# Date 2008-01-16 Time 02:52:53 PST -0800 (1200480773.59 s)
#phil __OFF__

Command line arguments: "../1015.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3333
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1015

-------------------------------------------------------------------------------
  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, 46.6953, 85.5261, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98104
Completeness in resolution range: 0.958694
Completeness with d_max=infinity: 0.955794

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1145
                             d_min =   1.9810

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, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98104
Completeness in resolution range: 0.958694
Completeness with d_max=infinity: 0.955794

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1149 -  4.2396 [2142/2168]  1931   211   9.9%
  bin  2:  4.2396 -  3.3774 [2064/2083]  1856   208  10.1%
  bin  3:  3.3774 -  2.9541 [2031/2050]  1826   205  10.1%
  bin  4:  2.9541 -  2.6857 [2015/2045]  1814   201  10.0%
  bin  5:  2.6857 -  2.4941 [2016/2035]  1819   197   9.8%
  bin  6:  2.4941 -  2.3476 [1983/2008]  1777   206  10.4%
  bin  7:  2.3476 -  2.2304 [1992/2020]  1793   199  10.0%
  bin  8:  2.2304 -  2.1336 [1970/2006]  1779   191   9.7%
  bin  9:  2.1336 -  2.0517 [1973/2015]  1772   201  10.2%
  bin 10:  2.0517 -  1.9810 [1403/2003]  1263   140  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1015/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: 16
        2.42 -     3.04: 2194
        3.04 -     3.66: 4691
        3.66 -     4.28: 9066
        4.28 -     4.90: 12324
  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 107 " - " O   HOH Z 340 "  2.096 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.180 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.180 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.214 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28286 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_1015/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1015/model_refine_001.geo

