# Date 2008-01-16 Time 02:56:35 PST -0800 (1200480995.25 s)
#phil __OFF__

Command line arguments: "../1035.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21226
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1035

-------------------------------------------------------------------------------
  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, 47.1647, 84.6622, 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: 3.24, 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, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96132
Completeness in resolution range: 0.930196
Completeness with d_max=infinity: 0.927422

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0711
                             d_min =   1.9613

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, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96132
Completeness in resolution range: 0.930196
Completeness with d_max=infinity: 0.927422

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0715 -  4.1980 [2210/2239]  1991   219   9.9%
  bin  2:  4.1980 -  3.3440 [2115/2138]  1904   211  10.0%
  bin  3:  3.3440 -  2.9248 [2092/2114]  1876   216  10.3%
  bin  4:  2.9248 -  2.6590 [2082/2101]  1885   197   9.5%
  bin  5:  2.6590 -  2.4693 [2063/2092]  1849   214  10.4%
  bin  6:  2.4693 -  2.3243 [2038/2080]  1838   200   9.8%
  bin  7:  2.3243 -  2.2082 [2044/2080]  1838   206  10.1%
  bin  8:  2.2082 -  2.1124 [2016/2053]  1816   200   9.9%
  bin  9:  2.1124 -  2.0313 [2053/2085]  1848   205  10.0%
  bin 10:  2.0313 -  1.9613 [ 876/2077]   785    91  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1035/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:
        1.73 -     2.36: 28
        2.36 -     3.00: 1912
        3.00 -     3.63: 4603
        3.63 -     4.27: 9133
        4.27 -     4.90: 12653
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.731 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.731 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.992 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.012 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28324 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_1035/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1035/model_refine_001.geo

CPU time processing inputs: 9.08


============================ 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 47.16465 84.6622 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: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4671   r_free= 0.4636   ksol= 0.00   Bsol= 0.00   scale= 0.801    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.268025                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6828 0.99   1427  159 0.3834 0.3767      6.5727      6.5495|
|  2:  4.6828 -  3.7355 0.99   1388  150 0.3759 0.3844      6.7436      6.8003|
|  3:  3.7355 -  3.2688 0.99   1355  156 0.4242 0.3933      6.6369      6.6402|
|  4:  3.2688 -  2.9724 0.99   1343  148 0.4472 0.4558      6.4905      6.4884|
|  5:  2.9724 -  2.7608 0.99   1325  146 0.4975 0.5154      6.3521       6.357|
|  6:  2.7608 -  2.5989 0.98   1325  152 0.4885 0.5180       6.261      6.2289|
|  7:  2.5989 -  2.4693 0.99   1342  146 0.5136 0.4463      6.2457      6.1346|
|  8:  2.4693 -  2.3622 0.99   1312  146 0.5219 0.5161      6.1563      6.1968|
|  9:  2.3622 -  2.2716 0.98   1312  149 0.5132 0.5142      6.1178      6.0963|
| 10:  2.2716 -  2.1935 0.98   1312  147 0.5166 0.5316      6.0808      6.0934|
| 11:  2.1935 -  2.1251 0.98   1315  138 0.5140 0.5157      6.0208      6.0294|
| 12:  2.1251 -  2.0645 0.99   1308  144 0.5298 0.5632      5.9493      5.9951|
| 13:  2.0645 -  2.0103 0.91   1198  143 0.5330 0.4852      5.8773      5.8287|
| 14:  2.0103 -  1.9613 0.27    368   35 0.5388 0.5937      5.8169       5.792|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6828  1427   159  0.72  32.65   0.80     0.74      65004.97|
|  2:  4.6828 -  3.7355  1388   150  0.71  33.92   0.89     0.79      97307.04|
|  3:  3.7355 -  3.2688  1355   156  0.61  43.33   0.84     0.73     108939.89|
|  4:  3.2688 -  2.9724  1343   148  0.50  51.66   0.82     0.61     101489.10|
|  5:  2.9724 -  2.7608  1325   146  0.41  59.00   0.74     0.50      84054.82|
|  6:  2.7608 -  2.5989  1325   152  0.41  59.28   0.75     0.49      70430.47|
|  7:  2.5989 -  2.4693  1342   146  0.43  57.66   0.73     0.48      58881.02|
|  8:  2.4693 -  2.3622  1312   146  0.42  58.58   0.72     0.50      54487.03|
|  9:  2.3622 -  2.2716  1312   149  0.39  60.49   0.75     0.46      49517.40|
| 10:  2.2716 -  2.1935  1312   147  0.36  63.08   0.75     0.43      49572.86|
| 11:  2.1935 -  2.1251  1315   138  0.31  67.16   0.78     0.37      46837.93|
| 12:  2.1251 -  2.0645  1308   144  0.25  71.73   0.74     0.32      46497.90|
| 13:  2.0645 -  2.0103  1198   143  0.24  72.50   0.73     0.30      40250.26|
| 14:  2.0103 -  1.9613   368    35  0.27  69.73   0.68     0.33      32565.63|
|alpha:            min =        0.30 max =            0.79 mean =         0.52|
|beta:             min =    32565.63 max =       108939.89 mean =     66906.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.13|
|phase err.(test): min =        0.00 max =           89.95 mean =        56.28|
|-----------------------------------------------------------------------------|

============================== 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 = 13.676122             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.956   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.138454              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.141   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      706 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1502 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2643 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3933 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5042 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6588 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7731 |
|-----------------------------------------------------------------------------|
|-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 |       53.703 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.824 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    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 = 11.914)------------------------------------------|
|    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: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4733   r_free= 0.4715   ksol= 0.00   Bsol= 0.00   scale= 0.771    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.270528                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4592   r_free= 0.4530   ksol= 0.30   Bsol= 20.00   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.91,7.60,8.65,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.267778                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.002092             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.253   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.041364              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.923   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4592      final r-factor (work) = 0.3731          |
