=    3.854 closest distance to " CG  ASN A  60 " =    1.122
peak=    3.853 closest distance to " O   HOH Z 316 " =    3.085
peak=    3.848 closest distance to " O   HOH Z 437 " =    1.878
peak=    3.839 closest distance to " O   HOH Z 112 " =    1.001
peak=    3.838 closest distance to " O   PRO A 198 " =    1.337
peak=    3.836 closest distance to " CG  PRO A 198 " =    1.297
peak=    3.836 closest distance to " O   TYR A 116 " =    1.250
peak=    3.834 closest distance to " O   HOH Z 117 " =    1.051
peak=    3.833 closest distance to " O   HOH Z 392 " =    1.276
peak=    3.826 closest distance to " O   HOH Z 251 " =    1.761
peak=    3.802 closest distance to " O   HOH Z 414 " =    1.239
peak=    3.796 closest distance to " OE2 GLU A   2 " =    2.239
peak=    3.786 closest distance to " O   HOH Z 258 " =    1.230
peak=    3.773 closest distance to " O   HOH Z  78 " =    1.769
peak=    3.769 closest distance to " O   HOH Z 361 " =    1.338
peak=    3.768 closest distance to " CB  GLU A 277 " =    3.668
peak=    3.765 closest distance to " CB  ASN A  39 " =    0.942
peak=    3.759 closest distance to " CG  PRO A 213 " =    1.322
peak=    3.758 closest distance to " C   GLN A  73 " =    1.094
peak=    3.758 closest distance to " NH1AARG A 145 " =    1.225
peak=    3.754 closest distance to " CA  ALA A 160 " =    1.127
peak=    3.750 closest distance to " O   HOH Z 145 " =    2.140
peak=    3.733 closest distance to " CG  PRO A 243 " =    1.038
peak=    3.732 closest distance to " O   HOH Z 258 " =    1.500
peak=    3.727 closest distance to " O   HOH Z 410 " =    1.641
peak=    3.723 closest distance to " CG1 ILE A 151 " =    1.193
peak=    3.722 closest distance to " CG2 THR A 221 " =    1.327
peak=    3.718 closest distance to " O   HOH Z 248 " =    1.125
peak=    3.715 closest distance to " O   HOH Z 143 " =    1.514
peak=    3.702 closest distance to " O   HOH Z  61 " =    1.671
peak=    3.701 closest distance to " O   HOH Z 359 " =    1.512
peak=    3.698 closest distance to " CB  MET A  40 " =    0.841
peak=    3.698 closest distance to " O   HOH Z 111 " =    1.867
peak=    3.697 closest distance to " CG  GLN A  58 " =    1.240
peak=    3.697 closest distance to " CD1 ILE A  33 " =    2.040
peak=    3.689 closest distance to " O   ASP A 200 " =    1.479
peak=    3.688 closest distance to " O   HOH Z 156 " =    3.088
peak=    3.677 closest distance to " ND1 HIS A  81 " =    1.965
peak=    3.669 closest distance to " CA  ARG A 195 " =    1.316
peak=    3.664 closest distance to " O   HOH Z 257 " =    1.208
peak=    3.656 closest distance to " O   HOH Z 211 " =    1.573
peak=    3.650 closest distance to " NH2 ARG A  56 " =    1.100
peak=    3.648 closest distance to " O   HOH Z 126 " =    1.591
peak=    3.646 closest distance to " O   THR A 294 " =    1.101
peak=    3.643 closest distance to " O   HOH Z 182 " =    1.224
peak=    3.623 closest distance to " ND2BASN A 224 " =    0.894
peak=    3.623 closest distance to " O   HOH Z 245 " =    1.249
peak=    3.615 closest distance to " CB  ASN A 110 " =    1.095
peak=    3.613 closest distance to " CA  ASN A 127 " =    1.109
peak=    3.609 closest distance to " O   HOH Z 380 " =    1.837
peak=    3.596 closest distance to " O   HOH Z 421 " =    2.347
peak=    3.595 closest distance to " CG2 VAL A 257 " =    0.921
peak=    3.595 closest distance to " O   HOH Z 303 " =    2.136
peak=    3.588 closest distance to " CB  MET A  47 " =    1.091
peak=    3.580 closest distance to " CB  ASN A  60 " =    0.946
peak=    3.576 closest distance to " CD  ARG A 138 " =    1.225
peak=    3.576 closest distance to " CD  ARG A 269 " =    0.901
peak=    3.575 closest distance to " O   HOH Z 153 " =    3.785
peak=    3.565 closest distance to " CB  TYR A 169 " =    0.894
peak=    3.564 closest distance to " CB  ARG A 275 " =    1.048
peak=    3.558 closest distance to " N   ALA A 256 " =    1.055
peak=    3.558 closest distance to " CD  PRO A  54 " =    1.083
peak=    3.557 closest distance to " CA  GLY A 267 " =    1.269
peak=    3.557 closest distance to " O   HOH Z  68 " =    2.219
peak=    3.554 closest distance to " O   HOH Z  88 " =    3.687
peak=    3.546 closest distance to " NE AARG A 275 " =    1.666
peak=    3.544 closest distance to " CA  ARG A 156 " =    1.078
peak=    3.543 closest distance to " O   HOH Z  27 " =    1.136
peak=    3.539 closest distance to " O   HOH Z  30 " =    1.906
peak=    3.538 closest distance to " CG  GLN A  89 " =    1.640
peak=    3.537 closest distance to " O   HOH Z 434 " =    1.467
peak=    3.535 closest distance to " CA  TYR A 116 " =    1.424
peak=    3.534 closest distance to " O   HOH Z 218 " =    1.633
peak=    3.531 closest distance to " O   HOH Z 273 " =    2.677
peak=    3.531 closest distance to " N   CYS A 260 " =    0.944
peak=    3.529 closest distance to " N   PHE A 130 " =    1.373
peak=    3.528 closest distance to " O   HOH Z 332 " =    1.589
peak=    3.528 closest distance to " NZ  LYS A 119 " =    3.011
peak=    3.528 closest distance to " CE3 TRP A 150 " =    1.129
peak=    3.526 closest distance to " C   PRO A  54 " =    0.789
peak=    3.512 closest distance to " CD2 TRP A 179 " =    1.281