CPU time processing inputs: 9.33


============================ 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 46.69535 85.5261 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: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4430   r_free= 0.4293   ksol= 0.00   Bsol= 0.00   scale= 0.816    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.238817                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7289 0.99   1392  155 0.3757 0.3688      6.5386      6.4979|
|  2:  4.7289 -  3.7727 0.99   1342  146 0.3423 0.3536      6.6808      6.6856|
|  3:  3.7727 -  3.3014 0.99   1314  147 0.3920 0.3548      6.5777      6.6101|
|  4:  3.3014 -  3.0022 0.99   1315  153 0.4166 0.3955      6.4682      6.4053|
|  5:  3.0022 -  2.7884 0.99   1297  139 0.4633 0.4750      6.3262       6.339|
|  6:  2.7884 -  2.6249 0.99   1286  143 0.4628 0.4633      6.2371      6.2198|
|  7:  2.6249 -  2.4941 0.99   1300  139 0.4967 0.4764      6.2414      6.2087|
|  8:  2.4941 -  2.3859 0.98   1261  151 0.4954 0.4455      6.1435      6.1338|
|  9:  2.3859 -  2.2944 0.98   1281  145 0.4727 0.4597      6.0962      6.0954|
| 10:  2.2944 -  2.2155 0.99   1279  138 0.4963 0.4768      6.0911      6.0764|
| 11:  2.2155 -  2.1464 0.98   1286  138 0.5004 0.4547      6.0312      5.9856|
| 12:  2.1464 -  2.0852 0.97   1241  139 0.4816 0.5420      5.9565      6.0176|
| 13:  2.0852 -  2.0305 1.00   1263  140 0.5284 0.5077      5.8792       5.818|
| 14:  2.0305 -  1.9810 0.59    773   86 0.5145 0.4789      5.8398      5.7648|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7289  1392   155  0.72  32.70   0.81     0.75      64445.94|
|  2:  4.7289 -  3.7727  1342   146  0.76  29.89   0.90     0.82      81116.31|
|  3:  3.7727 -  3.3014  1314   147  0.68  36.84   0.87     0.79      84476.56|
|  4:  3.3014 -  3.0022  1315   153  0.62  42.23   0.83     0.71      76881.45|
|  5:  3.0022 -  2.7884  1297   139  0.52  50.58   0.76     0.60      67747.59|
|  6:  2.7884 -  2.6249  1286   143  0.49  53.11   0.76     0.56      61890.19|
|  7:  2.6249 -  2.4941  1300   139  0.48  53.93   0.75     0.53      55984.92|
|  8:  2.4941 -  2.3859  1261   151  0.47  54.56   0.73     0.56      49747.19|
|  9:  2.3859 -  2.2944  1281   145  0.50  52.28   0.76     0.56      42828.78|
| 10:  2.2944 -  2.2155  1279   138  0.48  53.29   0.78     0.55      39290.48|
| 11:  2.2155 -  2.1464  1286   138  0.45  56.20   0.78     0.53      38436.09|
| 12:  2.1464 -  2.0852  1241   139  0.42  58.61   0.77     0.50      38181.73|
| 13:  2.0852 -  2.0305  1263   140  0.38  61.47   0.74     0.48      33882.32|
| 14:  2.0305 -  1.9810   773    86  0.45  56.42   0.72     0.49      25609.80|
|alpha:            min =        0.48 max =            0.82 mean =         0.61|
|beta:             min =    25609.80 max =        84476.56 mean =     55482.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.97 mean =        48.99|
|phase err.(test): min =        0.00 max =           89.95 mean =        49.05|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.155171              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.755   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.737954              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.695   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      166 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      687 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1512 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2648 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3902 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5078 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6558 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7748 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.716 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.667 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    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: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4502   r_free= 0.4377   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.242681                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4341   r_free= 0.4197   ksol= 0.34   Bsol= 13.74   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.90,8.15,8.10,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.232984                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.329104              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.699   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.719548              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.401   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4341      final r-factor (work) = 0.3327          |
| start r-factor (free) = 0.4197      final r-factor (free) = 0.3594          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 79.7264 = 8.33 * 0.50 * 6.2456 + 1.00 * 53.7165                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.5226 = 8.33 * 0.50 * 6.0986 + 1.00 * 0.1245                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3327      final r-factor (work) = 0.2746          |
| start r-factor (free) = 0.3594      final r-factor (free) = 0.3206          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4030 = 0.72 * 1.00 * 6.0986 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2899 = 0.72 * 1.00 * 5.9451 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.96   11.08    None  None   None       |
|    all(noH): 2823   0      0.00    72.96   11.08    None  None   None       |
|    Sol.    : 438    0      0.00    70.09   27.97    None  None   None       |
|    Mac.    : 2385   0      0.00    72.96   7.98     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.297: 1420   |   5:    36.482 -  43.779:   79        |
|      1:     7.297 -  14.593:  739   |   6:    43.779 -  51.075:   44        |
|      2:    14.593 -  21.890:  241   |   7:    51.075 -  58.372:   15        |
|      3:    21.890 -  29.186:  161   |   8:    58.372 -  65.668:    3        |
|      4:    29.186 -  36.482:  118   |   9:    65.668 -  72.965:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2746 r_free = 0.3206             target_work(ml) = 5.897         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2738 r_free = 0.3214             target_work(ml) = 5.896         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2738   r_free= 0.3214   ksol= 0.34   Bsol= 13.74   scale= 1.094   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.90,8.15,8.10,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.896229                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2692   r_free= 0.3153   ksol= 0.33   Bsol= 41.80   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.14,4.13,5.13,0.00,0.00,0.00); trace/3= 4.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.893362                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.032893              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.946   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.342452              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.484  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2692      final r-factor (work) = 0.1809          |
| start r-factor (free) = 0.3153      final r-factor (free) = 0.2270          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1198 = 4.03 * 0.50 * 5.9489 + 1.00 * 0.1241                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6153 = 4.03 * 0.50 * 5.7287 + 1.00 * 0.0637                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1809      final r-factor (work) = 0.1629          |
| start r-factor (free) = 0.2270      final r-factor (free) = 0.2076          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9738 = 0.34 * 1.00 * 5.7287 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8904 = 0.34 * 1.00 * 5.4900 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.79   11.51    None  None   None       |
|    all(noH): 2823   0      0.00    70.79   11.51    None  None   None       |
|    Sol.    : 438    0      0.64    69.00   32.24    None  None   None       |
|    Mac.    : 2385   0      0.00    70.79   7.71     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.079: 1480   |   5:    35.393 -  42.471:  126        |
|      1:     7.079 -  14.157:  676   |   6:    42.471 -  49.550:   75        |
|      2:    14.157 -  21.236:  202   |   7:    49.550 -  56.629:   23        |
|      3:    21.236 -  28.314:  114   |   8:    56.629 -  63.707:   11        |
|      4:    28.314 -  35.393:  112   |   9:    63.707 -  70.786:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1629 r_free = 0.2076             target_work(ml) = 5.450         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1628 r_free = 0.2075             target_work(ml) = 5.450         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1628   r_free= 0.2075   ksol= 0.33   Bsol= 41.80   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.14,4.13,5.13,0.00,0.00,0.00); trace/3= 4.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.450136                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1615   r_free= 0.2060   ksol= 0.34   Bsol= 46.99   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.40,2.86,3.93,0.00,0.00,0.00); trace/3= 3.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.450077                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.946631              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.974  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.036100              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.811  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1615      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.2060      final r-factor (free) = 0.1723          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1683 = 2.95 * 0.50 * 5.5009 + 1.00 * 0.0637                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9469 = 2.95 * 0.50 * 5.3496 + 1.00 * 0.0652                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1674          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5530 = 1.04 * 1.00 * 5.3496 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4278 = 1.04 * 1.00 * 5.2261 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.23   12.26    None  None   None       |
|    all(noH): 2823   0      0.00    80.23   12.26    None  None   None       |
|    Sol.    : 438    0      1.54    77.62   35.77    None  None   None       |
|    Mac.    : 2385   0      0.00    80.23   7.94     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 -   8.023: 1624   |   5:    40.115 -  48.138:   88        |
|      1:     8.023 -  16.046:  601   |   6:    48.138 -  56.161:   74        |
|      2:    16.046 -  24.069:  167   |   7:    56.161 -  64.184:   40        |
|      3:    24.069 -  32.092:  103   |   8:    64.184 -  72.207:   12        |