| start r-factor (free) = 0.4530      final r-factor (free) = 0.4096          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 88.1779 = 11.00 * 0.50 * 6.2669 + 1.00 * 53.7032                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.0695 = 11.00 * 0.50 * 6.1679 + 1.00 * 0.1395                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3731      final r-factor (work) = 0.3273          |
| start r-factor (free) = 0.4096      final r-factor (free) = 0.3867          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4374 = 1.04 * 1.00 * 6.1679 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3397 = 1.04 * 1.00 * 6.0738 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.08   12.44    None  None   None       |
|    all(noH): 2823   0      0.00    82.08   12.44    None  None   None       |
|    Sol.    : 438    0      0.00    82.08   27.95    None  None   None       |
|    Mac.    : 2385   0      0.00    78.58   9.59     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.208: 1364   |   5:    41.040 -  49.249:   51        |
|      1:     8.208 -  16.416:  731   |   6:    49.249 -  57.457:   29        |
|      2:    16.416 -  24.624:  337   |   7:    57.457 -  65.665:   18        |
|      3:    24.624 -  32.832:  176   |   8:    65.665 -  73.873:    9        |
|      4:    32.832 -  41.040:  106   |   9:    73.873 -  82.081:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3273 r_free = 0.3867             target_work(ml) = 6.049         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3270 r_free = 0.3872             target_work(ml) = 6.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3270   r_free= 0.3872   ksol= 0.30   Bsol= 20.00   scale= 1.083   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.91,7.60,8.65,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.048756                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3244   r_free= 0.3830   ksol= 0.31   Bsol= 36.77   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.65,4.35,5.98,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.049251                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.212909              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.011   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.509174              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.392  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3244      final r-factor (work) = 0.2408          |
| start r-factor (free) = 0.3830      final r-factor (free) = 0.3048          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9607 = 5.21 * 0.50 * 6.0700 + 1.00 * 0.1395                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.5441 = 5.21 * 0.50 * 5.9360 + 1.00 * 0.0721                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2408      final r-factor (work) = 0.2235          |
| start r-factor (free) = 0.3048      final r-factor (free) = 0.2846          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0372 = 0.51 * 1.00 * 5.9360 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9606 = 0.51 * 1.00 * 5.7819 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.06   12.69    None  None   None       |
|    all(noH): 2823   0      0.00    82.06   12.69    None  None   None       |
|    Sol.    : 438    0      0.00    82.06   31.98    None  None   None       |
|    Mac.    : 2385   0      0.00    77.83   9.15     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 -   8.206: 1424   |   5:    41.028 -  49.234:   74        |
|      1:     8.206 -  16.411:  714   |   6:    49.234 -  57.439:   31        |
|      2:    16.411 -  24.617:  237   |   7:    57.439 -  65.645:   19        |
|      3:    24.617 -  32.823:  181   |   8:    65.645 -  73.851:    6        |
|      4:    32.823 -  41.028:  134   |   9:    73.851 -  82.056:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2235 r_free = 0.2846             target_work(ml) = 5.749         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2233 r_free = 0.2845             target_work(ml) = 5.748         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2233   r_free= 0.2845   ksol= 0.31   Bsol= 36.77   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.65,4.35,5.98,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.748419                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2217   r_free= 0.2814   ksol= 0.32   Bsol= 36.77   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,2.87,3.75,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.747877                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.730098              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.496  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.125559              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.358   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2217      final r-factor (work) = 0.1636          |
| start r-factor (free) = 0.2814      final r-factor (free) = 0.2158          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8646 = 3.73 * 0.50 * 5.7867 + 1.00 * 0.0721                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5686 = 3.73 * 0.50 * 5.6325 + 1.00 * 0.0637                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1636      final r-factor (work) = 0.1482          |
| start r-factor (free) = 0.2158      final r-factor (free) = 0.1996          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3541 = 1.13 * 1.00 * 5.6325 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1267 = 1.13 * 1.00 * 5.4309 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.47   13.52    None  None   None       |
|    all(noH): 2823   0      0.00    89.47   13.52    None  None   None       |
|    Sol.    : 438    0      1.81    82.35   38.29    None  None   None       |
|    Mac.    : 2385   0      0.00    89.47   8.98     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 -   8.947: 1614   |   5:    44.735 -  53.683:  114        |
|      1:     8.947 -  17.894:  598   |   6:    53.683 -  62.630:   59        |
|      2:    17.894 -  26.841:  185   |   7:    62.630 -  71.577:   25        |
|      3:    26.841 -  35.788:   99   |   8:    71.577 -  80.524:    6        |
|      4:    35.788 -  44.735:  120   |   9:    80.524 -  89.471:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1482 r_free = 0.1996             target_work(ml) = 5.393         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1480 r_free = 0.1994             target_work(ml) = 5.392         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1480   r_free= 0.1994   ksol= 0.32   Bsol= 36.77   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,2.87,3.75,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.392107                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1479   r_free= 0.1988   ksol= 0.32   Bsol= 36.77   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.26,2.29,2.71,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.391277                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.556991              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.364  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.439473              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.055  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1479      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1988      final r-factor (free) = 0.1735          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7302 = 3.56 * 0.50 * 5.4351 + 1.00 * 0.0639                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5452 = 3.56 * 0.50 * 5.3271 + 1.00 * 0.0709                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1206          |