peak=    3.510 closest distance to " O   HOH Z 180 " =    2.251
peak=    3.510 closest distance to " O   HOH Z 238 " =    1.523
peak=    3.509 closest distance to " CB  SER A  62 " =    0.834
peak=    3.505 closest distance to " CB  ARG A 138 " =    1.262
peak=    3.503 closest distance to " CB  VAL A 265 " =    1.359
peak=    3.499 closest distance to " CB  PRO A  90 " =    1.126
peak=    3.497 closest distance to " O   HOH Z   2 " =    1.618
peak=    3.495 closest distance to " O   HOH Z  80 " =    1.690
peak=    3.494 closest distance to " CA  TYR A  30 " =    1.064
peak=    3.491 closest distance to " O   HOH Z  53 " =    2.458
peak=    3.485 closest distance to " CB  SER A   3 " =    1.635
peak=    3.484 closest distance to " OE1 GLN A 278 " =    1.237
peak=    3.483 closest distance to " O   HOH Z 403 " =    1.541
peak=    3.478 closest distance to " CE  MET A  93 " =    1.497
peak=    3.474 closest distance to " O   HOH Z  59 " =    1.913
peak=    3.470 closest distance to " O   HOH Z 265 " =    1.836
peak=    3.467 closest distance to " CA  ASP A 162 " =    0.839
peak=    3.462 closest distance to " CB  VAL A 250 " =    1.140
peak=    3.462 closest distance to " O   HOH Z  71 " =    1.377
peak=    3.461 closest distance to " CB  TRP A 266 " =    1.008
peak=    3.459 closest distance to " O   HOH Z 172 " =    5.220
peak=    3.457 closest distance to " CB  THR A  52 " =    1.099
peak=    3.456 closest distance to " O   HOH Z   3 " =    2.270
peak=    3.455 closest distance to " OG  SER A 135 " =    1.243
peak=    3.453 closest distance to " OD1 ASN A 148 " =    1.936
peak=    3.448 closest distance to " CD1 LEU A 300 " =    1.118
peak=    3.443 closest distance to " OE1 GLN A 240 " =    1.569
peak=    3.442 closest distance to " CG2 ILE A  20 " =    1.633
peak=    3.441 closest distance to " N   TYR A  15 " =    1.065
peak=    3.437 closest distance to " O   HOH Z 193 " =    1.744
peak=    3.433 closest distance to " O   HOH Z  97 " =    1.420
peak=    3.433 closest distance to " CA  ARG A 159 " =    1.110
peak=    3.433 closest distance to " NE1 TRP A 274 " =    0.933
peak=    3.431 closest distance to " O   HOH Z  20 " =    1.651
peak=    3.430 closest distance to " O   HOH Z 193 " =    1.840
peak=    3.429 closest distance to " O   HOH Z 122 " =    2.027
peak=    3.428 closest distance to " CB  GLU A 152 " =    1.113
peak=    3.424 closest distance to " O   HOH Z 353 " =    1.679
peak=    3.416 closest distance to " OD1 ASP A  65 " =    1.691
peak=    3.414 closest distance to " CD  ARG A 195 " =    3.550
peak=    3.413 closest distance to " CA  ILE A 234 " =    1.050
peak=    3.408 closest distance to " O   HOH Z 422 " =    1.204
peak=    3.406 closest distance to " CZ3 TRP A 266 " =    0.966
peak=    3.397 closest distance to " CE3 TRP A  85 " =    1.032
peak=    3.397 closest distance to " O   HOH Z 132 " =    2.616
peak=    3.393 closest distance to " ND2 ASN A 187 " =    1.968
peak=    3.392 closest distance to " CD  ARG A  66 " =    2.326
peak=    3.391 closest distance to " NE2 GLN A  58 " =    4.651
peak=    3.390 closest distance to " CB  TRP A 179 " =    1.406
peak=    3.384 closest distance to " O   HOH Z 272 " =    1.857
peak=    3.382 closest distance to " CA  VAL A 125 " =    1.190
peak=    3.380 closest distance to " O   HOH Z  88 " =    3.028
peak=    3.375 closest distance to " CA  ARG A  36 " =    1.087
peak=    3.370 closest distance to " O   HOH Z 214 " =    2.632
peak=    3.368 closest distance to " O   HOH Z 218 " =    1.637
peak=    3.365 closest distance to " CB  ARG A 102 " =    0.852
peak=    3.363 closest distance to " OG1 THR A 264 " =    0.751
peak=    3.362 closest distance to " CB  HIS A 108 " =    0.844
peak=    3.362 closest distance to " O   HOH Z 188 " =    2.917
peak=    3.362 closest distance to " O   HOH Z 422 " =    2.531
peak=    3.360 closest distance to " CG1 ILE A  49 " =    1.838
peak=    3.357 closest distance to " CD2 TYR A 186 " =    1.093
peak=    3.355 closest distance to " CB  TRP A 150 " =    1.167
peak=    3.351 closest distance to " CZ3 TRP A  92 " =    1.210
peak=    3.348 closest distance to " N   SER A 271 " =    0.969
peak=    3.345 closest distance to " CB  GLU A 175 " =    1.000
peak=    3.345 closest distance to " CG  ARG A 159 " =    0.952
peak=    3.343 closest distance to " O   HOH Z 115 " =    1.677
peak=    3.339 closest distance to " O   HOH Z 184 " =    1.505
peak=    3.338 closest distance to " O   HOH Z 298 " =    2.418
peak=    3.337 closest distance to " O   HOH Z 148 " =    2.421
peak=    3.334 closest distance to " O   HOH Z 158 " =    2.837
peak=    3.332 closest distance to " O   THR A 182 " =    1.475
peak=    3.332 closest distance to " CB  THR A 235 " =    1.269
peak=    3.330 closest distance to " CA  GLN A  94 " =    0.757
peak=    3.329 closest distance to " CD BLYS A 290 " =    1.017
peak=    3.326 closest distance to " O   HOH Z  58 " =    1.911
peak=    3.318 closest distance to " CA  ASP A 124 " =    0.803
peak=    3.317 closest distance to " NZ  LYS A 117 " =    2.981
peak=    3.314 closest distance to " O   HOH Z 417 " =    1.136
peak=    3.312 closest distance to " O   HOH Z 158 " =    3.029
peak=    3.309 closest distance to " O   HOH Z 154 " =    1.883