|      4:    32.092 -  40.115:  108   |   9:    72.207 -  80.230:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1217 r_free = 0.1674             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1216 r_free = 0.1672             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1672   ksol= 0.34   Bsol= 46.99   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.40,2.86,3.93,0.00,0.00,0.00); trace/3= 3.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.210805                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1668   ksol= 0.34   Bsol= 46.99   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,2.63,3.59,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.211167                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.801316              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.441  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.156108              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.717  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1219      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1668      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3872 = 2.80 * 0.50 * 5.2276 + 1.00 * 0.0652                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3295 = 2.80 * 0.50 * 5.1812 + 1.00 * 0.0724                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8218 = 0.16 * 1.00 * 5.1812 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8163 = 0.16 * 1.00 * 5.1696 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.89   11.63    None  None   None       |
|    all(noH): 2823   0      0.00    78.89   11.63    None  None   None       |
|    Sol.    : 438    0      1.65    75.48   32.70    None  None   None       |
|    Mac.    : 2385   0      0.00    78.89   7.76     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.889: 1647   |   5:    39.444 -  47.333:   87        |
|      1:     7.889 -  15.778:  611   |   6:    47.333 -  55.221:   59        |
|      2:    15.778 -  23.666:  152   |   7:    55.221 -  63.110:   25        |
|      3:    23.666 -  31.555:  127   |   8:    63.110 -  70.999:    8        |
|      4:    31.555 -  39.444:  104   |   9:    70.999 -  78.887:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1589             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1144 r_free = 0.1587             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1587   ksol= 0.34   Bsol= 46.99   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,2.63,3.59,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.160832                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1586   ksol= 0.34   Bsol= 46.99   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,2.59,3.50,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.160785                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.402347              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.027  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.205720              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.713  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6967 = 1.40 * 0.50 * 5.1689 + 1.00 * 0.0724                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6799 = 1.40 * 0.50 * 5.1694 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0727 = 0.21 * 1.00 * 5.1694 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0726 = 0.21 * 1.00 * 5.1680 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.91   11.65    None  None   None       |
|    all(noH): 2823   0      0.00    78.91   11.65    None  None   None       |
|    Sol.    : 438    0      1.68    75.19   32.71    None  None   None       |
|    Mac.    : 2385   0      0.00    78.91   7.78     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.891: 1638   |   5:    39.453 -  47.344:   83        |
|      1:     7.891 -  15.781:  619   |   6:    47.344 -  55.234:   61        |
|      2:    15.781 -  23.672:  151   |   7:    55.234 -  63.125:   23        |
|      3:    23.672 -  31.562:  129   |   8:    63.125 -  71.015:    8        |
|      4:    31.562 -  39.453:  108   |   9:    71.015 -  78.906:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1590             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1158 r_free = 0.1590             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1590   ksol= 0.34   Bsol= 46.99   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,2.59,3.50,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168487                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7289 0.99   1392  155 0.1028 0.1310      5.4054      5.5313|
|  2:  4.7289 -  3.7727 0.99   1342  146 0.0903 0.1128      5.4691        5.64|
|  3:  3.7727 -  3.3014 0.99   1314  147 0.1080 0.1565      5.4883      5.8801|
|  4:  3.3014 -  3.0022 0.99   1315  153 0.1230 0.1549      5.4715      5.5853|
|  5:  3.0022 -  2.7884 0.99   1297  139 0.1378 0.1795      5.3506      5.5667|
|  6:  2.7884 -  2.6249 0.99   1286  143 0.1253 0.1813      5.2231      5.4773|
|  7:  2.6249 -  2.4941 0.99   1300  139 0.1311 0.1601       5.205      5.3599|
|  8:  2.4941 -  2.3859 0.98   1261  151 0.1220 0.1812      5.0818      5.3737|
|  9:  2.3859 -  2.2944 0.98   1281  145 0.1220 0.1749      5.0674      5.3279|
| 10:  2.2944 -  2.2155 0.99   1279  138 0.1172 0.1742       4.976      5.2173|
| 11:  2.2155 -  2.1464 0.98   1286  138 0.1192 0.1781        4.97      5.3034|
| 12:  2.1464 -  2.0852 0.97   1241  139 0.1133 0.1637       4.893      5.1085|
| 13:  2.0852 -  2.0305 1.00   1263  140 0.1237 0.1828      4.8216      5.1058|
| 14:  2.0305 -  1.9810 0.59    773   86 0.1062 0.1688      4.6699       4.903|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7289  1392   155  0.94   8.91   0.98     0.96       7192.81|
|  2:  4.7289 -  3.7727  1342   146  0.95   8.13   1.01     1.00       9219.09|
|  3:  3.7727 -  3.3014  1314   147  0.93  11.45   1.02     1.01      10616.30|
|  4:  3.3014 -  3.0022  1315   153  0.92  13.62   1.00     0.98      10450.70|
|  5:  3.0022 -  2.7884  1297   139  0.90  16.16   0.99     0.96       8354.90|
|  6:  2.7884 -  2.6249  1286   143  0.90  15.86   0.98     0.95       7119.06|
|  7:  2.6249 -  2.4941  1300   139  0.91  15.60   0.99     0.97       6481.53|
|  8:  2.4941 -  2.3859  1261   151  0.90  15.71   0.99     0.96       5359.83|
|  9:  2.3859 -  2.2944  1281   145  0.91  15.49   1.01     0.98       5212.87|
| 10:  2.2944 -  2.2155  1279   138  0.90  15.51   1.00     0.97       4349.39|
| 11:  2.2155 -  2.1464  1286   138  0.90  16.27   1.00     0.96       4449.87|
| 12:  2.1464 -  2.0852  1241   139  0.92  14.96   1.01     1.01       4026.80|
| 13:  2.0852 -  2.0305  1263   140  0.90  16.78   1.01     1.00       3484.17|
| 14:  2.0305 -  1.9810   773    86  0.91  14.57   0.99     0.96       2537.28|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2537.28 max =        10616.30 mean =      6498.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.14|
|phase err.(test): min =        0.00 max =           88.45 mean =        13.61|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1590   ksol= 0.34   Bsol= 49.90   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.16,-0.38,0.53,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168469                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1590   ksol= 0.34   Bsol= 49.90   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.16,-0.38,0.53,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168469                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7289 0.99   1392  155 0.1028 0.1310      5.4051      5.5309|
|  2:  4.7289 -  3.7727 0.99   1342  146 0.0903 0.1128      5.4689      5.6401|
|  3:  3.7727 -  3.3014 0.99   1314  147 0.1080 0.1565      5.4882        5.88|
|  4:  3.3014 -  3.0022 0.99   1315  153 0.1230 0.1548      5.4715      5.5853|
|  5:  3.0022 -  2.7884 0.99   1297  139 0.1378 0.1795      5.3507      5.5669|
|  6:  2.7884 -  2.6249 0.99   1286  143 0.1253 0.1813      5.2232      5.4773|
|  7:  2.6249 -  2.4941 0.99   1300  139 0.1311 0.1601      5.2049      5.3598|
|  8:  2.4941 -  2.3859 0.98   1261  151 0.1220 0.1812      5.0817      5.3738|
|  9:  2.3859 -  2.2944 0.98   1281  145 0.1220 0.1749      5.0674      5.3278|
| 10:  2.2944 -  2.2155 0.99   1279  138 0.1172 0.1742       4.976      5.2174|
| 11:  2.2155 -  2.1464 0.98   1286  138 0.1192 0.1782        4.97      5.3034|
| 12:  2.1464 -  2.0852 0.97   1241  139 0.1134 0.1637      4.8931      5.1085|
| 13:  2.0852 -  2.0305 1.00   1263  140 0.1237 0.1829      4.8217       5.106|
| 14:  2.0305 -  1.9810 0.59    773   86 0.1062 0.1688        4.67      4.9031|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7289  1392   155  0.94   8.91   0.98     0.96       7187.70|
|  2:  4.7289 -  3.7727  1342   146  0.95   8.13   1.01     1.00       9214.65|
|  3:  3.7727 -  3.3014  1314   147  0.93  11.45   1.02     1.01      10614.39|
|  4:  3.3014 -  3.0022  1315   153  0.92  13.62   1.00     0.98      10451.90|
|  5:  3.0022 -  2.7884  1297   139  0.90  16.16   0.99     0.96       8356.22|
|  6:  2.7884 -  2.6249  1286   143  0.90  15.86   0.98     0.95       7119.42|
|  7:  2.6249 -  2.4941  1300   139  0.91  15.59   0.99     0.97       6480.98|
|  8:  2.4941 -  2.3859  1261   151  0.90  15.71   0.98     0.96       5359.72|
|  9:  2.3859 -  2.2944  1281   145  0.91  15.49   1.00     0.98       5212.35|
| 10:  2.2944 -  2.2155  1279   138  0.90  15.51   1.00     0.96       4349.27|
| 11:  2.2155 -  2.1464  1286   138  0.90  16.27   1.00     0.96       4449.60|
| 12:  2.1464 -  2.0852  1241   139  0.92  14.96   1.01     1.00       4027.87|
| 13:  2.0852 -  2.0305  1263   140  0.90  16.78   1.00     1.00       3484.91|
| 14:  2.0305 -  1.9810   773    86  0.91  14.57   0.98     0.95       2537.89|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2537.89 max =        10614.39 mean =      6498.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.14|
|phase err.(test): min =        0.00 max =           88.45 mean =        13.61|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.91    81.82   14.56    None  None   None       |
|    all(noH): 2823   0      2.91    81.82   14.56    None  None   None       |
|    Sol.    : 438    0      4.59    78.10   35.62    None  None   None       |
|    Mac.    : 2385   0      2.91    81.82   10.69    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:     2.909 -  10.800: 1638   |   5:    42.362 -  50.253:   83        |
|      1:    10.800 -  18.690:  619   |   6:    50.253 -  58.143:   61        |
|      2:    18.690 -  26.581:  151   |   7:    58.143 -  66.034:   23        |
|      3:    26.581 -  34.472:  129   |   8:    66.034 -  73.924:    8        |
|      4:    34.472 -  42.362:  108   |   9:    73.924 -  81.815:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.420 - 4.673
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 322
   mapped sites are within: 0.721 - 4.673