| start r-factor (free) = 0.1735      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6820 = 1.44 * 1.00 * 5.3271 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5475 = 1.44 * 1.00 * 5.2335 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.94  13.48    None  None   None       |
|    all(noH): 2823   0      0.00    100.94  13.48    None  None   None       |
|    Sol.    : 438    0      1.75    87.86   38.60    None  None   None       |
|    Mac.    : 2385   0      0.00    100.94  8.86     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.094: 1764   |   5:    50.471 -  60.566:   67        |
|      1:    10.094 -  20.189:  544   |   6:    60.566 -  70.660:   44        |
|      2:    20.189 -  30.283:  139   |   7:    70.660 -  80.754:   13        |
|      3:    30.283 -  40.377:  119   |   8:    80.754 -  90.848:    5        |
|      4:    40.377 -  50.471:  125   |   9:    90.848 - 100.943:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1206 r_free = 0.1694             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1204 r_free = 0.1692             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1692   ksol= 0.32   Bsol= 36.77   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.26,2.29,2.71,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.219860                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1693   ksol= 0.32   Bsol= 44.62   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.26,2.29,2.71,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.221536                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.479082              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.842  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.382443              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.413  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1693      final r-factor (free) = 0.1679          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9418 = 1.48 * 0.50 * 5.2342 + 1.00 * 0.0709                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9177 = 1.48 * 0.50 * 5.2262 + 1.00 * 0.0527                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1679      final r-factor (free) = 0.1665          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0126 = 0.38 * 1.00 * 5.2262 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0100 = 0.38 * 1.00 * 5.2247 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.48  13.09    None  None   None       |
|    all(noH): 2823   0      0.00    100.48  13.09    None  None   None       |
|    Sol.    : 438    0      1.57    84.90   37.03    None  None   None       |
|    Mac.    : 2385   0      0.00    100.48  8.70     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.048: 1778   |   5:    50.240 -  60.288:   64        |
|      1:    10.048 -  20.096:  544   |   6:    60.288 -  70.335:   37        |
|      2:    20.096 -  30.144:  145   |   7:    70.335 -  80.383:   11        |
|      3:    30.144 -  40.192:  126   |   8:    80.383 -  90.431:    5        |
|      4:    40.192 -  50.240:  110   |   9:    90.431 - 100.479:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1211 r_free = 0.1665             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1211 r_free = 0.1663             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1663   ksol= 0.32   Bsol= 44.62   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.26,2.29,2.71,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.219057                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6828 0.99   1427  159 0.1005 0.1288      5.3912      5.5383|
|  2:  4.6828 -  3.7355 0.99   1388  150 0.0923 0.1141      5.4755      5.6892|
|  3:  3.7355 -  3.2688 0.99   1355  156 0.1112 0.1680      5.5148      5.8933|
|  4:  3.2688 -  2.9724 0.99   1343  148 0.1333 0.1514      5.5078      5.6218|
|  5:  2.9724 -  2.7608 0.99   1325  146 0.1421 0.1814      5.3814      5.5519|
|  6:  2.7608 -  2.5989 0.98   1325  152 0.1356 0.2037      5.2934      5.5451|
|  7:  2.5989 -  2.4693 0.99   1342  146 0.1358 0.1830      5.2511      5.4514|
|  8:  2.4693 -  2.3622 0.99   1312  146 0.1263 0.1846      5.1261      5.3535|
|  9:  2.3622 -  2.2716 0.98   1312  149 0.1281 0.2043      5.0941      5.3782|
| 10:  2.2716 -  2.1935 0.98   1312  147 0.1264 0.1734      5.0486      5.2588|
| 11:  2.1935 -  2.1251 0.98   1315  138 0.1264 0.1907      5.0067      5.3373|
| 12:  2.1251 -  2.0645 0.99   1308  144 0.1267 0.1831      4.9526      5.1411|
| 13:  2.0645 -  2.0103 0.91   1198  143 0.1267 0.1931       4.859      5.1268|
| 14:  2.0103 -  1.9613 0.27    368   35 0.1179 0.1903      4.7351      4.9909|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6828  1427   159  0.94   8.90   0.97     0.95       7214.98|
|  2:  4.6828 -  3.7355  1388   150  0.95   8.35   1.01     0.99       9162.25|
|  3:  3.7355 -  3.2688  1355   156  0.93  11.96   1.03     1.04      11215.33|
|  4:  3.2688 -  2.9724  1343   148  0.91  14.77   1.01     0.99      11187.28|
|  5:  2.9724 -  2.7608  1325   146  0.89  17.17   0.99     0.97       9278.90|
|  6:  2.7608 -  2.5989  1325   152  0.89  17.78   0.99     0.96       8385.41|
|  7:  2.5989 -  2.4693  1342   146  0.89  16.97   0.99     0.97       7365.53|
|  8:  2.4693 -  2.3622  1312   146  0.89  17.12   0.99     0.95       6059.10|
|  9:  2.3622 -  2.2716  1312   149  0.89  17.26   1.01     0.98       5676.12|
| 10:  2.2716 -  2.1935  1312   147  0.90  16.75   1.00     0.97       5225.18|
| 11:  2.1935 -  2.1251  1315   138  0.89  17.52   1.00     0.95       4896.72|
| 12:  2.1251 -  2.0645  1308   144  0.89  17.31   1.01     1.00       4607.68|
| 13:  2.0645 -  2.0103  1198   143  0.89  17.68   1.00     0.99       3859.88|
| 14:  2.0103 -  1.9613   368    35  0.88  17.79   1.00     0.97       3088.63|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3088.63 max =        11215.33 mean =      7203.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.31|
|phase err.(test): min =        0.00 max =           89.99 mean =        14.78|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1663   ksol= 0.32   Bsol= 46.89   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.14,-0.08,0.22,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.218907                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1663   ksol= 0.32   Bsol= 46.89   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.14,-0.08,0.22,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.218907                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6828 0.99   1427  159 0.1004 0.1287      5.3902      5.5373|