peak=    3.308 closest distance to " CG  GLN A  88 " =    1.054
peak=    3.307 closest distance to " NH2AARG A 145 " =    1.129
peak=    3.307 closest distance to " O   HOH Z 273 " =    1.262
peak=    3.306 closest distance to " CB  GLU A 236 " =    1.338
peak=    3.304 closest distance to " O   HOH Z 145 " =    1.642
peak=    3.302 closest distance to " NH1 ARG A  14 " =    0.959
peak=    3.302 closest distance to " O   HOH Z 104 " =    1.775
peak=    3.301 closest distance to " O   HOH Z 345 " =    4.275
peak=    3.297 closest distance to " OG  SER A  62 " =    2.699
peak=    3.291 closest distance to " CA  ASN A 284 " =    0.931
peak=    3.290 closest distance to " O   ASN A 209 " =    1.555
peak=    3.289 closest distance to " CB  GLN A  88 " =    1.356
peak=    3.283 closest distance to " CB  GLN A  89 " =    1.142
peak=    3.278 closest distance to " CZ3 TRP A 177 " =    1.127
peak=    3.272 closest distance to " O   HOH Z 357 " =    2.478
peak=    3.270 closest distance to " O   HOH Z  10 " =    1.690
peak=    3.269 closest distance to " CG  GLU A  37 " =    0.973
peak=    3.261 closest distance to " O   HOH Z 328 " =    1.675
peak=    3.260 closest distance to " CG  PHE A 204 " =    0.846
peak=    3.260 closest distance to " CG1 ILE A 120 " =    1.301
peak=    3.254 closest distance to " O   HOH Z 234 " =    3.886
peak=    3.253 closest distance to " O   MET A 105 " =    1.720
peak=    3.251 closest distance to " O   HOH Z  28 " =    1.343
peak=    3.251 closest distance to " CB  SER A 212 " =    1.562
peak=    3.242 closest distance to " CG ALYS A 290 " =    1.078
peak=    3.242 closest distance to " CB  ALA A  43 " =    0.840
peak=    3.240 closest distance to " CA  ASN A 215 " =    1.172
peak=    3.237 closest distance to " CD1 ILE A 199 " =    1.031
peak=    3.235 closest distance to " O   HOH Z 225 " =    1.797
peak=    3.233 closest distance to " CA  ALA A  21 " =    1.168
peak=    3.232 closest distance to " CG1 VAL A 153 " =    0.935
peak=    3.230 closest distance to " O   HOH Z 280 " =    3.075
peak=    3.224 closest distance to " CA  VAL A 112 " =    1.200
peak=    3.218 closest distance to " O   HOH Z 368 " =    4.261
peak=    3.216 closest distance to " O   HOH Z 119 " =    1.751
peak=    3.214 closest distance to " O   HOH Z 281 " =    2.446
peak=    3.209 closest distance to " O   HOH Z  57 " =    1.385
peak=    3.208 closest distance to " CA  ARG A 139 " =    1.134
peak=    3.208 closest distance to " O   HOH Z 197 " =    1.801
peak=    3.203 closest distance to " CA  SER A  12 " =    1.570
peak=    3.195 closest distance to " O   GLY A 211 " =    1.118
peak=    3.193 closest distance to " O   HOH Z  76 " =    1.413
peak=    3.188 closest distance to " O   HOH Z 290 " =    1.505
peak=    3.184 closest distance to " NE2 HIS A 207 " =    1.038
peak=    3.182 closest distance to " O   HOH Z 248 " =    1.897
peak=    3.173 closest distance to " O   HOH Z 403 " =    1.334
peak=    3.172 closest distance to " CA  ALA A 129 " =    1.344
peak=    3.172 closest distance to " CA  ALA A 154 " =    1.072
peak=    3.170 closest distance to " N   SER A 135 " =    1.318
peak=    3.163 closest distance to " CA  LEU A 282 " =    1.201
peak=    3.157 closest distance to " O   HOH Z 357 " =    2.177
peak=    3.153 closest distance to " O   HOH Z 109 " =    2.801
peak=    3.152 closest distance to " O   HOH Z  64 " =    2.440
peak=    3.149 closest distance to " O   HOH Z 172 " =    2.671
peak=    3.148 closest distance to " CA  ARG A 102 " =    1.119
peak=    3.144 closest distance to " O   HOH Z 368 " =    3.358
peak=    3.141 closest distance to " O   HOH Z 409 " =    3.072
peak=    3.137 closest distance to " O   HOH Z 227 " =    1.948
peak=    3.134 closest distance to " O   HOH Z  85 " =    2.098
peak=    3.131 closest distance to " CA  ALA A 184 " =    1.183
peak=    3.131 closest distance to " N   ASN A 127 " =    1.388
peak=    3.131 closest distance to " CA  ALA A 299 " =    0.999
peak=    3.128 closest distance to " CB  ALA A   1 " =    4.839
peak=    3.128 closest distance to " O   HOH Z  78 " =    2.046
peak=    3.112 closest distance to " O   HOH Z 216 " =    3.642
peak=    3.109 closest distance to " CZ3 TRP A  92 " =    1.036
peak=    3.106 closest distance to " CA  MET A 105 " =    0.870
peak=    3.106 closest distance to " CB  ALA A  10 " =    0.892
peak=    3.104 closest distance to " O   HOH Z 325 " =    2.213
peak=    3.102 closest distance to " O   HOH Z 303 " =    2.646
peak=    3.101 closest distance to " OE2 GLU A  53 " =    0.897
peak=    3.098 closest distance to " O   HOH Z 343 " =    2.838
peak=    3.095 closest distance to " CB  LYS A 290 " =    0.990
peak=    3.084 closest distance to " O   HOH Z 425 " =    2.102
peak=    3.081 closest distance to " O   HOH Z 194 " =    2.198
peak=    3.079 closest distance to " N   GLU A   2 " =    1.533
peak=    3.076 closest distance to " CE AMET A  47 " =    1.320
peak=    3.075 closest distance to " O   HOH Z 423 " =    1.327
peak=    3.074 closest distance to " OG  SER A  28 " =    1.329
peak=    3.069 closest distance to " O   HOH Z 359 " =    4.302
peak=    3.068 closest distance to " CA  ILE A 106 " =    0.833