peak=   11.037 closest distance to " CB  VAL A 230 " =    1.501
peak=    7.486 closest distance to " CG2 VAL A 296 " =    1.143
peak=    6.112 closest distance to " NH2 ARG A  56 " =    2.202
peak=    6.067 closest distance to " CG  LEU A   5 " =    1.254
peak=    6.021 closest distance to " CD2 LEU A   5 " =    1.253
peak=    5.420 closest distance to " CB  GLN A 223 " =    1.407
peak=    5.361 closest distance to " CG  LEU A 228 " =    1.169
peak=    4.988 closest distance to " O   HOH Z 232 " =    2.264
peak=    4.969 closest distance to " NE2 GLN A  11 " =    1.165
peak=    4.928 closest distance to " CG  PRO A 213 " =    1.251
peak=    4.923 closest distance to " O   HOH Z 126 " =    1.949
peak=    4.908 closest distance to " CB  SER A  63 " =    1.333
peak=    4.819 closest distance to " CD2 LEU A 228 " =    1.195
peak=    4.794 closest distance to " CG  PRO A 198 " =    1.313
peak=    4.718 closest distance to " CB  GLN A 183 " =    1.188
peak=    4.715 closest distance to " C   PRO A 198 " =    1.574
peak=    4.666 closest distance to " CB  VAL A 296 " =    1.150
peak=    4.657 closest distance to " O   HOH Z 144 " =    1.750
peak=    4.596 closest distance to " CG  PRO A 243 " =    1.133
peak=    4.553 closest distance to " CB  GLU A 152 " =    1.186
peak=    4.528 closest distance to " CB  VAL A 230 " =    1.207
peak=    4.521 closest distance to " O   HOH Z 298 " =    1.767
peak=    4.457 closest distance to " CB  ASN A 148 " =    1.348
peak=    4.448 closest distance to " O   HOH Z 427 " =    3.029
peak=    4.443 closest distance to " CB  GLU A 128 " =    1.033
peak=    4.437 closest distance to " CB  SER A   3 " =    1.461
peak=    4.426 closest distance to " CB  ARG A 275 " =    0.873
peak=    4.414 closest distance to " O   HOH Z 316 " =    3.052
peak=    4.395 closest distance to " O   HOH Z 272 " =    1.882
peak=    4.339 closest distance to " O   HOH Z 236 " =    1.917
peak=    4.291 closest distance to " ND2 ASN A 187 " =    1.526
peak=    4.289 closest distance to " O   HOH Z 263 " =    1.637
peak=    4.284 closest distance to " O   HOH Z 368 " =    2.127
peak=    4.273 closest distance to " CB  SER A 216 " =    0.808
peak=    4.256 closest distance to " CB  TRP A 266 " =    0.931
peak=    4.243 closest distance to " CB  VAL A 265 " =    1.287
peak=    4.207 closest distance to " O   HOH Z 425 " =    1.441
peak=    4.191 closest distance to " OD1 ASN A  69 " =    2.636
peak=    4.182 closest distance to " CB  TYR A 169 " =    0.734
peak=    4.157 closest distance to " NH1AARG A 145 " =    1.109
peak=    4.130 closest distance to " CA  ALA A  51 " =    1.023
peak=    4.108 closest distance to " O   HOH Z 403 " =    1.694
peak=    4.107 closest distance to " O   HOH Z 303 " =    2.073
peak=    4.101 closest distance to " O   HOH Z 369 " =    2.040
peak=    4.049 closest distance to " CB  ASN A 187 " =    1.115
peak=    4.029 closest distance to " O   HOH Z 265 " =    2.403
peak=    4.017 closest distance to " O   HOH Z 193 " =    1.878
peak=    4.001 closest distance to " CD  ARG A 159 " =    0.756
peak=    3.992 closest distance to " O   HOH Z   9 " =    2.134
peak=    3.980 closest distance to " CA  TYR A  30 " =    0.956
peak=    3.970 closest distance to " O   HOH Z 193 " =    1.780
peak=    3.960 closest distance to " O   HOH Z 346 " =    1.580
peak=    3.947 closest distance to " OD2 ASP A 286 " =    2.854
peak=    3.938 closest distance to " O   HOH Z  78 " =    1.713
peak=    3.925 closest distance to " O   HOH Z 209 " =    2.371
peak=    3.920 closest distance to " O   HOH Z 411 " =    3.738
peak=    3.905 closest distance to " CA  ASN A 215 " =    1.129
peak=    3.892 closest distance to " CB  ARG A  79 " =    1.438
peak=    3.889 closest distance to " CD1 LEU A 300 " =    1.207
peak=    3.888 closest distance to " CA  SER A  87 " =    0.945
peak=    3.888 closest distance to " CB  ASN A  39 " =    0.881
peak=    3.881 closest distance to " CG1BVAL A  72 " =    1.611
peak=    3.869 closest distance to " CA  THR A 264 " =    0.803
peak=    3.868 closest distance to " O   HOH Z  88 " =    3.303
peak=    3.868 closest distance to " ND2 ASN A 249 " =    1.935
peak=    3.867 closest distance to " CZ  PHE A 192 " =    0.915
peak=    3.858 closest distance to " O   SER A  87 " =    2.343
peak=    3.857 closest distance to " CZ  PHE A 218 " =    1.057
peak=    3.855 closest distance to " O   HOH Z  61 " =    1.656
peak=    3.841 closest distance to " CD  ARG A  66 " =    2.587
peak=    3.839 closest distance to " O   HOH Z 234 " =    3.719
peak=    3.829 closest distance to " N   PHE A 130 " =    1.279
peak=    3.821 closest distance to " CA  ALA A  21 " =    1.172
peak=    3.812 closest distance to " CG2 VAL A 257 " =    0.987
peak=    3.794 closest distance to " O   HOH Z  97 " =    2.003
peak=    3.781 closest distance to " CB  LEU A 143 " =    1.151
peak=    3.781 closest distance to " O   HOH Z  68 " =    2.066
peak=    3.776 closest distance to " CD  ARG A 269 " =    0.997
peak=    3.765 closest distance to " CD2 LEU A 255 " =    1.636
peak=    3.754 closest distance to " CG  LEU A 167 " =    1.186
peak=    3.751 closest distance to " CB  ASP A 140 " =    0.798
peak=    3.748 closest distance to " CG  GLN A  88 " =    1.057
peak=    3.747 closest distance to " O   HOH Z 344 " =    2.951
peak=    3.745 closest distance to " O   TRP A 274 " =    1.858
peak=    3.727 closest distance to " CG2 THR A 221 " =    1.041
peak=    3.724 closest distance to " O   HOH Z 132 " =    2.537
peak=    3.721 closest distance to " O   HOH Z 158 " =    3.023
peak=    3.715 closest distance to " O   HOH Z 128 " =    2.007
peak=    3.709 closest distance to " NH2 ARG A 156 " =    1.128
peak=    3.708 closest distance to " O   HOH Z 371 " =    2.959
peak=    3.708 closest distance to " CB  PRO A  54 " =    0.769
peak=    3.704 closest distance to " O   HOH Z 247 " =    1.346
peak=    3.702 closest distance to " O   HOH Z  10 " =    1.800
peak=    3.699 closest distance to " CB  TRP A 179 " =    1.431
peak=    3.690 closest distance to " O   HOH Z 193 " =    1.885
peak=    3.690 closest distance to " CB  ASN A 142 " =    0.982
peak=    3.689 closest distance to " CB  LEU A 228 " =    1.254
peak=    3.686 closest distance to " CB  MET A  40 " =    0.808
peak=    3.675 closest distance to " CG  ARG A 138 " =    1.075
peak=    3.674 closest distance to " O   HOH Z  43 " =    1.889
peak=    3.671 closest distance to " O   HOH Z 203 " =    1.741
peak=    3.670 closest distance to " O   HOH Z 133 " =    1.718
peak=    3.660 closest distance to " O   HOH Z 112 " =    1.477
peak=    3.637 closest distance to " O   HOH Z 189 " =    2.766
peak=    3.633 closest distance to " O   HOH Z 280 " =    2.968
peak=    3.629 closest distance to " O   HOH Z 261 " =    2.140
peak=    3.627 closest distance to " CB  ALA A 291 " =    1.338
peak=    3.623 closest distance to " CD BLYS A 290 " =    1.078
peak=    3.621 closest distance to " CA  LEU A 282 " =    1.017
peak=    3.619 closest distance to " CA  THR A 221 " =    0.872
peak=    3.608 closest distance to " CA  ALA A 158 " =    1.131
peak=    3.608 closest distance to " OG  SER A 206 " =    1.208
peak=    3.606 closest distance to " N   ASN A  39 " =    1.142
peak=    3.605 closest distance to " O   HOH Z 437 " =    2.048
peak=    3.600 closest distance to " CB  GLU A 277 " =    3.552
peak=    3.596 closest distance to " O   HOH Z 197 " =    3.218
peak=    3.591 closest distance to " CA  VAL A  41 " =    0.860
peak=    3.580 closest distance to " O   HOH Z 273 " =    2.629
peak=    3.567 closest distance to " CG1 VAL A 153 " =    0.926
peak=    3.549 closest distance to " N   ARG A 156 " =    1.326
peak=    3.545 closest distance to " CB  VAL A 202 " =    1.571
peak=    3.544 closest distance to " CB  SER A 212 " =    1.256
peak=    3.542 closest distance to " CG1 VAL A 296 " =    1.171
peak=    3.539 closest distance to " CB  GLN A  88 " =    1.241
peak=    3.539 closest distance to " CG BARG A 275 " =    1.472
peak=    3.537 closest distance to " NH1 ARG A  56 " =    0.941
peak=    3.537 closest distance to " CA  LYS A 117 " =    1.193
peak=    3.532 closest distance to " O   HOH Z 135 " =    1.831
peak=    3.523 closest distance to " O   HOH Z 171 " =    3.831
peak=    3.511 closest distance to " O   HOH Z 368 " =    3.604
peak=    3.508 closest distance to " O   HOH Z 207 " =    1.783
peak=    3.505 closest distance to " O   HOH Z 184 " =    1.396
peak=    3.499 closest distance to " CE  LYS A  76 " =    0.937
peak=    3.499 closest distance to " O   HOH Z 216 " =    2.564
peak=    3.497 closest distance to " O   HOH Z 350 " =    1.603
peak=    3.494 closest distance to " CB  ARG A 139 " =    0.956
peak=    3.489 closest distance to " N   VAL A 126 " =    1.339
peak=    3.489 closest distance to " OG BSER A 164 " =    2.240
peak=    3.475 closest distance to " O   HOH Z 227 " =    2.051
peak=    3.473 closest distance to " C   ALA A 299 " =    0.963
peak=    3.472 closest distance to " CA  ALA A 154 " =    1.137
peak=    3.465 closest distance to " CG1 ILE A 151 " =    1.055
peak=    3.465 closest distance to " O   MET A 105 " =    1.753
peak=    3.463 closest distance to " CG  MET A 185 " =    1.002
peak=    3.458 closest distance to " O   HOH Z  30 " =    1.330
peak=    3.453 closest distance to " CB  HIS A 108 " =    0.803
peak=    3.453 closest distance to " CE1 TYR A 186 " =    1.339
peak=    3.448 closest distance to " O   HOH Z 227 " =    1.663
peak=    3.439 closest distance to " CA  ILE A 234 " =    0.909
peak=    3.438 closest distance to " NE AARG A 275 " =    1.344
peak=    3.437 closest distance to " NZ  LYS A 117 " =    3.281
peak=    3.432 closest distance to " CG1 ILE A  33 " =    1.326
peak=    3.430 closest distance to " O   HOH Z 214 " =    1.920
peak=    3.429 closest distance to " O   HOH Z  21 " =    1.696
peak=    3.428 closest distance to " O   HOH Z 329 " =    3.824
peak=    3.426 closest distance to " N   SER A 135 " =    1.305
peak=    3.422 closest distance to " CB  THR A  82 " =    1.389
peak=    3.421 closest distance to " O   HOH Z 271 " =    2.021
peak=    3.414 closest distance to " CB  ALA A   9 " =    1.585