|  2:  4.6828 -  3.7355 0.99   1388  150 0.0922 0.1141       5.475      5.6892|
|  3:  3.7355 -  3.2688 0.99   1355  156 0.1113 0.1681      5.5149      5.8936|
|  4:  3.2688 -  2.9724 0.99   1343  148 0.1333 0.1514      5.5078      5.6219|
|  5:  2.9724 -  2.7608 0.99   1325  146 0.1421 0.1813      5.3814      5.5518|
|  6:  2.7608 -  2.5989 0.98   1325  152 0.1356 0.2040      5.2936      5.5462|
|  7:  2.5989 -  2.4693 0.99   1342  146 0.1359 0.1829      5.2514      5.4514|
|  8:  2.4693 -  2.3622 0.99   1312  146 0.1263 0.1846      5.1262      5.3535|
|  9:  2.3622 -  2.2716 0.98   1312  149 0.1281 0.2043      5.0941      5.3785|
| 10:  2.2716 -  2.1935 0.98   1312  147 0.1264 0.1735      5.0484      5.2581|
| 11:  2.1935 -  2.1251 0.98   1315  138 0.1264 0.1907      5.0063      5.3367|
| 12:  2.1251 -  2.0645 0.99   1308  144 0.1266 0.1829      4.9521      5.1401|
| 13:  2.0645 -  2.0103 0.91   1198  143 0.1267 0.1929      4.8589      5.1263|
| 14:  2.0103 -  1.9613 0.27    368   35 0.1180 0.1910      4.7354      4.9935|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6828  1427   159  0.94   8.89   0.97     0.95       7200.89|
|  2:  4.6828 -  3.7355  1388   150  0.95   8.35   1.01     0.99       9154.10|
|  3:  3.7355 -  3.2688  1355   156  0.93  11.96   1.03     1.03      11215.45|
|  4:  3.2688 -  2.9724  1343   148  0.91  14.77   1.01     0.98      11187.55|
|  5:  2.9724 -  2.7608  1325   146  0.89  17.18   0.99     0.96       9284.92|
|  6:  2.7608 -  2.5989  1325   152  0.89  17.79   0.99     0.96       8392.02|
|  7:  2.5989 -  2.4693  1342   146  0.89  16.97   0.99     0.96       7370.69|
|  8:  2.4693 -  2.3622  1312   146  0.89  17.12   0.98     0.94       6063.30|
|  9:  2.3622 -  2.2716  1312   149  0.89  17.25   1.00     0.97       5676.23|
| 10:  2.2716 -  2.1935  1312   147  0.90  16.75   1.00     0.96       5223.99|
| 11:  2.1935 -  2.1251  1315   138  0.89  17.50   0.99     0.94       4890.91|
| 12:  2.1251 -  2.0645  1308   144  0.89  17.29   1.00     1.00       4599.78|
| 13:  2.0645 -  2.0103  1198   143  0.89  17.67   0.99     0.98       3859.30|
| 14:  2.0103 -  1.9613   368    35  0.88  17.79   0.99     0.96       3092.73|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     3092.73 max =        11215.45 mean =      7202.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.31|
|phase err.(test): min =        0.00 max =           89.99 mean =        14.78|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.27    102.75  15.37    None  None   None       |
|    all(noH): 2823   0      2.27    102.75  15.37    None  None   None       |
|    Sol.    : 438    0      3.84    87.18   39.30    None  None   None       |
|    Mac.    : 2385   0      2.27    102.75  10.97    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:     2.274 -  12.322: 1778   |   5:    52.514 -  62.562:   64        |
|      1:    12.322 -  22.370:  544   |   6:    62.562 -  72.610:   37        |
|      2:    22.370 -  32.418:  145   |   7:    72.610 -  82.658:   11        |
|      3:    32.418 -  42.466:  126   |   8:    82.658 -  92.705:    5        |
|      4:    42.466 -  52.514:  110   |   9:    92.705 - 102.753:    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)= 353         
Filter by distance & map next to the model:
   mapped sites are within: 0.444 - 5.838
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 348 from: 353
   mapped sites are within: 0.731 - 5.838

peak=   10.319 closest distance to " CB  VAL A 230 " =    1.459
peak=    8.984 closest distance to " CG2 VAL A 296 " =    1.278
peak=    7.084 closest distance to " CG  ARG A 138 " =    1.157
peak=    6.307 closest distance to " NH2 ARG A  56 " =    2.267
peak=    5.950 closest distance to " CG  LEU A   5 " =    1.320
peak=    5.840 closest distance to " CD2 LEU A   5 " =    1.245
peak=    5.743 closest distance to " O   HOH Z  37 " =    1.303
peak=    5.547 closest distance to " O   HOH Z 278 " =    1.172
peak=    5.459 closest distance to " CB  GLN A 223 " =    1.408
peak=    5.354 closest distance to " O   HOH Z 247 " =    1.535
peak=    5.343 closest distance to " CD1AILE A 234 " =    1.119
peak=    5.209 closest distance to " CG  PRO A 198 " =    1.336
peak=    5.189 closest distance to " NH1 ARG A 138 " =    0.993
peak=    5.133 closest distance to " CB  PRO A  54 " =    0.924
peak=    5.084 closest distance to " CG  PRO A  54 " =    1.306
peak=    4.977 closest distance to " NH2BARG A 102 " =    0.982
peak=    4.883 closest distance to " O   HOH Z  48 " =    1.756
peak=    4.869 closest distance to " CD  ARG A 138 " =    1.091
peak=    4.771 closest distance to " O   HOH Z 132 " =    1.141
peak=    4.768 closest distance to " CG  PRO A 213 " =    1.313
peak=    4.728 closest distance to " O   HOH Z 124 " =    1.415
peak=    4.678 closest distance to " CG  LEU A 228 " =    1.280
peak=    4.657 closest distance to " CG  PRO A 280 " =    0.860
peak=    4.611 closest distance to " CB  SER A  63 " =    1.361
peak=    4.590 closest distance to " CB  GLN A 183 " =    1.252
peak=    4.568 closest distance to " CB  VAL A 230 " =    1.243
peak=    4.531 closest distance to " CB  ARG A 275 " =    0.857
peak=    4.468 closest distance to " NE2 GLN A  11 " =    1.129
peak=    4.467 closest distance to " O   HOH Z 126 " =    1.913
peak=    4.433 closest distance to " CB  GLU A 128 " =    1.153
peak=    4.428 closest distance to " O   HOH Z 368 " =    2.023
peak=    4.398 closest distance to " CB  SER A   3 " =    1.436
peak=    4.395 closest distance to " CA  ALA A  21 " =    1.214
peak=    4.385 closest distance to " O   HOH Z 120 " =    1.074
peak=    4.369 closest distance to " O   HOH Z 128 " =    2.016
peak=    4.367 closest distance to " CD2 LEU A 228 " =    1.220
peak=    4.339 closest distance to " CG  PRO A 243 " =    1.170
peak=    4.299 closest distance to " O   HOH Z 371 " =    3.252
peak=    4.275 closest distance to " CB  ASN A 148 " =    1.342
peak=    4.268 closest distance to " O   HOH Z 263 " =    1.498
peak=    4.265 closest distance to " O   HOH Z 272 " =    1.916
peak=    4.262 closest distance to " O   HOH Z  97 " =    2.014
peak=    4.246 closest distance to " O   HOH Z 316 " =    2.773
peak=    4.231 closest distance to " O   HOH Z  11 " =    1.217
peak=    4.226 closest distance to " CB  TYR A 169 " =    0.884
peak=    4.216 closest distance to " O   HOH Z 298 " =    1.784
peak=    4.202 closest distance to " O   HOH Z 389 " =    1.922
peak=    4.195 closest distance to " O   HOH Z 369 " =    1.950
peak=    4.195 closest distance to " O   HOH Z 260 " =    1.225
peak=    4.175 closest distance to " O   PRO A 198 " =    1.522
peak=    4.138 closest distance to " O   HOH Z 411 " =    3.575
peak=    4.135 closest distance to " O   HOH Z 277 " =    1.048
peak=    4.135 closest distance to " O   HOH Z 126 " =    1.546
peak=    4.133 closest distance to " CB  LEU A 228 " =    1.363
peak=    4.118 closest distance to " CB  GLU A 152 " =    1.162
peak=    4.101 closest distance to " OD2 ASP A 286 " =    2.827
peak=    4.101 closest distance to " O   HOH Z 236 " =    1.823
peak=    4.099 closest distance to " O   HOH Z 427 " =    3.180
peak=    4.097 closest distance to " O   HOH Z  15 " =    2.273