peak=    3.059 closest distance to " N   ASP A 162 " =    1.211
peak=    3.053 closest distance to " CB  ASP A 140 " =    0.900
peak=    3.051 closest distance to " CB  THR A  31 " =    1.431
peak=    3.043 closest distance to " O   CYS A 168 " =    1.435
peak=    3.029 closest distance to " CD  LYS A 119 " =    1.670
peak=    3.018 closest distance to " O   HOH Z 148 " =    2.025
peak=    3.016 closest distance to " CG2 ILE A 120 " =    1.279
peak=    3.014 closest distance to " O   HOH Z 302 " =    1.671
peak=    3.010 closest distance to " O   HOH Z 368 " =    2.069
peak=    3.007 closest distance to " CB  ALA A 114 " =    0.739
peak=    3.003 closest distance to " CB  MET A  40 " =    0.990

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 228         
Filter by distance & map next to the model:
   mapped sites are within: 0.263 - 5.576
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 225 from: 228
   mapped sites are within: 0.713 - 5.576

peak=   -4.850 closest distance to " CB  VAL A 230 " =    1.128
peak=   -4.643 closest distance to " O   PRO A 198 " =    1.387
peak=   -4.431 closest distance to " OE1 GLN A  88 " =    0.922
peak=   -4.426 closest distance to " CZ2 TRP A  92 " =    2.838
peak=   -4.377 closest distance to " CG2 VAL A 230 " =    0.857
peak=   -4.287 closest distance to " CD  ARG A 138 " =    1.425
peak=   -4.273 closest distance to " CD  ARG A  14 " =    3.144
peak=   -4.263 closest distance to " CB  ASP A  27 " =    2.543
peak=   -4.257 closest distance to " CB  PRO A 243 " =    2.687
peak=   -4.160 closest distance to " O   HOH Z 100 " =    0.848
peak=   -4.112 closest distance to " CG  ARG A 219 " =    2.364
peak=   -4.093 closest distance to " O   PRO A 163 " =    1.961
peak=   -4.069 closest distance to " O   HOH Z 368 " =    1.329
peak=   -4.050 closest distance to " O   HOH Z 111 " =    1.532
peak=   -4.048 closest distance to " CD  GLN A  55 " =    1.085
peak=   -3.994 closest distance to " CG1 VAL A 250 " =    2.622
peak=   -3.978 closest distance to " O   HOH Z 255 " =    1.034
peak=   -3.953 closest distance to " O   HOH Z 103 " =    0.713
peak=   -3.938 closest distance to " O   HOH Z 231 " =    0.754
peak=   -3.923 closest distance to " O   HOH Z 216 " =    1.284
peak=   -3.904 closest distance to " O   HOH Z  39 " =    0.829
peak=   -3.893 closest distance to " O   HOH Z  69 " =    1.860
peak=   -3.886 closest distance to " CD2 LEU A   5 " =    0.920
peak=   -3.881 closest distance to " CG2 VAL A 296 " =    1.123
peak=   -3.876 closest distance to " O   HOH Z  60 " =    1.461
peak=   -3.855 closest distance to " CG2 VAL A 202 " =    2.808
peak=   -3.800 closest distance to " O   HOH Z 275 " =    1.895
peak=   -3.793 closest distance to " CD  ARG A 156 " =    2.030
peak=   -3.792 closest distance to " CG1 VAL A 112 " =    2.682
peak=   -3.787 closest distance to " CG  GLN A  88 " =    0.807
peak=   -3.784 closest distance to " O   HOH Z 177 " =    2.628
peak=   -3.781 closest distance to " OG BSER A 134 " =    1.624
peak=   -3.769 closest distance to " O   HOH Z  44 " =    0.953
peak=   -3.759 closest distance to " O   HOH Z  52 " =    2.208
peak=   -3.736 closest distance to " CD  LYS A 289 " =    2.299
peak=   -3.729 closest distance to " O   HOH Z 231 " =    1.902
peak=   -3.718 closest distance to " O   HOH Z 128 " =    2.518
peak=   -3.712 closest distance to " CB  PRO A 163 " =    2.296
peak=   -3.703 closest distance to " CE2 TYR A  30 " =    2.569
peak=   -3.698 closest distance to " O   HOH Z 207 " =    1.168
peak=   -3.693 closest distance to " OG  SER A 141 " =    1.692
peak=   -3.689 closest distance to " CG2 ILE A  20 " =    2.752
peak=   -3.684 closest distance to " CG  ARG A 219 " =    2.756
peak=   -3.683 closest distance to " CD  PRO A 213 " =    2.163
peak=   -3.681 closest distance to " CB  ALA A  43 " =    2.681
peak=   -3.675 closest distance to " N   ALA A  43 " =    2.774
peak=   -3.670 closest distance to " CB  GLN A  55 " =    1.249
peak=   -3.654 closest distance to " O   HOH Z 298 " =    2.836
peak=   -3.654 closest distance to " OD1 ASN A  60 " =    0.800
peak=   -3.651 closest distance to " CG  ARG A 259 " =    2.438
peak=   -3.630 closest distance to " NE2 GLN A 223 " =    1.513
peak=   -3.630 closest distance to " O   HOH Z 412 " =    4.493
peak=   -3.617 closest distance to " CG2 THR A 178 " =    2.284
peak=   -3.614 closest distance to " O   HOH Z  32 " =    1.584
peak=   -3.594 closest distance to " CD1 LEU A 101 " =    2.320
peak=   -3.589 closest distance to " CG  GLU A 277 " =    1.274
peak=   -3.588 closest distance to " O   HOH Z 131 " =    3.970
peak=   -3.584 closest distance to " CD1 LEU A 255 " =    2.973
peak=   -3.582 closest distance to " CG  MET A 105 " =    0.956
peak=   -3.575 closest distance to " CG2BVAL A  41 " =    2.338
peak=   -3.574 closest distance to " O   SER A 276 " =    1.677
peak=   -3.571 closest distance to " O   HOH Z 147 " =    2.083
peak=   -3.570 closest distance to " OG  SER A  28 " =    2.144
peak=   -3.570 closest distance to " O   HOH Z 183 " =    1.413
peak=   -3.562 closest distance to " C   GLU A   2 " =    1.803
peak=   -3.559 closest distance to " O   HOH Z 143 " =    1.415
peak=   -3.555 closest distance to " O   HOH Z 193 " =    1.074