peak=    3.413 closest distance to " CB  ALA A 161 " =    0.880
peak=    3.411 closest distance to " O   HOH Z 286 " =    2.353
peak=    3.409 closest distance to " O   HOH Z 163 " =    1.883
peak=    3.406 closest distance to " ND1 HIS A  81 " =    1.669
peak=    3.404 closest distance to " ND1 HIS A  86 " =    1.683
peak=    3.404 closest distance to " O   HOH Z  58 " =    1.539
peak=    3.397 closest distance to " O   GLN A 278 " =    1.322
peak=    3.396 closest distance to " O   HOH Z   2 " =    1.678
peak=    3.393 closest distance to " O   HOH Z 248 " =    1.817
peak=    3.388 closest distance to " CB  ARG A 190 " =    1.717
peak=    3.385 closest distance to " CB  VAL A 250 " =    1.192
peak=    3.385 closest distance to " CG  MET A 185 " =    1.185
peak=    3.379 closest distance to " CD  LYS A 166 " =    1.312
peak=    3.379 closest distance to " O   HOH Z 145 " =    1.725
peak=    3.378 closest distance to " CB  THR A 157 " =    1.120
peak=    3.375 closest distance to " O   HOH Z 302 " =    1.892
peak=    3.374 closest distance to " O   HOH Z 410 " =    1.531
peak=    3.374 closest distance to " CB  ALA A 248 " =    1.375
peak=    3.371 closest distance to " CB  PRO A 198 " =    0.923
peak=    3.368 closest distance to " CG BARG A 102 " =    1.830
peak=    3.365 closest distance to " O   HOH Z   3 " =    1.767
peak=    3.361 closest distance to " CB  ALA A 137 " =    1.073
peak=    3.361 closest distance to " CZ3 TRP A 123 " =    1.278
peak=    3.356 closest distance to " CD1 ILE A 106 " =    0.987
peak=    3.353 closest distance to " O   ALA A 158 " =    1.427
peak=    3.352 closest distance to " CA  ASP A 140 " =    1.291
peak=    3.351 closest distance to " O   HOH Z  59 " =    2.006
peak=    3.345 closest distance to " O   HOH Z  48 " =    1.385
peak=    3.345 closest distance to " NH1 ARG A  14 " =    0.934
peak=    3.344 closest distance to " O   HOH Z   9 " =    1.894
peak=    3.343 closest distance to " O   ALA A   1 " =    1.590
peak=    3.341 closest distance to " NH2BARG A 145 " =    1.962
peak=    3.340 closest distance to " O   HOH Z 175 " =    2.079
peak=    3.338 closest distance to " CA  ILE A 106 " =    0.800
peak=    3.338 closest distance to " C   LYS A 290 " =    1.346
peak=    3.334 closest distance to " O   HOH Z  22 " =    2.080
peak=    3.332 closest distance to " CD1 ILE A  33 " =    1.639
peak=    3.331 closest distance to " CB  ALA A 104 " =    0.752
peak=    3.329 closest distance to " NH2AARG A 190 " =    1.783
peak=    3.327 closest distance to " CB  ALA A 248 " =    1.056
peak=    3.326 closest distance to " O   HOH Z   1 " =    1.843
peak=    3.323 closest distance to " OG BSER A 134 " =    2.952
peak=    3.322 closest distance to " CD1 LEU A   5 " =    1.353
peak=    3.321 closest distance to " CD1 LEU A  96 " =    0.749
peak=    3.319 closest distance to " O   HOH Z 355 " =    1.752
peak=    3.312 closest distance to " O   HOH Z 280 " =    1.780
peak=    3.310 closest distance to " O   HOH Z 147 " =    1.683
peak=    3.310 closest distance to " CB  LYS A 117 " =    1.189
peak=    3.308 closest distance to " O   HOH Z 172 " =    3.622
peak=    3.304 closest distance to " O   HOH Z 303 " =    1.822
peak=    3.300 closest distance to " O   HOH Z 250 " =    1.334
peak=    3.299 closest distance to " CB  ALA A 114 " =    1.245
peak=    3.296 closest distance to " O   HOH Z 402 " =    1.430
peak=    3.296 closest distance to " CB  SER A 210 " =    0.831
peak=    3.295 closest distance to " OG1 THR A 294 " =    1.741
peak=    3.294 closest distance to " O   HOH Z 124 " =    1.327
peak=    3.287 closest distance to " CD  ARG A 219 " =    1.065
peak=    3.286 closest distance to " O   HOH Z 128 " =    1.987
peak=    3.285 closest distance to " CB  ILE A 120 " =    1.276
peak=    3.284 closest distance to " O   HOH Z 271 " =    2.565
peak=    3.284 closest distance to " O   HOH Z 185 " =    1.802
peak=    3.284 closest distance to " O   HOH Z 334 " =    1.585
peak=    3.282 closest distance to " OG  SER A  22 " =    2.839
peak=    3.281 closest distance to " NE2 HIS A 207 " =    1.443
peak=    3.278 closest distance to " CA  ASN A 284 " =    0.907
peak=    3.277 closest distance to " CB  ALA A  34 " =    0.972
peak=    3.269 closest distance to " O   HOH Z 286 " =    2.497
peak=    3.269 closest distance to " CA  ALA A 291 " =    0.988
peak=    3.267 closest distance to " O   HOH Z 313 " =    1.781
peak=    3.266 closest distance to " CB  VAL A 268 " =    0.847
peak=    3.265 closest distance to " CB BVAL A  41 " =    1.260
peak=    3.264 closest distance to " CB  LEU A 255 " =    0.854
peak=    3.264 closest distance to " O   HOH Z 291 " =    1.590
peak=    3.262 closest distance to " CG  GLN A 278 " =    1.326
peak=    3.261 closest distance to " O   HOH Z 305 " =    3.531
peak=    3.261 closest distance to " CB  GLU A 236 " =    1.132
peak=    3.260 closest distance to " O   HOH Z 345 " =    3.530
peak=    3.259 closest distance to " CD2 LEU A 167 " =    0.723
peak=    3.256 closest distance to " O   HOH Z 282 " =    1.962
peak=    3.254 closest distance to " N   GLN A 278 " =    0.967
peak=    3.254 closest distance to " O   HOH Z 327 " =    2.121
peak=    3.254 closest distance to " O   HOH Z 126 " =    1.544
peak=    3.252 closest distance to " CA  GLY A 267 " =    0.985
peak=    3.251 closest distance to " CB  MET A  47 " =    1.026
peak=    3.251 closest distance to " O   HOH Z   1 " =    1.842
peak=    3.250 closest distance to " O   HOH Z  49 " =    2.542
peak=    3.248 closest distance to " CD  ARG A  14 " =    1.240
peak=    3.247 closest distance to " O   HOH Z 145 " =    3.474
peak=    3.243 closest distance to " NH2 ARG A 219 " =    1.844
peak=    3.242 closest distance to " CB  SER A  62 " =    1.188
peak=    3.239 closest distance to " O   HOH Z  93 " =    2.620
peak=    3.230 closest distance to " O   HOH Z 295 " =    1.490
peak=    3.227 closest distance to " CB  ASN A 110 " =    1.160
peak=    3.219 closest distance to " O   HOH Z 417 " =    2.049
peak=    3.218 closest distance to " O   HOH Z 116 " =    1.668
peak=    3.212 closest distance to " O   HOH Z 407 " =    2.301
peak=    3.208 closest distance to " O   HOH Z  61 " =    1.607
peak=    3.207 closest distance to " CG2 ILE A 106 " =    0.928
peak=    3.206 closest distance to " O   HOH Z 189 " =    3.132
peak=    3.202 closest distance to " OH  TYR A 214 " =    1.179
peak=    3.199 closest distance to " O   HOH Z 281 " =    4.673
peak=    3.196 closest distance to " O   HOH Z 185 " =    2.201
peak=    3.190 closest distance to " CB  ILE A 234 " =    1.010
peak=    3.189 closest distance to " CB  GLU A  46 " =    1.052
peak=    3.188 closest distance to " CA  ASP A 162 " =    1.026
peak=    3.186 closest distance to " CG2 THR A 220 " =    0.932
peak=    3.184 closest distance to " CB  SER A  28 " =    1.043
peak=    3.183 closest distance to " CB  TRP A 150 " =    1.580
peak=    3.182 closest distance to " O   HOH Z 367 " =    2.178
peak=    3.180 closest distance to " CA  VAL A 126 " =    0.882
peak=    3.174 closest distance to " O   HOH Z 109 " =    2.632
peak=    3.173 closest distance to " O   TYR A 116 " =    1.254
peak=    3.165 closest distance to " O   GLN A  58 " =    1.585
peak=    3.165 closest distance to " C   TYR A 214 " =    1.474
peak=    3.164 closest distance to " NZ  LYS A  48 " =    1.440
peak=    3.164 closest distance to " CA  ARG A  36 " =    1.133
peak=    3.156 closest distance to " CA  ASP A 191 " =    0.721
peak=    3.155 closest distance to " C   SER A  32 " =    1.035
peak=    3.154 closest distance to " CA  ALA A 233 " =    1.473
peak=    3.154 closest distance to " O   HOH Z 425 " =    2.043
peak=    3.153 closest distance to " CB  LEU A 237 " =    0.753
peak=    3.146 closest distance to " O   HOH Z 293 " =    1.969
peak=    3.146 closest distance to " O   HOH Z 411 " =    1.867
peak=    3.145 closest distance to " O   HOH Z 151 " =    1.696
peak=    3.143 closest distance to " CB  ASN A 224 " =    1.011
peak=    3.140 closest distance to " O   HOH Z 151 " =    1.807
peak=    3.140 closest distance to " CA  GLN A 194 " =    1.219
peak=    3.138 closest distance to " CB  GLN A 278 " =    0.877
peak=    3.134 closest distance to " O   HOH Z 294 " =    1.559
peak=    3.129 closest distance to " CB  ALA A 227 " =    1.012
peak=    3.126 closest distance to " N   ASN A 127 " =    1.252
peak=    3.124 closest distance to " N   TYR A  15 " =    0.800
peak=    3.124 closest distance to " O   HOH Z 409 " =    3.029
peak=    3.124 closest distance to " CG1 VAL A 174 " =    1.062
peak=    3.123 closest distance to " OG BSER A 212 " =    2.690
peak=    3.122 closest distance to " O   HOH Z  89 " =    2.291
peak=    3.114 closest distance to " CB  ALA A  10 " =    0.898
peak=    3.111 closest distance to " OD1 ASN A 217 " =    1.657
peak=    3.107 closest distance to " CE2 TYR A 186 " =    0.922
peak=    3.103 closest distance to " NZ  LYS A  76 " =    1.211
peak=    3.102 closest distance to " O   HOH Z 213 " =    2.141
peak=    3.099 closest distance to " O   HOH Z 353 " =    2.739
peak=    3.098 closest distance to " O   HOH Z 180 " =    2.069
peak=    3.095 closest distance to " O   HOH Z 422 " =    2.636
peak=    3.095 closest distance to " O   HOH Z 173 " =    2.103
peak=    3.090 closest distance to " O   HOH Z 141 " =    1.620
peak=    3.089 closest distance to " O   HOH Z 383 " =    2.123
peak=    3.088 closest distance to " O   THR A  31 " =    1.533
peak=    3.083 closest distance to " CA  THR A 246 " =    1.235
peak=    3.082 closest distance to " CA  ARG A  56 " =    2.078
peak=    3.080 closest distance to " OG  SER A  62 " =    2.892
peak=    3.078 closest distance to " O   HOH Z 392 " =    1.997
peak=    3.077 closest distance to " O   HOH Z  20 " =    1.666
peak=    3.071 closest distance to " CB  ILE A  20 " =    1.436
peak=    3.067 closest distance to " CB  ASN A 215 " =    1.140
peak=    3.049 closest distance to " O   HOH Z 271 " =    2.267
peak=    3.035 closest distance to " CD  LYS A 119 " =    1.442
peak=    3.026 closest distance to " ND2 ASN A 249 " =    0.859