peak=    4.095 closest distance to " O   HOH Z 202 " =    1.174
peak=    4.085 closest distance to " O   HOH Z 193 " =    1.871
peak=    4.075 closest distance to " O   HOH Z  80 " =    1.794
peak=    4.071 closest distance to " CB  VAL A 265 " =    1.193
peak=    4.066 closest distance to " OD1 ASN A  69 " =    2.650
peak=    4.058 closest distance to " O   HOH Z 295 " =    1.577
peak=    4.049 closest distance to " O   HOH Z  54 " =    2.390
peak=    4.048 closest distance to " O   HOH Z 284 " =    3.117
peak=    4.042 closest distance to " CD1 LEU A 300 " =    1.168
peak=    4.037 closest distance to " CB  TRP A 179 " =    1.331
peak=    4.035 closest distance to " NH1 ARG A  56 " =    0.996
peak=    4.025 closest distance to " O   HOH Z 133 " =    2.263
peak=    4.014 closest distance to " CG2 THR A 221 " =    0.956
peak=    4.014 closest distance to " CA  LEU A 282 " =    1.009
peak=    4.012 closest distance to " CD  ARG A 269 " =    0.957
peak=    4.009 closest distance to " CB  VAL A 202 " =    1.617
peak=    4.000 closest distance to " O   HOH Z 232 " =    2.169
peak=    3.986 closest distance to " O   TRP A 274 " =    1.818
peak=    3.983 closest distance to " O   HOH Z 134 " =    1.474
peak=    3.957 closest distance to " O   HOH Z  63 " =    2.076
peak=    3.951 closest distance to " CB  PRO A 198 " =    0.979
peak=    3.948 closest distance to " O   HOH Z 344 " =    2.861
peak=    3.947 closest distance to " O   HOH Z  78 " =    2.192
peak=    3.947 closest distance to " O   HOH Z 108 " =    1.427
peak=    3.924 closest distance to " CA  TYR A  30 " =    0.992
peak=    3.920 closest distance to " O   HOH Z  88 " =    3.200
peak=    3.917 closest distance to " CG1BVAL A  72 " =    1.606
peak=    3.914 closest distance to " O   HOH Z  92 " =    0.922
peak=    3.900 closest distance to " O   HOH Z 276 " =    1.320
peak=    3.895 closest distance to " O   SER A  87 " =    2.374
peak=    3.893 closest distance to " O   HOH Z 403 " =    1.697
peak=    3.890 closest distance to " O   ASP A 132 " =    3.777
peak=    3.880 closest distance to " O   HOH Z 112 " =    1.473
peak=    3.879 closest distance to " O   HOH Z 303 " =    2.128
peak=    3.865 closest distance to " O   HOH Z 426 " =    1.477
peak=    3.858 closest distance to " O   HOH Z 144 " =    1.661
peak=    3.842 closest distance to " O   HOH Z  78 " =    1.776
peak=    3.841 closest distance to " CB  TRP A 266 " =    0.947
peak=    3.837 closest distance to " CA  VAL A  41 " =    0.883
peak=    3.834 closest distance to " CB  ASP A 124 " =    0.731
peak=    3.825 closest distance to " O   HOH Z 279 " =    1.209
peak=    3.820 closest distance to " CD BLYS A 290 " =    1.061
peak=    3.818 closest distance to " CG1 VAL A 153 " =    1.023
peak=    3.807 closest distance to " CD  LYS A 119 " =    1.332
peak=    3.801 closest distance to " O   HOH Z 189 " =    2.402
peak=    3.783 closest distance to " CA  THR A 221 " =    0.918
peak=    3.780 closest distance to " O   HOH Z 374 " =    3.126
peak=    3.780 closest distance to " O   HOH Z 423 " =    1.731
peak=    3.774 closest distance to " CB  LEU A 143 " =    1.146
peak=    3.774 closest distance to " CA  ASP A 191 " =    0.779
peak=    3.768 closest distance to " O   HOH Z  58 " =    1.490
peak=    3.759 closest distance to " CB  SER A 216 " =    0.841
peak=    3.758 closest distance to " CA  MET A  40 " =    1.064
peak=    3.752 closest distance to " O   HOH Z 271 " =    1.927
peak=    3.751 closest distance to " CA  ALA A 295 " =    1.095
peak=    3.749 closest distance to " O   HOH Z 193 " =    2.018
peak=    3.745 closest distance to " CG  ARG A  66 " =    2.455
peak=    3.742 closest distance to " O   HOH Z 183 " =    1.417
peak=    3.737 closest distance to " CD  GLN A  58 " =    5.830
peak=    3.726 closest distance to " N   ASN A  39 " =    1.224
peak=    3.720 closest distance to " O   HOH Z  68 " =    1.620
peak=    3.717 closest distance to " CG  GLN A  88 " =    1.006
peak=    3.717 closest distance to " O   HOH Z 184 " =    1.430
peak=    3.714 closest distance to " OD1 ASN A 217 " =    1.590
peak=    3.714 closest distance to " CB  ARG A 139 " =    1.013
peak=    3.699 closest distance to " O   HOH Z  93 " =    2.639
peak=    3.694 closest distance to " CG2 VAL A 174 " =    1.325
peak=    3.675 closest distance to " O   HOH Z 345 " =    3.421
peak=    3.673 closest distance to " O   MET A 105 " =    1.808
peak=    3.670 closest distance to " CG2 VAL A 257 " =    0.925
peak=    3.669 closest distance to " CD  ARG A 159 " =    0.812
peak=    3.668 closest distance to " NH1 ARG A  14 " =    1.066
peak=    3.666 closest distance to " O   HOH Z 221 " =    1.409
peak=    3.636 closest distance to " CZ  PHE A 192 " =    1.096
peak=    3.636 closest distance to " CA  VAL A 296 " =    1.116
peak=    3.634 closest distance to " CB  ALA A 291 " =    1.327
peak=    3.634 closest distance to " CA  ASP A 140 " =    1.254
peak=    3.628 closest distance to " O   HOH Z 180 " =    2.131
peak=    3.628 closest distance to " CA  LYS A 117 " =    1.245
peak=    3.626 closest distance to " O   HOH Z 425 " =    1.448
peak=    3.622 closest distance to " O   HOH Z 332 " =    1.593
peak=    3.622 closest distance to " CA  ALA A  51 " =    1.047
peak=    3.619 closest distance to " O   THR A  31 " =    1.430
peak=    3.616 closest distance to " CB  GLU A 277 " =    3.651
peak=    3.612 closest distance to " CA  ALA A 160 " =    0.834
peak=    3.609 closest distance to " CD2 LEU A 255 " =    1.372
peak=    3.607 closest distance to " O   HOH Z 132 " =    2.802
peak=    3.598 closest distance to " CA  GLN A 194 " =    1.086
peak=    3.596 closest distance to " O   HOH Z 346 " =    1.513
peak=    3.594 closest distance to " CD  LYS A 166 " =    1.382
peak=    3.590 closest distance to " O   HOH Z 236 " =    1.661
peak=    3.588 closest distance to " OE1 GLN A  11 " =    1.701
peak=    3.585 closest distance to " O   HOH Z 215 " =    1.527
peak=    3.580 closest distance to " CA  VAL A 126 " =    1.104
peak=    3.579 closest distance to " CG1 ILE A  33 " =    1.406
peak=    3.577 closest distance to " O   HOH Z 118 " =    1.648
peak=    3.558 closest distance to " O   HOH Z 163 " =    1.562
peak=    3.554 closest distance to " O   HOH Z 394 " =    1.700
peak=    3.552 closest distance to " CB  ALA A 161 " =    0.939
peak=    3.548 closest distance to " CB  LEU A 255 " =    0.890
peak=    3.547 closest distance to " CG BARG A 102 " =    1.866
peak=    3.544 closest distance to " C   ALA A 299 " =    0.960
peak=    3.543 closest distance to " CA  ARG A  36 " =    1.126
peak=    3.543 closest distance to " O   HOH Z 327 " =    2.255
peak=    3.540 closest distance to " O   HOH Z  40 " =    1.459
peak=    3.532 closest distance to " CB  LYS A 193 " =    1.205
peak=    3.530 closest distance to " NH2BARG A 145 " =    2.163
peak=    3.527 closest distance to " CB  ILE A 234 " =    0.893
peak=    3.526 closest distance to " O   HOH Z  61 " =    1.513
peak=    3.525 closest distance to " CG  LEU A 167 " =    1.089
peak=    3.524 closest distance to " O   HOH Z  63 " =    1.306
peak=    3.523 closest distance to " NZ  LYS A 117 " =    3.362
peak=    3.511 closest distance to " O   HOH Z  44 " =    2.309