peak=   -3.546 closest distance to " O   SER A  22 " =    2.648
peak=   -3.546 closest distance to " O   HOH Z 134 " =    1.666
peak=   -3.542 closest distance to " CG2AVAL A  41 " =    2.833
peak=   -3.538 closest distance to " CG1 VAL A 125 " =    2.355
peak=   -3.537 closest distance to " NZ  LYS A 166 " =    1.173
peak=   -3.537 closest distance to " CB  TRP A  85 " =    2.411
peak=   -3.537 closest distance to " OG  SER A  87 " =    1.419
peak=   -3.532 closest distance to " O   HOH Z 377 " =    1.863
peak=   -3.531 closest distance to " O   HOH Z  68 " =    1.505
peak=   -3.529 closest distance to " OG  SER A  97 " =    2.209
peak=   -3.521 closest distance to " CG  ARG A 138 " =    1.034
peak=   -3.514 closest distance to " CG  TRP A 266 " =    1.684
peak=   -3.512 closest distance to " N   THR A 157 " =    1.539
peak=   -3.510 closest distance to " CD2 HIS A 207 " =    2.249
peak=   -3.509 closest distance to " NH2AARG A 275 " =    5.490
peak=   -3.506 closest distance to " CB  ALA A 291 " =    2.107
peak=   -3.500 closest distance to " O   HOH Z 276 " =    1.105
peak=   -3.492 closest distance to " CD1 TYR A 247 " =    2.589
peak=   -3.490 closest distance to " CA  HIS A 207 " =    1.078
peak=   -3.487 closest distance to " CA  GLY A 241 " =    3.101
peak=   -3.476 closest distance to " O   HOH Z  52 " =    0.762
peak=   -3.473 closest distance to " O   HOH Z 389 " =    2.463
peak=   -3.468 closest distance to " ND2 ASN A 285 " =    2.208
peak=   -3.463 closest distance to " O   HOH Z 286 " =    1.608
peak=   -3.462 closest distance to " O   HOH Z 268 " =    1.080
peak=   -3.461 closest distance to " O   HOH Z 133 " =    1.559
peak=   -3.460 closest distance to " OE1 GLN A 278 " =    1.166
peak=   -3.458 closest distance to " O   HOH Z 411 " =    5.242
peak=   -3.451 closest distance to " O   HOH Z 139 " =    0.903
peak=   -3.449 closest distance to " CB  ASP A 132 " =    2.362
peak=   -3.439 closest distance to " O   ALA A  84 " =    1.725
peak=   -3.439 closest distance to " O   HOH Z 155 " =    1.071
peak=   -3.438 closest distance to " O   GLY A 203 " =    2.623
peak=   -3.431 closest distance to " CB  ALA A 129 " =    2.559
peak=   -3.430 closest distance to " O   HOH Z 359 " =    3.224
peak=   -3.429 closest distance to " CG1 VAL A 112 " =    3.072
peak=   -3.422 closest distance to " CG2 ILE A 151 " =    2.613
peak=   -3.422 closest distance to " CB  PHE A 130 " =    1.289
peak=   -3.417 closest distance to " O   HOH Z 118 " =    1.156
peak=   -3.415 closest distance to " O   HOH Z 144 " =    0.986
peak=   -3.414 closest distance to " CA  GLY A 241 " =    2.382
peak=   -3.409 closest distance to " CE BMET A  47 " =    1.413
peak=   -3.408 closest distance to " CA  ASP A 298 " =    1.116
peak=   -3.403 closest distance to " OG ASER A 134 " =    1.175
peak=   -3.402 closest distance to " CA  ASN A 110 " =    1.013
peak=   -3.400 closest distance to " CB  ASP A 200 " =    2.611
peak=   -3.396 closest distance to " CB  ALA A 227 " =    2.351
peak=   -3.388 closest distance to " CD2 TYR A 116 " =    2.267
peak=   -3.386 closest distance to " CD1 PHE A 218 " =    1.501
peak=   -3.385 closest distance to " O   HOH Z 149 " =    2.166
peak=   -3.383 closest distance to " O   HOH Z 394 " =    1.708
peak=   -3.378 closest distance to " CB  ALA A 161 " =    1.706
peak=   -3.378 closest distance to " C   ASN A 285 " =    2.405
peak=   -3.375 closest distance to " O   HOH Z 275 " =    1.613
peak=   -3.366 closest distance to " CD2 LEU A 143 " =    2.398
peak=   -3.365 closest distance to " CB  ALA A   9 " =    2.631
peak=   -3.363 closest distance to " O   HOH Z 198 " =    2.071
peak=   -3.361 closest distance to " CD2 PHE A  61 " =    2.004
peak=   -3.358 closest distance to " O   HOH Z 389 " =    1.426
peak=   -3.358 closest distance to " O   HOH Z 165 " =    1.797
peak=   -3.357 closest distance to " OD2 ASP A  50 " =    1.687
peak=   -3.352 closest distance to " CD2 TYR A 293 " =    1.982
peak=   -3.342 closest distance to " CA  GLY A  98 " =    1.945
peak=   -3.334 closest distance to " NH2 ARG A 219 " =    1.755
peak=   -3.333 closest distance to " NH2 ARG A  79 " =    2.213
peak=   -3.326 closest distance to " O   HOH Z 435 " =    2.379
peak=   -3.325 closest distance to " N   ALA A 244 " =    1.325
peak=   -3.325 closest distance to " O   HOH Z 112 " =    1.003
peak=   -3.314 closest distance to " O   HOH Z 434 " =    1.871
peak=   -3.310 closest distance to " O   HOH Z 103 " =    0.928
peak=   -3.299 closest distance to " C   ARG A 269 " =    1.464
peak=   -3.299 closest distance to " O   HOH Z 368 " =    1.932
peak=   -3.293 closest distance to " CD1 ILE A 199 " =    2.501
peak=   -3.292 closest distance to " O   HOH Z  53 " =    1.559
peak=   -3.290 closest distance to " CG2 THR A  31 " =    2.441
peak=   -3.285 closest distance to " O   HOH Z 163 " =    1.792
peak=   -3.285 closest distance to " OE1 GLN A  77 " =    1.063
peak=   -3.285 closest distance to " O   HOH Z  11 " =    1.667
peak=   -3.283 closest distance to " CG  LEU A 281 " =    1.989
peak=   -3.282 closest distance to " C   HIS A 108 " =    1.220
peak=   -3.280 closest distance to " O   HOH Z  24 " =    1.093