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.488 - 5.399
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 201
   mapped sites are within: 0.737 - 5.399

peak=   -5.975 closest distance to " CG2 VAL A 230 " =    0.737
peak=   -4.711 closest distance to " O   HOH Z 290 " =    1.129
peak=   -4.441 closest distance to " CD  ARG A 156 " =    1.975
peak=   -4.204 closest distance to " O   HOH Z 231 " =    1.489
peak=   -4.203 closest distance to " CD  ARG A  14 " =    3.184
peak=   -4.062 closest distance to " CG1 VAL A 296 " =    1.341
peak=   -4.042 closest distance to " CZ3 TRP A 179 " =    1.189
peak=   -4.012 closest distance to " CB  PRO A 243 " =    2.624
peak=   -3.993 closest distance to " O   HOH Z  52 " =    1.383
peak=   -3.946 closest distance to " N   ALA A  43 " =    2.383
peak=   -3.939 closest distance to " CG  GLN A 223 " =    1.893
peak=   -3.933 closest distance to " CG  ASP A 231 " =    0.759
peak=   -3.930 closest distance to " O   HOH Z 351 " =    1.548
peak=   -3.918 closest distance to " O   HOH Z 266 " =    4.863
peak=   -3.887 closest distance to " O   HOH Z 231 " =    1.070
peak=   -3.854 closest distance to " CG  MET A 105 " =    0.950
peak=   -3.843 closest distance to " C   ALA A 158 " =    1.333
peak=   -3.839 closest distance to " O   HOH Z 389 " =    1.942
peak=   -3.814 closest distance to " CB  PRO A 163 " =    2.596
peak=   -3.808 closest distance to " O   VAL A  67 " =    2.547
peak=   -3.808 closest distance to " CB  ALA A 161 " =    2.552
peak=   -3.760 closest distance to " CG2 VAL A 296 " =    1.126
peak=   -3.749 closest distance to " CE2 TYR A  30 " =    2.865
peak=   -3.717 closest distance to " O   HOH Z 388 " =    2.131
peak=   -3.712 closest distance to " O   HOH Z 435 " =    2.810
peak=   -3.710 closest distance to " O   HOH Z 211 " =    1.537
peak=   -3.704 closest distance to " ND2 ASN A  45 " =    1.234
peak=   -3.685 closest distance to " CD1 LEU A 228 " =    2.323
peak=   -3.666 closest distance to " CD2 LEU A 237 " =    2.859
peak=   -3.661 closest distance to " OG  SER A  87 " =    1.409
peak=   -3.660 closest distance to " O   PRO A 198 " =    1.184
peak=   -3.656 closest distance to " O   GLY A 196 " =    1.154
peak=   -3.649 closest distance to " N   THR A 157 " =    1.472
peak=   -3.647 closest distance to " CB  VAL A 296 " =    1.220
peak=   -3.637 closest distance to " O   PRO A 163 " =    1.967
peak=   -3.635 closest distance to " OG BSER A 134 " =    1.227
peak=   -3.633 closest distance to " CA  GLY A 241 " =    2.299
peak=   -3.629 closest distance to " N   GLN A  58 " =    1.845
peak=   -3.621 closest distance to " NH2AARG A 275 " =    5.316
peak=   -3.618 closest distance to " O   HOH Z 185 " =    2.262
peak=   -3.617 closest distance to " C   ASN A 285 " =    2.476
peak=   -3.610 closest distance to " O   HOH Z 166 " =    1.556
peak=   -3.608 closest distance to " OE1 GLN A  88 " =    1.098
peak=   -3.608 closest distance to " NH2 ARG A  79 " =    1.901
peak=   -3.604 closest distance to " O   HOH Z  38 " =    1.750
peak=   -3.599 closest distance to " CD1 LEU A 101 " =    2.790
peak=   -3.593 closest distance to " CG2 THR A   4 " =    1.981
peak=   -3.589 closest distance to " O   HOH Z 417 " =    2.919
peak=   -3.587 closest distance to " C   HIS A 108 " =    1.162
peak=   -3.584 closest distance to " O   HOH Z 275 " =    1.537
peak=   -3.565 closest distance to " O   HOH Z 407 " =    3.179
peak=   -3.557 closest distance to " O   HOH Z 309 " =    2.425
peak=   -3.551 closest distance to " CD2 LEU A 300 " =    2.852
peak=   -3.546 closest distance to " CD1 LEU A 101 " =    2.473
peak=   -3.545 closest distance to " CD  LYS A 289 " =    2.617
peak=   -3.545 closest distance to " CB  PHE A 192 " =    1.770
peak=   -3.535 closest distance to " CG  LEU A 101 " =    2.500
peak=   -3.534 closest distance to " O   HOH Z 118 " =    2.912
peak=   -3.528 closest distance to " OG BSER A 134 " =    1.748
peak=   -3.513 closest distance to " O   GLY A 211 " =    1.371
peak=   -3.506 closest distance to " CG1 VAL A 112 " =    2.965
peak=   -3.497 closest distance to " C   LEU A 222 " =    0.797
peak=   -3.497 closest distance to " CB  ALA A  43 " =    2.494
peak=   -3.494 closest distance to " O   HOH Z 184 " =    1.914
peak=   -3.491 closest distance to " CG  PRO A 163 " =    2.527
peak=   -3.491 closest distance to " O   HOH Z  92 " =    1.532
peak=   -3.490 closest distance to " C   ASP A 231 " =    2.542
peak=   -3.488 closest distance to " CD  GLN A  58 " =    0.938
peak=   -3.485 closest distance to " OD1 ASN A 148 " =    1.516
peak=   -3.471 closest distance to " OD1 ASN A 187 " =    1.652
peak=   -3.466 closest distance to " CG  ASP A  50 " =    2.384
peak=   -3.465 closest distance to " O   HOH Z 372 " =    2.390
peak=   -3.465 closest distance to " CG1 VAL A 112 " =    2.605
peak=   -3.458 closest distance to " CB  ALA A 248 " =    2.034
peak=   -3.453 closest distance to " O   HOH Z  98 " =    2.089
peak=   -3.452 closest distance to " CD2 TYR A 293 " =    2.093
peak=   -3.449 closest distance to " CE  MET A 105 " =    2.207
peak=   -3.449 closest distance to " O   HOH Z  43 " =    1.747
peak=   -3.448 closest distance to " O   HOH Z 241 " =    1.208
peak=   -3.443 closest distance to " O   HOH Z 394 " =    1.519
peak=   -3.441 closest distance to " O   GLY A 203 " =    2.386
peak=   -3.437 closest distance to " CG  LEU A 228 " =    0.915
peak=   -3.429 closest distance to " CG  TRP A 266 " =    1.807
peak=   -3.426 closest distance to " O   VAL A  67 " =    2.582
peak=   -3.420 closest distance to " O   HOH Z 198 " =    1.498
peak=   -3.419 closest distance to " CD2 LEU A 237 " =    2.720
peak=   -3.416 closest distance to " O   HOH Z 103 " =    1.957
peak=   -3.411 closest distance to " CG2 VAL A 112 " =    2.613
peak=   -3.406 closest distance to " CD  GLN A  88 " =    0.784
peak=   -3.402 closest distance to " O   HOH Z 166 " =    2.014
peak=   -3.401 closest distance to " NZ  LYS A 119 " =    3.373
peak=   -3.398 closest distance to " CE3 TRP A 150 " =    2.015
peak=   -3.390 closest distance to " C   MET A 188 " =    1.495
peak=   -3.387 closest distance to " O   ARG A 145 " =    1.676
peak=   -3.385 closest distance to " CB  ASN A  39 " =    2.079
peak=   -3.378 closest distance to " O   HOH Z 191 " =    5.399
peak=   -3.374 closest distance to " OXT GLY A 302 " =    2.927