peak=    3.507 closest distance to " O   HOH Z 227 " =    1.730
peak=    3.506 closest distance to " O   HOH Z 193 " =    1.586
peak=    3.505 closest distance to " O   HOH Z   4 " =    1.908
peak=    3.499 closest distance to " CA  ALA A 154 " =    1.218
peak=    3.483 closest distance to " CB  ILE A 199 " =    0.853
peak=    3.480 closest distance to " O   HOH Z 102 " =    1.308
peak=    3.475 closest distance to " CA  ALA A 248 " =    1.164
peak=    3.474 closest distance to " O   HOH Z  54 " =    1.539
peak=    3.464 closest distance to " CB  MET A  47 " =    1.088
peak=    3.463 closest distance to " CB  TYR A  30 " =    1.455
peak=    3.444 closest distance to " CA  ALA A 158 " =    1.079
peak=    3.444 closest distance to " CA  GLY A 211 " =    1.202
peak=    3.442 closest distance to " O   ALA A 158 " =    1.334
peak=    3.440 closest distance to " O   GLN A 278 " =    1.326
peak=    3.438 closest distance to " O   HOH Z 261 " =    1.909
peak=    3.435 closest distance to " CB  ASN A  39 " =    0.854
peak=    3.427 closest distance to " O   HOH Z 126 " =    1.729
peak=    3.419 closest distance to " CB  SER A  28 " =    0.968
peak=    3.418 closest distance to " O   HOH Z  21 " =    1.771
peak=    3.418 closest distance to " CA  SER A  87 " =    0.872
peak=    3.417 closest distance to " O   HOH Z 116 " =    1.757
peak=    3.413 closest distance to " OG BSER A 164 " =    2.220
peak=    3.411 closest distance to " CB  GLU A 236 " =    1.125
peak=    3.410 closest distance to " OG  SER A  22 " =    2.846
peak=    3.409 closest distance to " O   HOH Z 214 " =    1.994
peak=    3.408 closest distance to " O   HOH Z 290 " =    1.178
peak=    3.407 closest distance to " O   HOH Z 203 " =    1.739
peak=    3.404 closest distance to " O   HOH Z 281 " =    4.279
peak=    3.401 closest distance to " O   HOH Z  49 " =    2.555
peak=    3.397 closest distance to " NH2 ARG A 156 " =    1.117
peak=    3.395 closest distance to " CZ  PHE A 218 " =    1.049
peak=    3.392 closest distance to " CD1 ILE A  33 " =    1.622
peak=    3.388 closest distance to " O   HOH Z 128 " =    2.010
peak=    3.384 closest distance to " O   HOH Z 131 " =    2.450
peak=    3.381 closest distance to " O   HOH Z 374 " =    2.448
peak=    3.381 closest distance to " OD1 ASP A 231 " =    1.856
peak=    3.379 closest distance to " CB  SER A 273 " =    0.844
peak=    3.378 closest distance to " CE1 TYR A 186 " =    1.289
peak=    3.377 closest distance to " CB  ALA A 248 " =    1.034
peak=    3.377 closest distance to " O   HOH Z 155 " =    1.544
peak=    3.375 closest distance to " O   HOH Z  49 " =    1.903
peak=    3.372 closest distance to " CB  ARG A  79 " =    1.541
peak=    3.370 closest distance to " O   HOH Z  20 " =    1.904
peak=    3.368 closest distance to " CA  THR A 264 " =    0.785
peak=    3.367 closest distance to " NH1AARG A 145 " =    0.995
peak=    3.363 closest distance to " CB  LYS A 117 " =    1.160
peak=    3.362 closest distance to " CB  MET A  40 " =    0.750
peak=    3.360 closest distance to " CA  LEU A 101 " =    1.674
peak=    3.357 closest distance to " O   HOH Z 273 " =    2.608
peak=    3.355 closest distance to " OG1 THR A 294 " =    1.753
peak=    3.342 closest distance to " O   HOH Z  48 " =    1.767
peak=    3.337 closest distance to " NZ  LYS A  76 " =    1.275
peak=    3.337 closest distance to " NE2 GLN A  58 " =    4.064
peak=    3.335 closest distance to " OD1 ASN A 252 " =    1.257
peak=    3.328 closest distance to " O   ALA A  10 " =    1.592
peak=    3.326 closest distance to " O   HOH Z 133 " =    1.828
peak=    3.325 closest distance to " N   ALA A 291 " =    1.324
peak=    3.324 closest distance to " O   HOH Z 410 " =    1.510
peak=    3.323 closest distance to " O   HOH Z 151 " =    1.754
peak=    3.323 closest distance to " O   HOH Z 280 " =    1.558
peak=    3.322 closest distance to " O   HOH Z  48 " =    2.238
peak=    3.320 closest distance to " ND1 HIS A  86 " =    1.666
peak=    3.317 closest distance to " CG  MET A 188 " =    1.388
peak=    3.316 closest distance to " CB  GLU A 152 " =    1.429
peak=    3.315 closest distance to " CB  ALA A 295 " =    1.360
peak=    3.314 closest distance to " OE1 GLN A  58 " =    1.292
peak=    3.310 closest distance to " O   HOH Z 291 " =    1.465
peak=    3.306 closest distance to " O   HOH Z 420 " =    2.071
peak=    3.303 closest distance to " O   HOH Z 145 " =    1.868
peak=    3.302 closest distance to " CB  PHE A  16 " =    1.052
peak=    3.302 closest distance to " O   HOH Z  43 " =    2.172
peak=    3.298 closest distance to " O   HOH Z 197 " =    1.996
peak=    3.298 closest distance to " CE1 PHE A 208 " =    1.090
peak=    3.298 closest distance to " CA  TYR A 186 " =    1.376
peak=    3.297 closest distance to " O   HOH Z 422 " =    2.706
peak=    3.296 closest distance to " O   HOH Z  30 " =    1.366
peak=    3.295 closest distance to " CD2 HIS A  81 " =    1.129
peak=    3.294 closest distance to " C   SER A  32 " =    1.054
peak=    3.293 closest distance to " O   HOH Z 171 " =    3.762
peak=    3.292 closest distance to " O   HOH Z 271 " =    2.136
peak=    3.292 closest distance to " O   HOH Z 409 " =    3.545
peak=    3.290 closest distance to " O   HOH Z 172 " =    3.980
peak=    3.287 closest distance to " CG1 VAL A 296 " =    1.197
peak=    3.276 closest distance to " OE1 GLU A   2 " =    2.133
peak=    3.276 closest distance to " O   HOH Z  68 " =    1.900
peak=    3.273 closest distance to " O   HOH Z 175 " =    3.572
peak=    3.272 closest distance to " CD  ARG A  14 " =    1.247
peak=    3.271 closest distance to " CD1 TRP A 266 " =    1.146
peak=    3.269 closest distance to " O   HOH Z  50 " =    1.898
peak=    3.269 closest distance to " O   HOH Z 437 " =    2.367
peak=    3.263 closest distance to " O   HOH Z 383 " =    2.164
peak=    3.261 closest distance to " O   ASN A 217 " =    1.322
peak=    3.258 closest distance to " CA  THR A 246 " =    1.231
peak=    3.258 closest distance to " O   HOH Z 355 " =    1.822
peak=    3.257 closest distance to " C   GLY A  80 " =    1.145
peak=    3.254 closest distance to " CA  THR A  42 " =    0.963
peak=    3.248 closest distance to " CB  TRP A 123 " =    1.037
peak=    3.243 closest distance to " O   HOH Z 423 " =    3.183
peak=    3.240 closest distance to " CB  THR A  82 " =    1.308
peak=    3.239 closest distance to " O   HOH Z  53 " =    2.554
peak=    3.238 closest distance to " O   HOH Z 114 " =    1.342
peak=    3.238 closest distance to " CD  GLU A 152 " =    0.909
peak=    3.237 closest distance to " CG1 ILE A 151 " =    1.173
peak=    3.237 closest distance to " CA  GLU A 152 " =    0.776
peak=    3.236 closest distance to " CB  SER A 141 " =    1.077
peak=    3.236 closest distance to " CB  PRO A 243 " =    1.225
peak=    3.235 closest distance to " OD1 ASP A 238 " =    0.822
peak=    3.232 closest distance to " O   HOH Z 427 " =    3.107
peak=    3.232 closest distance to " CA  ILE A 263 " =    0.930
peak=    3.232 closest distance to " NZ ALYS A 290 " =    1.280
peak=    3.231 closest distance to " CB  ASN A 142 " =    0.991
peak=    3.229 closest distance to " O   HOH Z 186 " =    1.056
peak=    3.228 closest distance to " CB  ALA A 256 " =    1.078