peak=   -3.277 closest distance to " O   HOH Z 292 " =    1.670
peak=   -3.277 closest distance to " O   HOH Z  30 " =    1.745
peak=   -3.271 closest distance to " O   ALA A  51 " =    1.428
peak=   -3.267 closest distance to " O   HOH Z 313 " =    1.537
peak=   -3.253 closest distance to " CE1 PHE A  16 " =    2.751
peak=   -3.248 closest distance to " OE2 GLU A 152 " =    1.196
peak=   -3.242 closest distance to " O   HOH Z  73 " =    2.350
peak=   -3.241 closest distance to " O   HOH Z   9 " =    1.726
peak=   -3.237 closest distance to " OE1 GLN A  89 " =    1.651
peak=   -3.236 closest distance to " O   HOH Z 351 " =    1.516
peak=   -3.233 closest distance to " O   HOH Z 219 " =    4.529
peak=   -3.218 closest distance to " O   HOH Z  77 " =    1.694
peak=   -3.213 closest distance to " CB  ALA A 100 " =    2.090
peak=   -3.212 closest distance to " O   HOH Z 398 " =    0.933
peak=   -3.211 closest distance to " C   GLN A 205 " =    1.882
peak=   -3.209 closest distance to " CD1 LEU A   5 " =    2.422
peak=   -3.206 closest distance to " CD2 TYR A 247 " =    2.418
peak=   -3.205 closest distance to " OD1 ASP A 171 " =    1.607
peak=   -3.204 closest distance to " O   HOH Z 191 " =    5.576
peak=   -3.203 closest distance to " O   HOH Z 281 " =    2.688
peak=   -3.202 closest distance to " O   HOH Z  10 " =    1.541
peak=   -3.200 closest distance to " CB  ALA A   7 " =    1.937
peak=   -3.191 closest distance to " CB  ALA A 248 " =    2.064
peak=   -3.189 closest distance to " O   HOH Z 407 " =    3.010
peak=   -3.186 closest distance to " O   HOH Z 350 " =    1.751
peak=   -3.184 closest distance to " C   VAL A  72 " =    0.988
peak=   -3.181 closest distance to " CG1 VAL A  78 " =    2.475
peak=   -3.180 closest distance to " CB  PRO A  54 " =    2.471
peak=   -3.179 closest distance to " O   GLY A  80 " =    2.550
peak=   -3.179 closest distance to " O   ILE A  49 " =    1.707
peak=   -3.179 closest distance to " O   HOH Z 117 " =    0.860
peak=   -3.179 closest distance to " NH2 ARG A  66 " =    3.741
peak=   -3.178 closest distance to " OE1 GLU A 277 " =    2.260
peak=   -3.174 closest distance to " CG2BVAL A  72 " =    2.140
peak=   -3.168 closest distance to " ND2 ASN A  45 " =    2.566
peak=   -3.167 closest distance to " CZ2 TRP A 274 " =    1.065
peak=   -3.164 closest distance to " O   SER A 271 " =    2.127
peak=   -3.163 closest distance to " CD1 LEU A 228 " =    2.353
peak=   -3.161 closest distance to " CA  GLY A 133 " =    2.072
peak=   -3.160 closest distance to " O   HOH Z 357 " =    2.211
peak=   -3.159 closest distance to " OG  SER A 245 " =    1.497
peak=   -3.159 closest distance to " O   HOH Z 371 " =    1.372
peak=   -3.158 closest distance to " O   HOH Z 364 " =    1.361
peak=   -3.157 closest distance to " CB  HIS A  86 " =    1.194
peak=   -3.155 closest distance to " O   HOH Z 236 " =    1.336
peak=   -3.154 closest distance to " CD1 TRP A  85 " =    1.050
peak=   -3.147 closest distance to " O   HOH Z 165 " =    2.281
peak=   -3.146 closest distance to " C   ALA A 158 " =    1.321
peak=   -3.140 closest distance to " O   ASP A 253 " =    1.766
peak=   -3.138 closest distance to " CB  ALA A 161 " =    2.635
peak=   -3.137 closest distance to " O   HOH Z 251 " =    4.722
peak=   -3.136 closest distance to " O   HOH Z 166 " =    2.009
peak=   -3.135 closest distance to " C   ASN A 176 " =    1.346
peak=   -3.132 closest distance to " C   MET A 188 " =    1.517
peak=   -3.128 closest distance to " O   HOH Z 140 " =    1.418
peak=   -3.126 closest distance to " O   HOH Z 295 " =    1.753
peak=   -3.125 closest distance to " CG  LEU A 282 " =    2.555
peak=   -3.123 closest distance to " O   HOH Z 147 " =    0.891
peak=   -3.122 closest distance to " O   HOH Z 426 " =    1.833
peak=   -3.117 closest distance to " O   HOH Z 244 " =    1.843
peak=   -3.115 closest distance to " C   ASN A 148 " =    1.616
peak=   -3.111 closest distance to " CE3 TRP A  70 " =    1.645
peak=   -3.105 closest distance to " O   HOH Z 387 " =    0.981
peak=   -3.104 closest distance to " O   HOH Z 353 " =    1.839
peak=   -3.099 closest distance to " O   HOH Z  52 " =    2.010
peak=   -3.098 closest distance to " O   PHE A 218 " =    1.622
peak=   -3.096 closest distance to " CB  ALA A 291 " =    2.293
peak=   -3.094 closest distance to " CB  GLN A  11 " =    1.663
peak=   -3.076 closest distance to " CA  TYR A  68 " =    1.143
peak=   -3.073 closest distance to " CA  LEU A   5 " =    2.823
peak=   -3.066 closest distance to " O   HOH Z 252 " =    3.844
peak=   -3.048 closest distance to " CE1 TYR A 247 " =    2.638
peak=   -3.040 closest distance to " O   HOH Z 365 " =    1.793
peak=   -3.036 closest distance to " O   HOH Z 356 " =    4.369
peak=   -3.035 closest distance to " O   HOH Z  86 " =    2.746
peak=   -3.023 closest distance to " CA  GLY A 133 " =    2.342
peak=   -3.017 closest distance to " CG2 VAL A 230 " =    1.056

================= 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    :  0.5080 0.4988   6.307397e+00   6.291587e+00
   1_bss:  0.5007 0.4873   6.304266e+00   6.287298e+00
   1_xyz:  0.4332 0.4573   6.228846e+00   6.250158e+00
   1_adp:  0.3917 0.4486   6.174940e+00   6.245191e+00