peak=   -3.371 closest distance to " OG  SER A 206 " =    1.722
peak=   -3.370 closest distance to " C   ASN A 187 " =    1.764
peak=   -3.370 closest distance to " O   GLY A  80 " =    2.469
peak=   -3.366 closest distance to " CE2 PHE A 218 " =    2.580
peak=   -3.365 closest distance to " CE1 TYR A 169 " =    2.458
peak=   -3.365 closest distance to " O   HOH Z 377 " =    1.935
peak=   -3.361 closest distance to " CD1 ILE A 199 " =    2.620
peak=   -3.357 closest distance to " O   HOH Z  22 " =    2.411
peak=   -3.352 closest distance to " O   HOH Z 353 " =    2.110
peak=   -3.344 closest distance to " CG  PHE A 283 " =    2.765
peak=   -3.342 closest distance to " CG1 VAL A 197 " =    2.289
peak=   -3.341 closest distance to " CA  GLY A 241 " =    2.994
peak=   -3.338 closest distance to " O   HOH Z  44 " =    2.198
peak=   -3.337 closest distance to " CA  ASP A  27 " =    2.440
peak=   -3.336 closest distance to " CD  ARG A 139 " =    1.629
peak=   -3.334 closest distance to " NE2 GLN A  88 " =    2.187
peak=   -3.334 closest distance to " O   HOH Z 423 " =    1.152
peak=   -3.330 closest distance to " CB  ALA A 248 " =    2.461
peak=   -3.329 closest distance to " O   HOH Z 134 " =    2.617
peak=   -3.325 closest distance to " CE BMET A  47 " =    1.722
peak=   -3.312 closest distance to " N   ALA A 226 " =    2.169
peak=   -3.311 closest distance to " O   HOH Z 437 " =    1.791
peak=   -3.307 closest distance to " N   SER A 212 " =    1.721
peak=   -3.305 closest distance to " CD1 ILE A 239 " =    2.106
peak=   -3.302 closest distance to " O   HOH Z  13 " =    1.255
peak=   -3.296 closest distance to " O   HOH Z 210 " =    0.898
peak=   -3.294 closest distance to " C   GLY A 229 " =    1.213
peak=   -3.294 closest distance to " OG  SER A  97 " =    2.219
peak=   -3.293 closest distance to " O   HOH Z  60 " =    2.134
peak=   -3.293 closest distance to " CG  ARG A 259 " =    2.520
peak=   -3.291 closest distance to " O   VAL A 121 " =    1.177
peak=   -3.288 closest distance to " CB  ASP A 132 " =    2.313
peak=   -3.284 closest distance to " OG1 THR A 178 " =    1.253
peak=   -3.282 closest distance to " O   HOH Z 140 " =    1.468
peak=   -3.279 closest distance to " O   HOH Z 295 " =    1.429
peak=   -3.269 closest distance to " O   HOH Z 179 " =    2.279
peak=   -3.269 closest distance to " O   HOH Z 281 " =    2.729
peak=   -3.265 closest distance to " O   HOH Z 128 " =    4.104
peak=   -3.257 closest distance to " CD1 PHE A  59 " =    1.835
peak=   -3.257 closest distance to " CA  SER A 135 " =    1.367
peak=   -3.256 closest distance to " O   HOH Z  51 " =    1.247
peak=   -3.253 closest distance to " O   ALA A 161 " =    1.504
peak=   -3.249 closest distance to " O   HOH Z 196 " =    2.246
peak=   -3.248 closest distance to " OG ASER A 134 " =    1.686
peak=   -3.245 closest distance to " CB  VAL A 230 " =    1.017
peak=   -3.244 closest distance to " CZ3 TRP A 274 " =    1.063
peak=   -3.244 closest distance to " CG2 ILE A 263 " =    2.418
peak=   -3.242 closest distance to " O   HOH Z 222 " =    1.421
peak=   -3.236 closest distance to " OD1 ASP A 191 " =    1.561
peak=   -3.228 closest distance to " O   HOH Z 377 " =    1.052
peak=   -3.226 closest distance to " CG1 VAL A 296 " =    1.265
peak=   -3.224 closest distance to " CB  ALA A 291 " =    2.164
peak=   -3.216 closest distance to " O   SER A  22 " =    2.184
peak=   -3.215 closest distance to " O   HOH Z 436 " =    1.391
peak=   -3.214 closest distance to " CB  TYR A  15 " =    2.163
peak=   -3.211 closest distance to " CA  GLY A 203 " =    2.329
peak=   -3.208 closest distance to " CG  ARG A 269 " =    2.345
peak=   -3.197 closest distance to " O   HOH Z  63 " =    1.214
peak=   -3.194 closest distance to " ND2 ASN A  60 " =    1.787
peak=   -3.193 closest distance to " ND2 ASN A  60 " =    1.528
peak=   -3.189 closest distance to " CD  GLN A  11 " =    0.738
peak=   -3.183 closest distance to " CG  GLU A 277 " =    1.198
peak=   -3.183 closest distance to " C   LEU A 143 " =    1.197
peak=   -3.180 closest distance to " O   VAL A 189 " =    2.573
peak=   -3.178 closest distance to " CB  ALA A 291 " =    2.210
peak=   -3.175 closest distance to " O   HOH Z 417 " =    2.734
peak=   -3.159 closest distance to " O   HOH Z 359 " =    3.278
peak=   -3.157 closest distance to " O   HOH Z 174 " =    2.549
peak=   -3.154 closest distance to " CB  TRP A  85 " =    2.470
peak=   -3.154 closest distance to " CA  ARG A 139 " =    1.007
peak=   -3.148 closest distance to " CD  PRO A 243 " =    2.116
peak=   -3.145 closest distance to " CB  ALA A 114 " =    2.457
peak=   -3.145 closest distance to " O   HOH Z 177 " =    1.655
peak=   -3.141 closest distance to " CB  TYR A 172 " =    2.289
peak=   -3.141 closest distance to " NH1AARG A 275 " =    1.842
peak=   -3.139 closest distance to " O   HOH Z 148 " =    1.779
peak=   -3.137 closest distance to " NH2 ARG A  66 " =    2.133
peak=   -3.134 closest distance to " CZ  PHE A  59 " =    1.502
peak=   -3.133 closest distance to " O   PRO A 198 " =    1.312
peak=   -3.131 closest distance to " NH2 ARG A  36 " =    2.344
peak=   -3.127 closest distance to " CD2 LEU A   5 " =    1.027
peak=   -3.123 closest distance to " O   TYR A  30 " =    2.849
peak=   -3.118 closest distance to " O   HOH Z 390 " =    2.392
peak=   -3.118 closest distance to " CZ  ARG A 259 " =    0.804
peak=   -3.118 closest distance to " N   THR A  18 " =    1.386
peak=   -3.116 closest distance to " O   HOH Z 423 " =    2.137
peak=   -3.115 closest distance to " ND2 ASN A 249 " =    2.338
peak=   -3.114 closest distance to " O   HOH Z 148 " =    3.240
peak=   -3.105 closest distance to " CA  GLY A  98 " =    1.976
peak=   -3.103 closest distance to " CA  ASP A 298 " =    1.062
peak=   -3.101 closest distance to " ND2 ASN A 285 " =    2.215
peak=   -3.093 closest distance to " O   HOH Z 350 " =    1.864
peak=   -3.074 closest distance to " NH2BARG A 275 " =    1.758
peak=   -3.065 closest distance to " O   HOH Z  10 " =    1.500
peak=   -3.061 closest distance to " O   HOH Z 359 " =    1.605
peak=   -3.059 closest distance to " CB  ASP A 132 " =    2.266
peak=   -3.053 closest distance to " O   HOH Z  71 " =    1.088
peak=   -3.047 closest distance to " OXT GLY A 302 " =    3.522
peak=   -3.043 closest distance to " OD1 ASP A 231 " =    1.019
peak=   -3.024 closest distance to " N   ALA A 248 " =    1.634