peak=    3.227 closest distance to " O   HOH Z 209 " =    2.451
peak=    3.226 closest distance to " CA  ASN A 176 " =    1.097
peak=    3.225 closest distance to " CZ2 TRP A 274 " =    1.903
peak=    3.221 closest distance to " CG2 THR A 220 " =    1.025
peak=    3.220 closest distance to " O   HOH Z 217 " =    1.254
peak=    3.217 closest distance to " O   HOH Z 109 " =    2.807
peak=    3.213 closest distance to " CB  LEU A 237 " =    0.950
peak=    3.211 closest distance to " O   HOH Z 279 " =    2.286
peak=    3.210 closest distance to " O   HOH Z 185 " =    1.722
peak=    3.208 closest distance to " CG AARG A 275 " =    1.050
peak=    3.205 closest distance to " CE  MET A  93 " =    1.513
peak=    3.204 closest distance to " O   HOH Z 377 " =    1.335
peak=    3.202 closest distance to " O   HOH Z 158 " =    2.947
peak=    3.199 closest distance to " N   GLN A 278 " =    0.984
peak=    3.199 closest distance to " N   LYS A 166 " =    0.881
peak=    3.198 closest distance to " O   HOH Z  66 " =    2.161
peak=    3.198 closest distance to " CB  ASN A 187 " =    1.096
peak=    3.197 closest distance to " CB  THR A  31 " =    1.512
peak=    3.197 closest distance to " CA  PHE A 283 " =    1.082
peak=    3.197 closest distance to " OG1 THR A 246 " =    3.316
peak=    3.196 closest distance to " O   HOH Z 207 " =    2.297
peak=    3.193 closest distance to " OG  SER A 206 " =    1.246
peak=    3.190 closest distance to " CA  ASN A 215 " =    1.187
peak=    3.189 closest distance to " OG  SER A  97 " =    3.596
peak=    3.189 closest distance to " C   TYR A 214 " =    1.560
peak=    3.187 closest distance to " O   HOH Z 420 " =    5.838
peak=    3.181 closest distance to " OD2 ASP A 200 " =    1.401
peak=    3.179 closest distance to " CA  ALA A 233 " =    1.920
peak=    3.179 closest distance to " ND1 HIS A  81 " =    1.593
peak=    3.179 closest distance to " O   HOH Z 426 " =    3.058
peak=    3.176 closest distance to " CG1 VAL A 174 " =    1.239
peak=    3.176 closest distance to " NE  ARG A 156 " =    1.020
peak=    3.174 closest distance to " O   HOH Z 417 " =    1.973
peak=    3.170 closest distance to " O   HOH Z 211 " =    2.364
peak=    3.167 closest distance to " O   HOH Z 313 " =    1.956
peak=    3.164 closest distance to " O   HOH Z 329 " =    3.669
peak=    3.162 closest distance to " CG2 ILE A 120 " =    1.270
peak=    3.161 closest distance to " O   HOH Z 407 " =    2.470
peak=    3.160 closest distance to " CB BVAL A  41 " =    1.241
peak=    3.157 closest distance to " ND2 ASN A 187 " =    1.676
peak=    3.154 closest distance to " O   HOH Z 216 " =    2.463
peak=    3.142 closest distance to " CE  LYS A 289 " =    1.344
peak=    3.138 closest distance to " O   HOH Z 151 " =    1.728
peak=    3.137 closest distance to " CG2AVAL A 121 " =    2.259
peak=    3.137 closest distance to " O   HOH Z 298 " =    2.346
peak=    3.136 closest distance to " CD1 LEU A 222 " =    0.878
peak=    3.135 closest distance to " NH1 ARG A 269 " =    0.849
peak=    3.131 closest distance to " O   HOH Z 365 " =    5.758
peak=    3.120 closest distance to " CD  ARG A 219 " =    1.011
peak=    3.116 closest distance to " O   HOH Z  71 " =    1.107
peak=    3.116 closest distance to " N   ALA A 256 " =    1.045
peak=    3.109 closest distance to " O   HOH Z 395 " =    1.358
peak=    3.107 closest distance to " CG2 VAL A 202 " =    1.162
peak=    3.099 closest distance to " CH2 TRP A 150 " =    1.086
peak=    3.099 closest distance to " O   HOH Z 406 " =    1.639
peak=    3.097 closest distance to " O   THR A 220 " =    1.342
peak=    3.092 closest distance to " O   HOH Z 215 " =    1.279
peak=    3.092 closest distance to " O   HOH Z 156 " =    2.862
peak=    3.077 closest distance to " NH2BARG A 190 " =    1.728
peak=    3.073 closest distance to " O   HOH Z 357 " =    2.041
peak=    3.045 closest distance to " O   HOH Z 366 " =    2.954
peak=    3.043 closest distance to " O   HOH Z 344 " =    1.442
peak=    3.034 closest distance to " O   HOH Z  18 " =    1.534

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 191         
Filter by distance & map next to the model:
   mapped sites are within: 0.750 - 5.311
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 191
   mapped sites are within: 0.750 - 5.311

peak=   -5.367 closest distance to " CG2 VAL A 230 " =    0.850
peak=   -4.903 closest distance to " CD  ARG A 138 " =    1.179
peak=   -4.865 closest distance to " CG  ARG A 138 " =    0.894
peak=   -4.353 closest distance to " OG ASER A 134 " =    1.249
peak=   -4.220 closest distance to " O   HOH Z  19 " =    2.076
peak=   -4.200 closest distance to " O   HOH Z 198 " =    2.596
peak=   -4.151 closest distance to " O   ILE A 109 " =    2.664
peak=   -4.119 closest distance to " O   HOH Z 290 " =    1.065
peak=   -4.090 closest distance to " CG2BVAL A  41 " =    2.576
peak=   -4.086 closest distance to " O   HOH Z 266 " =    4.451
peak=   -4.048 closest distance to " O   HOH Z 388 " =    1.829
peak=   -4.044 closest distance to " O   HOH Z  13 " =    1.237
peak=   -4.043 closest distance to " OG1 THR A   4 " =    1.894
peak=   -4.031 closest distance to " O   HOH Z 166 " =    1.849
peak=   -4.029 closest distance to " CG  ASP A 231 " =    0.862
peak=   -4.004 closest distance to " O   HOH Z 231 " =    1.675
peak=   -3.950 closest distance to " NH2 ARG A  66 " =    1.699
peak=   -3.947 closest distance to " O   HOH Z  92 " =    1.353
peak=   -3.940 closest distance to " O   HOH Z 266 " =    4.616
peak=   -3.938 closest distance to " C   ASN A 187 " =    1.786
peak=   -3.918 closest distance to " O   HOH Z 151 " =    1.338
peak=   -3.918 closest distance to " CD  ARG A 156 " =    2.047
peak=   -3.871 closest distance to " C   ALA A 158 " =    1.245
peak=   -3.857 closest distance to " CE2 TYR A  30 " =    2.801
peak=   -3.856 closest distance to " CG1 VAL A 296 " =    1.249
peak=   -3.839 closest distance to " CA  SER A 164 " =    2.000
peak=   -3.815 closest distance to " O   HOH Z 274 " =    2.773
peak=   -3.808 closest distance to " O   HOH Z  11 " =    1.693
peak=   -3.803 closest distance to " CB  TYR A  15 " =    2.235
peak=   -3.791 closest distance to " CD1 LEU A 228 " =    2.437
peak=   -3.753 closest distance to " CG  GLN A 223 " =    2.347
peak=   -3.749 closest distance to " CD2 LEU A 237 " =    2.631
peak=   -3.744 closest distance to " CD  GLN A  88 " =    2.251
peak=   -3.739 closest distance to " O   HOH Z  43 " =    1.669
peak=   -3.730 closest distance to " CD  LYS A 289 " =    2.522
peak=   -3.727 closest distance to " OD1 ASN A 249 " =    1.188
peak=   -3.703 closest distance to " O   HOH Z 377 " =    1.605
peak=   -3.693 closest distance to " O   HOH Z  71 " =    0.879
peak=   -3.669 closest distance to " C   ASN A 285 " =    2.525
peak=   -3.663 closest distance to " CG  ASP A  50 " =    2.206
peak=   -3.654 closest distance to " CB  GLN A  55 " =    1.479
peak=   -3.653 closest distance to " N   GLN A  58 " =    1.821
peak=   -3.643 closest distance to " CG  MET A 105 " =    0.916
peak=   -3.635 closest distance to " O   HOH Z 103 " =    1.776
peak=   -3.633 closest distance to " O   HOH Z 221 " =    1.263
peak=   -3.624 closest distance to " CD1 PHE A  59 " =    1.800
peak=   -3.618 closest distance to " O   HOH Z  37 " =    1.407