   1_occ:  0.3910 0.4492   6.174818e+00   6.246048e+00
   2_bss:  0.3892 0.4473   6.176757e+00   6.246189e+00
   2_xyz:  0.3144 0.3791   6.007884e+00   6.134646e+00
   2_adp:  0.2903 0.3581   5.959107e+00   6.095855e+00
   2_occ:  0.2902 0.3575   5.958256e+00   6.094781e+00
   3_bss:  0.2882 0.3568   5.958915e+00   6.094711e+00
   3_xyz:  0.2276 0.2910   5.761941e+00   5.945049e+00
   3_adp:  0.2057 0.2741   5.691803e+00   5.898197e+00
   3_occ:  0.2056 0.2739   5.691398e+00   5.897991e+00
   4_bss:  0.2057 0.2743   5.692399e+00   5.897732e+00
   4_xyz:  0.1638 0.2261   5.492956e+00   5.726609e+00
   4_adp:  0.1555 0.2099   5.433827e+00   5.652907e+00
   4_occ:  0.1554 0.2097   5.433064e+00   5.652082e+00
   5_bss:  0.1556 0.2096   5.433114e+00   5.650643e+00
   5_xyz:  0.1348 0.1865   5.313340e+00   5.544543e+00
   5_adp:  0.1293 0.1822   5.282628e+00   5.519998e+00
   5_occ:  0.1292 0.1822   5.282214e+00   5.519576e+00
   5_bss:  0.1292 0.1822   5.282216e+00   5.519695e+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:  0.328  20.000   6.607   7.120  10.306   0.000   0.000   0.000
   1_xyz:  0.328  20.000   6.607   7.120  10.306   0.000   0.000   0.000
   1_adp:  0.328  20.000   6.607   7.120  10.306   0.000   0.000   0.000
   1_occ:  0.328  20.000   6.607   7.120  10.306   0.000   0.000   0.000
   2_bss:  0.348  62.666   3.992   3.898   6.905   0.000   0.000   0.000
   2_xyz:  0.348  62.666   3.992   3.898   6.905   0.000   0.000   0.000
   2_adp:  0.348  62.666   3.992   3.898   6.905   0.000   0.000   0.000
   2_occ:  0.348  62.666   3.992   3.898   6.905   0.000   0.000   0.000
   3_bss:  0.334  62.666   1.674   1.369   4.199   0.000   0.000   0.000
   3_xyz:  0.334  62.666   1.674   1.369   4.199   0.000   0.000   0.000
   3_adp:  0.334  62.666   1.674   1.369   4.199   0.000   0.000   0.000
   3_occ:  0.334  62.666   1.674   1.369   4.199   0.000   0.000   0.000
   4_bss:  0.331  71.263   0.874   0.570   3.112   0.000   0.000   0.000
   4_xyz:  0.331  71.263   0.874   0.570   3.112   0.000   0.000   0.000
   4_adp:  0.331  71.263   0.874   0.570   3.112   0.000   0.000   0.000
   4_occ:  0.331  71.263   0.874   0.570   3.112   0.000   0.000   0.000
   5_bss:  0.324  65.976   0.391   0.045   2.341   0.000   0.000   0.000
   5_xyz:  0.324  65.976   0.391   0.045   2.341   0.000   0.000   0.000
   5_adp:  0.324  65.976   0.391   0.045   2.341   0.000   0.000   0.000
   5_occ:  0.324  65.976   0.391   0.045   2.341   0.000   0.000   0.000
   5_bss:  0.320  64.915  -0.469  -0.875   1.344  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.465 0.3479  0.4151    79253.893
   1_bss:  62.771 0.3566  0.5339    78350.985
   1_xyz:  55.169 0.4538  0.6646    63783.701
   1_adp:  52.757 0.4849  0.7955    61579.124
   1_occ:  52.923 0.4827  0.7908    61913.595
   2_bss:  52.714 0.4853  0.7174    61651.033
   2_xyz:  41.998 0.6170  0.8869    40321.922
   2_adp:  38.877 0.6551  0.9252    35939.330
   2_occ:  38.849 0.6554  0.9246    35790.169
   3_bss:  38.770 0.6564  0.8492    35777.121
   3_xyz:  30.224 0.7539  0.9472    22698.462
   3_adp:  27.874 0.7801  0.9536    19943.091
   3_occ:  27.880 0.7799  0.9527    19906.166
   4_bss:  27.865 0.7802  0.9236    19932.036
   4_xyz:  22.396 0.8371  0.9696    13348.153
   4_adp:  20.265 0.8590  0.9782    11568.537
   4_occ:  20.242 0.8592  0.9781    11526.166
   5_bss:  20.216 0.8594  0.9583    11497.392
   5_xyz:  17.540 0.8845  0.9711     8986.788
   5_adp:  16.962 0.8898  0.9670     8515.921
   5_occ:  16.948 0.8899  0.9669     8499.733
   5_bss:  16.948 0.8899  0.9646     8503.993
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.4190e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.4190e+01
   1_xyz:   1.832  0.015  0.115 18.694  0.007  4.107   1.6390e-01
   1_adp:   1.832  0.015  0.115 18.694  0.007  4.107   1.6390e-01
   1_occ:   1.832  0.015  0.115 18.694  0.007  4.107   1.6390e-01
   2_bss:   1.832  0.015  0.115 18.694  0.007  4.107   1.6390e-01
   2_xyz:   1.319  0.010  0.093 17.260  0.006  4.108   1.0757e-01
   2_adp:   1.319  0.010  0.093 17.260  0.006  4.108   1.0757e-01
   2_occ:   1.319  0.010  0.093 17.260  0.006  4.108   1.0757e-01
   3_bss:   1.319  0.010  0.093 17.260  0.006  4.108   1.0757e-01
   3_xyz:   1.087  0.008  0.081 16.166  0.004  4.128   7.1648e-02
   3_adp:   1.087  0.008  0.081 16.166  0.004  4.128   7.1648e-02
   3_occ:   1.087  0.008  0.081 16.166  0.004  4.128   7.1648e-02
   4_bss:   1.087  0.008  0.081 16.166  0.004  4.128   7.1648e-02
   4_xyz:   1.092  0.008  0.080 15.924  0.004  4.113   7.2975e-02
   4_adp:   1.092  0.008  0.080 15.924  0.004  4.113   7.2975e-02
   4_occ:   1.092  0.008  0.080 15.924  0.004  4.113   7.2975e-02
   5_bss:   1.092  0.008  0.080 15.924  0.004  4.113   7.2975e-02
   5_xyz:   1.164  0.010  0.087 15.774  0.004  4.125   8.0305e-02
   5_adp:   1.164  0.010  0.087 15.774  0.004  4.125   8.0305e-02
   5_occ:   1.164  0.010  0.087 15.774  0.004  4.125   8.0305e-02
   5_bss:   1.164  0.010  0.087 15.774  0.004  4.125   8.0305e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0251e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0251e+00
   1_xyz:  14.701  0.188  0.474 85.785  0.033  2.153   1.1368e-01