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.4430 0.4293   6.238817e+00   6.222492e+00
   1_bss:  0.4341 0.4197   6.232984e+00   6.212172e+00
   1_xyz:  0.3327 0.3594   6.048439e+00   6.100381e+00
   1_adp:  0.2746 0.3206   5.897000e+00   6.015173e+00
   1_occ:  0.2738 0.3214   5.896229e+00   6.016554e+00
   2_bss:  0.2692 0.3153   5.893362e+00   6.012552e+00
   2_xyz:  0.1809 0.2270   5.543805e+00   5.729049e+00
   2_adp:  0.1629 0.2076   5.450378e+00   5.645640e+00
   2_occ:  0.1628 0.2075   5.450136e+00   5.645554e+00
   3_bss:  0.1615 0.2060   5.450077e+00   5.645486e+00
   3_xyz:  0.1283 0.1723   5.250737e+00   5.476016e+00
   3_adp:  0.1217 0.1674   5.211252e+00   5.447835e+00
   3_occ:  0.1216 0.1672   5.210805e+00   5.447308e+00
   4_bss:  0.1219 0.1668   5.211167e+00   5.446113e+00
   4_xyz:  0.1132 0.1607   5.161853e+00   5.410917e+00
   4_adp:  0.1145 0.1589   5.161460e+00   5.400355e+00
   4_occ:  0.1144 0.1587   5.160832e+00   5.399536e+00
   5_bss:  0.1144 0.1586   5.160785e+00   5.399476e+00
   5_xyz:  0.1163 0.1588   5.170245e+00   5.401676e+00
   5_adp:  0.1158 0.1590   5.168642e+00   5.403049e+00
   5_occ:  0.1158 0.1590   5.168487e+00   5.402833e+00
   5_bss:  0.1158 0.1590   5.168469e+00   5.402822e+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:  0.344  13.743   8.896   8.148   8.095   0.000   0.000   0.000
   1_xyz:  0.344  13.743   8.896   8.148   8.095   0.000   0.000   0.000
   1_adp:  0.344  13.743   8.896   8.148   8.095   0.000   0.000   0.000
   1_occ:  0.344  13.743   8.896   8.148   8.095   0.000   0.000   0.000
   2_bss:  0.332  41.800   5.142   4.131   5.133   0.000   0.000   0.000
   2_xyz:  0.332  41.800   5.142   4.131   5.133   0.000   0.000   0.000
   2_adp:  0.332  41.800   5.142   4.131   5.133   0.000   0.000   0.000
   2_occ:  0.332  41.800   5.142   4.131   5.133   0.000   0.000   0.000
   3_bss:  0.335  46.993   3.402   2.859   3.927   0.000   0.000   0.000
   3_xyz:  0.335  46.993   3.402   2.859   3.927   0.000   0.000   0.000
   3_adp:  0.335  46.993   3.402   2.859   3.927   0.000   0.000   0.000
   3_occ:  0.335  46.993   3.402   2.859   3.927   0.000   0.000   0.000
   4_bss:  0.335  46.993   3.001   2.627   3.586   0.000   0.000   0.000
   4_xyz:  0.335  46.993   3.001   2.627   3.586   0.000   0.000   0.000
   4_adp:  0.335  46.993   3.001   2.627   3.586   0.000   0.000   0.000
   4_occ:  0.335  46.993   3.001   2.627   3.586   0.000   0.000   0.000
   5_bss:  0.335  46.993   2.828   2.588   3.499   0.000   0.000   0.000
   5_xyz:  0.335  46.993   2.828   2.588   3.499   0.000   0.000   0.000
   5_adp:  0.335  46.993   2.828   2.588   3.499   0.000   0.000   0.000
   5_occ:  0.335  46.993   2.828   2.588   3.499   0.000   0.000   0.000
   5_bss:  0.335  49.902  -0.157  -0.375   0.532  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.001 0.5344  0.6083    55486.296
   1_bss:  49.477 0.5261  0.7646    53195.248
   1_xyz:  39.136 0.6521  0.9254    35812.199
   1_adp:  33.039 0.7241  1.0244    27473.394
   1_occ:  33.103 0.7233  1.0227    27571.239
   2_bss:  32.748 0.7271  0.9052    27060.833
   2_xyz:  21.972 0.8422  1.0013    12959.596
   2_adp:  19.623 0.8658  1.0198    10972.973
   2_occ:  19.626 0.8658  1.0196    10968.306
   3_bss:  19.591 0.8661  0.9688    10949.833
   3_xyz:  15.765 0.9002  0.9877     7617.105
   3_adp:  15.146 0.9057  0.9897     7198.531
   3_occ:  15.131 0.9059  0.9897     7186.155
   4_bss:  15.100 0.9061  0.9779     7162.066
   4_xyz:  14.391 0.9120  0.9793     6621.279
   4_adp:  14.087 0.9147  0.9814     6502.645
   4_occ:  14.074 0.9148  0.9814     6488.597
   5_bss:  14.072 0.9148  0.9778     6486.479
   5_xyz:  14.068 0.9149  0.9774     6483.994
   5_adp:  14.092 0.9147  0.9774     6500.441
   5_occ:  14.090 0.9147  0.9774     6499.626
   5_bss:  14.089 0.9148  0.9752     6498.995
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3716e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3716e+01
   1_xyz:   1.562  0.012  0.102 18.057  0.006  4.121   1.2455e-01
   1_adp:   1.562  0.012  0.102 18.057  0.006  4.121   1.2455e-01
   1_occ:   1.562  0.012  0.102 18.057  0.006  4.121   1.2455e-01
   2_bss:   1.562  0.012  0.102 18.057  0.006  4.121   1.2455e-01
   2_xyz:   0.988  0.007  0.071 16.359  0.004  4.123   6.3718e-02
   2_adp:   0.988  0.007  0.071 16.359  0.004  4.123   6.3718e-02
   2_occ:   0.988  0.007  0.071 16.359  0.004  4.123   6.3718e-02
   3_bss:   0.988  0.007  0.071 16.359  0.004  4.123   6.3718e-02
   3_xyz:   1.032  0.007  0.080 16.142  0.003  4.130   6.5202e-02
   3_adp:   1.032  0.007  0.080 16.142  0.003  4.130   6.5202e-02
   3_occ:   1.032  0.007  0.080 16.142  0.003  4.130   6.5202e-02
   4_bss:   1.032  0.007  0.080 16.142  0.003  4.130   6.5202e-02
   4_xyz:   1.080  0.008  0.087 16.222  0.004  4.112   7.2375e-02
   4_adp:   1.080  0.008  0.087 16.222  0.004  4.112   7.2375e-02
   4_occ:   1.080  0.008  0.087 16.222  0.004  4.112   7.2375e-02
   5_bss:   1.080  0.008  0.087 16.222  0.004  4.112   7.2375e-02
   5_xyz:   0.920  0.006  0.074 15.693  0.003  4.112   5.5270e-02
   5_adp:   0.920  0.006  0.074 15.693  0.003  4.112   5.5270e-02
   5_occ:   0.920  0.006  0.074 15.693  0.003  4.112   5.5270e-02
   5_bss:   0.920  0.006  0.074 15.693  0.003  4.112   5.5270e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9650e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9650e+00
   1_xyz:  13.583  0.152  0.438 87.676  0.035  2.275   9.2582e-02
   1_adp:  13.583  0.152  0.438 87.676  0.035  2.275   9.2582e-02
   1_occ:  13.583  0.152  0.438 87.676  0.035  2.275   9.2582e-02
   2_bss:  13.583  0.152  0.438 87.676  0.035  2.275   9.2582e-02
   2_xyz:   6.835  0.062  0.258 89.162  0.045  2.344   4.5632e-02
   2_adp:   6.835  0.062  0.258 89.162  0.045  2.344   4.5632e-02
   2_occ:   6.835  0.062  0.258 89.162  0.045  2.344   4.5632e-02
   3_bss:   6.835  0.062  0.258 89.162  0.045  2.344   4.5632e-02
   3_xyz:   8.029  0.061  0.457 82.803  0.037  2.319   4.6849e-02
   3_adp:   8.029  0.061  0.457 82.803  0.037  2.319   4.6849e-02
   3_occ:   8.029  0.061  0.457 82.803  0.037  2.319   4.6849e-02
   4_bss:   8.029  0.061  0.457 82.803  0.037  2.319   4.6849e-02
   4_xyz:   8.167  0.063  0.607 84.203  0.038  2.329   6.8015e-02
   4_adp:   8.167  0.063  0.607 84.203  0.038  2.329   6.8015e-02
   4_occ:   8.167  0.063  0.607 84.203  0.038  2.329   6.8015e-02
   5_bss:   8.167  0.063  0.607 84.203  0.038  2.329   6.8015e-02
   5_xyz:   7.524  0.038  0.457 83.823  0.035  2.351   3.0830e-02
   5_adp:   7.524  0.038  0.457 83.823  0.035  2.351   3.0830e-02
   5_occ:   7.524  0.038  0.457 83.823  0.035  2.351   3.0830e-02
   5_bss:   7.524  0.038  0.457 83.823  0.035  2.351   3.0830e-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:  72.96   0.00  11.08  72.96   0.00   7.98  70.09   0.00  27.97
   1_occ:  72.96   0.00  11.08  72.96   0.00   7.98  70.09   0.00  27.97
   2_bss:  72.96   0.00  11.08  72.96   0.00   7.98  70.09   0.00  27.97
   2_xyz:  72.96   0.00  11.08  72.96   0.00   7.98  70.09   0.00  27.97
   2_adp:  70.79   0.00  11.51  70.79   0.00   7.71  69.00   0.64  32.24
   2_occ:  70.79   0.00  11.51  70.79   0.00   7.71  69.00   0.64  32.24
   3_bss:  70.79   0.00  11.51  70.79   0.00   7.71  69.00   0.64  32.24
   3_xyz:  70.79   0.00  11.51  70.79   0.00   7.71  69.00   0.64  32.24
   3_adp:  80.23   0.00  12.26  80.23   0.00   7.94  77.62   1.54  35.77
   3_occ:  80.23   0.00  12.26  80.23   0.00   7.94  77.62   1.54  35.77
   4_bss:  80.23   0.00  12.26  80.23   0.00   7.94  77.62   1.54  35.77
   4_xyz:  80.23   0.00  12.26  80.23   0.00   7.94  77.62   1.54  35.77
   4_adp:  78.89   0.00  11.63  78.89   0.00   7.76  75.48   1.65  32.70
   4_occ:  78.89   0.00  11.63  78.89   0.00   7.76  75.48   1.65  32.70
   5_bss:  78.89   0.00  11.63  78.89   0.00   7.76  75.48   1.65  32.70
   5_xyz:  78.89   0.00  11.63  78.89   0.00   7.76  75.48   1.65  32.70
   5_adp:  78.91   0.00  11.65  78.91   0.00   7.78  75.19   1.68  32.71
   5_occ:  78.91   0.00  11.65  78.91   0.00   7.78  75.19   1.68  32.71
   5_bss:  81.82   2.91  14.56  81.82   2.91  10.69  78.10   4.59  35.62
------------------------------------------------------------------------
 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:    1.175    0.014    0.406
   1_adp:    1.175    0.014    0.406
   1_occ:    1.175    0.014    0.406
   2_bss:    1.175    0.014    0.406
   2_xyz:    1.388    0.033    0.532
   2_adp:    1.388    0.033    0.532
   2_occ:    1.388    0.033    0.532
   3_bss:    1.388    0.033    0.532
   3_xyz:    1.461    0.009    0.567
   3_adp:    1.461    0.009    0.567
   3_occ:    1.461    0.009    0.567
   4_bss:    1.461    0.009    0.567
   4_xyz:    1.728    0.045    0.591
   4_adp:    1.728    0.045    0.591
   4_occ:    1.728    0.045    0.591
   5_bss:    1.728    0.045    0.591
   5_xyz:    1.773    0.062    0.594
   5_adp:    1.773    0.062    0.594
   5_occ:    1.773    0.062    0.594
   5_bss:    1.773    0.062    0.594
------------------------------------------------------------------------

CPU time actual refinement: 323.56


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1015/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_1015/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1015/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1015/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1015/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.41 
  Macro-tasks:
    bulk solvent and scale       = 40.95  
    individual site refinement   = 135.48 
    weights calculation          = 31.21  
    collect and process          = 6.32   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 214.07 
  Micro-tasks:
    mask                            = 1.71   
    f_calc                          = 97.97  
    alpha_beta                      = 7.79   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 110.02 
    fmodel                         = 7.13   
    r_factors                      = 0.25   
    phase_errors                   = 10.49  
    foms                           = 0.34   
    TOTAL for micro-tasks          = 236.81 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.495 micro seconds
Total CPU time: 5.62 minutes
from_scatterers_fft:    655 calls, 97.62 s
gradients_fft:          600 calls, 95.99 s

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

# Date 2008-01-16 Time 02:58:28 PST -0800 (1200481108.95 s)
Start R-work = 0.4430, R-free = 0.4293 (no bulk solvent and anisotropic scale)
Final R-work = 0.1327, R-free = 0.1761 (no bulk solvent and anisotropic scale)

Start R-work = 0.4341, R-free = 0.4197
Final R-work = 0.1158, R-free = 0.1590