   1_adp:  14.701  0.188  0.474 85.785  0.033  2.153   1.1368e-01
   1_occ:  14.701  0.188  0.474 85.785  0.033  2.153   1.1368e-01
   2_bss:  14.701  0.188  0.474 85.785  0.033  2.153   1.1368e-01
   2_xyz:   7.225  0.093  0.319 86.339  0.037  2.176   6.9414e-02
   2_adp:   7.225  0.093  0.319 86.339  0.037  2.176   6.9414e-02
   2_occ:   7.225  0.093  0.319 86.339  0.037  2.176   6.9414e-02
   3_bss:   7.225  0.093  0.319 86.339  0.037  2.176   6.9414e-02
   3_xyz:   7.315  0.060  0.316 82.587  0.033  2.273   6.4657e-02
   3_adp:   7.315  0.060  0.316 82.587  0.033  2.273   6.4657e-02
   3_occ:   7.315  0.060  0.316 82.587  0.033  2.273   6.4657e-02
   4_bss:   7.315  0.060  0.316 82.587  0.033  2.273   6.4657e-02
   4_xyz:   7.077  0.056  0.324 89.578  0.043  2.240   4.6943e-02
   4_adp:   7.077  0.056  0.324 89.578  0.043  2.240   4.6943e-02
   4_occ:   7.077  0.056  0.324 89.578  0.043  2.240   4.6943e-02
   5_bss:   7.077  0.056  0.324 89.578  0.043  2.240   4.6943e-02
   5_xyz:  10.141  0.077  0.474 82.006  0.043  2.284   5.4704e-02
   5_adp:  10.141  0.077  0.474 82.006  0.043  2.284   5.4704e-02
   5_occ:  10.141  0.077  0.474 82.006  0.043  2.284   5.4704e-02
   5_bss:  10.141  0.077  0.474 82.006  0.043  2.284   5.4704e-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:  85.76   0.00  17.01  78.35   0.00  15.16  85.76   0.00  27.09
   1_occ:  85.76   0.00  17.01  78.35   0.00  15.16  85.76   0.00  27.09
   2_bss:  85.76   0.00  17.01  78.35   0.00  15.16  85.76   0.00  27.09
   2_xyz:  85.76   0.00  17.01  78.35   0.00  15.16  85.76   0.00  27.09
   2_adp:  85.70   0.00  15.71  65.96   0.00  12.55  85.70   0.00  32.88
   2_occ:  85.70   0.00  15.71  65.96   0.00  12.55  85.70   0.00  32.88
   3_bss:  85.70   0.00  15.71  65.96   0.00  12.55  85.70   0.00  32.88
   3_xyz:  85.70   0.00  15.71  65.96   0.00  12.55  85.70   0.00  32.88
   3_adp:  98.82   0.00  16.31  80.47   0.00  11.65  98.82   0.00  41.68
   3_occ:  98.82   0.00  16.31  80.47   0.00  11.65  98.82   0.00  41.68
   4_bss:  98.82   0.00  16.31  80.47   0.00  11.65  98.82   0.00  41.68
   4_xyz:  98.82   0.00  16.31  80.47   0.00  11.65  98.82   0.00  41.68
   4_adp:  97.39   0.00  15.48  77.53   0.00  10.77  97.39   3.02  41.11
   4_occ:  97.39   0.00  15.48  77.53   0.00  10.77  97.39   3.02  41.11
   5_bss:  97.39   0.00  15.48  77.53   0.00  10.77  97.39   3.02  41.11
   5_xyz:  97.39   0.00  15.48  77.53   0.00  10.77  97.39   3.02  41.11
   5_adp: 101.84   0.00  15.63  84.84   0.00  10.59 101.84   3.53  43.04
   5_occ: 101.84   0.00  15.63  84.84   0.00  10.59 101.84   3.53  43.04
   5_bss: 102.69   0.85  16.48  85.69   0.85  11.45 102.69   4.38  43.90
------------------------------------------------------------------------
 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:    1.278    0.018    0.419
   1_adp:    1.278    0.018    0.419
   1_occ:    1.278    0.018    0.419
   2_bss:    1.278    0.018    0.419
   2_xyz:    1.761    0.022    0.619
   2_adp:    1.761    0.022    0.619
   2_occ:    1.761    0.022    0.619
   3_bss:    1.761    0.022    0.619
   3_xyz:    1.779    0.084    0.712
   3_adp:    1.779    0.084    0.712
   3_occ:    1.779    0.084    0.712
   4_bss:    1.779    0.084    0.712
   4_xyz:    1.812    0.006    0.802
   4_adp:    1.812    0.006    0.802
   4_occ:    1.812    0.006    0.802
   5_bss:    1.812    0.006    0.802
   5_xyz:    1.844    0.034    0.835
   5_adp:    1.844    0.034    0.835
   5_occ:    1.844    0.034    0.835
   5_bss:    1.844    0.034    0.835
------------------------------------------------------------------------

CPU time actual refinement: 336.67


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1000/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_1000/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1000/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1000/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1000/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.52 
  Macro-tasks:
    bulk solvent and scale       = 41.20  
    individual site refinement   = 139.44 
    weights calculation          = 31.44  
    collect and process          = 6.27   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 218.46 
  Micro-tasks:
    mask                            = 2.40   
    f_calc                          = 106.39 
    alpha_beta                      = 7.99   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 115.11 
    fmodel                         = 6.75   
    r_factors                      = 0.18   
    phase_errors                   = 10.10  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 250.31 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.811 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    616 calls, 106.14 s
gradients_fft:          561 calls, 102.70 s

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

# Date 2008-01-16 Time 02:57:00 PST -0800 (1200481020.50 s)
Start R-work = 0.5080, R-free = 0.4988 (no bulk solvent and anisotropic scale)
Final R-work = 0.1460, R-free = 0.1991 (no bulk solvent and anisotropic scale)

Start R-work = 0.5007, R-free = 0.4873
Final R-work = 0.1292, R-free = 0.1822