peak=   -3.618 closest distance to " O   PRO A 198 " =    1.257
peak=   -3.617 closest distance to " O   HOH Z 222 " =    1.227
peak=   -3.615 closest distance to " O   HOH Z 275 " =    1.569
peak=   -3.614 closest distance to " O   HOH Z  15 " =    1.691
peak=   -3.610 closest distance to " CD2 TYR A 293 " =    2.141
peak=   -3.607 closest distance to " CD  ARG A 139 " =    1.644
peak=   -3.588 closest distance to " CD  ARG A  14 " =    3.255
peak=   -3.587 closest distance to " O   HOH Z 368 " =    1.673
peak=   -3.585 closest distance to " O   HOH Z 243 " =    1.593
peak=   -3.583 closest distance to " NE2 GLN A  88 " =    1.025
peak=   -3.582 closest distance to " O   HOH Z  17 " =    1.478
peak=   -3.578 closest distance to " N   ALA A 226 " =    2.099
peak=   -3.578 closest distance to " O   HOH Z 407 " =    3.246
peak=   -3.573 closest distance to " CG  GLU A  53 " =    1.509
peak=   -3.572 closest distance to " CD1 LEU A 101 " =    2.778
peak=   -3.562 closest distance to " OG  SER A  87 " =    1.498
peak=   -3.561 closest distance to " NH2AARG A 275 " =    5.311
peak=   -3.555 closest distance to " O   HOH Z 241 " =    1.210
peak=   -3.553 closest distance to " CG2 VAL A 112 " =    2.581
peak=   -3.552 closest distance to " CG  ASN A  45 " =    1.686
peak=   -3.527 closest distance to " CD2 LEU A 300 " =    2.816
peak=   -3.521 closest distance to " CD  GLN A  88 " =    0.844
peak=   -3.519 closest distance to " CD2 LEU A 167 " =    1.747
peak=   -3.518 closest distance to " N   ALA A  43 " =    2.498
peak=   -3.512 closest distance to " N   SER A 276 " =    1.311
peak=   -3.509 closest distance to " O   GLY A 211 " =    1.483
peak=   -3.508 closest distance to " O   HOH Z 351 " =    1.514
peak=   -3.505 closest distance to " CB  ALA A 248 " =    1.903
peak=   -3.505 closest distance to " O   HOH Z  98 " =    1.888
peak=   -3.500 closest distance to " O   HOH Z 185 " =    2.339
peak=   -3.496 closest distance to " N   THR A 157 " =    1.614
peak=   -3.496 closest distance to " O   HOH Z 184 " =    1.203
peak=   -3.495 closest distance to " O   GLY A 196 " =    1.129
peak=   -3.485 closest distance to " CE3 TRP A 150 " =    2.032
peak=   -3.484 closest distance to " O   HOH Z 317 " =    2.388
peak=   -3.484 closest distance to " O   HOH Z 341 " =    1.170
peak=   -3.482 closest distance to " C   HIS A 108 " =    1.118
peak=   -3.480 closest distance to " O   HOH Z  52 " =    1.736
peak=   -3.473 closest distance to " O   HOH Z 423 " =    2.149
peak=   -3.466 closest distance to " OE1 GLN A  88 " =    1.013
peak=   -3.463 closest distance to " O   HOH Z 165 " =    2.032
peak=   -3.455 closest distance to " CG  TRP A 266 " =    1.693
peak=   -3.453 closest distance to " CG  GLU A 277 " =    1.162
peak=   -3.448 closest distance to " O   HOH Z 113 " =    1.840
peak=   -3.447 closest distance to " O   HOH Z 292 " =    4.461
peak=   -3.428 closest distance to " ND2 ASN A  45 " =    0.920
peak=   -3.426 closest distance to " O   HOH Z  63 " =    0.874
peak=   -3.416 closest distance to " OE2 GLU A   2 " =    1.694
peak=   -3.415 closest distance to " O   HOH Z 389 " =    1.713
peak=   -3.414 closest distance to " NH2 ARG A  79 " =    1.928
peak=   -3.413 closest distance to " OG BSER A 134 " =    1.741
peak=   -3.412 closest distance to " CB  PRO A 163 " =    2.711
peak=   -3.410 closest distance to " CB  ALA A  43 " =    2.509
peak=   -3.401 closest distance to " O   HOH Z 210 " =    0.856
peak=   -3.396 closest distance to " CA  ASN A 127 " =    1.013
peak=   -3.389 closest distance to " OG  SER A  32 " =    1.064
peak=   -3.379 closest distance to " O   HOH Z 166 " =    1.530
peak=   -3.374 closest distance to " CD1 LEU A   5 " =    2.480
peak=   -3.367 closest distance to " CA  SER A 271 " =    2.292
peak=   -3.363 closest distance to " O   HOH Z 252 " =    4.229
peak=   -3.362 closest distance to " O   HOH Z 353 " =    2.394
peak=   -3.361 closest distance to " CZ  TYR A 169 " =    1.827
peak=   -3.351 closest distance to " O   HOH Z  38 " =    1.556
peak=   -3.351 closest distance to " CD2 LEU A 237 " =    2.805
peak=   -3.350 closest distance to " O   ASN A 187 " =    1.439
peak=   -3.349 closest distance to " CZ  TYR A 172 " =    1.714
peak=   -3.348 closest distance to " O   ALA A 100 " =    2.443
peak=   -3.335 closest distance to " O   HOH Z   9 " =    2.013
peak=   -3.335 closest distance to " O   HOH Z 189 " =    2.248
peak=   -3.332 closest distance to " O   HOH Z 234 " =    4.348
peak=   -3.330 closest distance to " CG  PHE A 283 " =    2.733
peak=   -3.329 closest distance to " CE2 PHE A 283 " =    2.533
peak=   -3.327 closest distance to " CA  ASN A 142 " =    1.372
peak=   -3.322 closest distance to " O   HOH Z 295 " =    1.383
peak=   -3.319 closest distance to " CH2 TRP A 179 " =    1.253
peak=   -3.317 closest distance to " ND2 ASN A  60 " =    1.588
peak=   -3.316 closest distance to " CB  CYS A 254 " =    2.193
peak=   -3.306 closest distance to " O   HOH Z 177 " =    1.406
peak=   -3.298 closest distance to " O   ALA A 161 " =    1.499
peak=   -3.287 closest distance to " O   HOH Z 211 " =    1.574
peak=   -3.282 closest distance to " O   HOH Z 396 " =    1.675
peak=   -3.267 closest distance to " OG BSER A 134 " =    1.255
peak=   -3.265 closest distance to " O   HOH Z 431 " =    1.638
peak=   -3.265 closest distance to " OD2 ASP A 171 " =    1.799
peak=   -3.262 closest distance to " CG2 VAL A 296 " =    1.798
peak=   -3.262 closest distance to " O   HOH Z  10 " =    1.531
peak=   -3.261 closest distance to " CE3 TRP A  70 " =    1.757
peak=   -3.239 closest distance to " NH1 ARG A 195 " =    2.336
peak=   -3.231 closest distance to " OG  SER A 206 " =    1.710
peak=   -3.230 closest distance to " O   HOH Z 411 " =    3.554
peak=   -3.227 closest distance to " O   HOH Z  60 " =    2.068
peak=   -3.225 closest distance to " OG1 THR A  82 " =    1.629
peak=   -3.225 closest distance to " O   HOH Z 184 " =    1.467
peak=   -3.224 closest distance to " O   ASN A 301 " =    1.868
peak=   -3.215 closest distance to " CB  SER A 245 " =    2.327
peak=   -3.215 closest distance to " O   VAL A  67 " =    2.428
peak=   -3.215 closest distance to " CD  GLU A 236 " =    1.031
peak=   -3.215 closest distance to " O   ALA A 256 " =    1.561
peak=   -3.208 closest distance to " O   HOH Z 202 " =    0.750
peak=   -3.207 closest distance to " O   VAL A 197 " =    1.196
peak=   -3.203 closest distance to " N   PHE A  59 " =    2.293
peak=   -3.203 closest distance to " O   TYR A 186 " =    2.281
peak=   -3.201 closest distance to " CD2 LEU A   5 " =    0.986
peak=   -3.201 closest distance to " CB  PRO A 243 " =    2.704
peak=   -3.201 closest distance to " CG  PRO A 163 " =    2.428
peak=   -3.200 closest distance to " CE  MET A 105 " =    2.135
peak=   -3.194 closest distance to " O   HOH Z 435 " =    2.742
peak=   -3.192 closest distance to " CH2 TRP A 177 " =    2.189
peak=   -3.191 closest distance to " OH  TYR A 169 " =    0.978
peak=   -3.187 closest distance to " CB  ASN A  39 " =    2.079
peak=   -3.187 closest distance to " NE2 GLN A  73 " =    1.627
peak=   -3.185 closest distance to " CB  TRP A  85 " =    2.354
peak=   -3.180 closest distance to " CB  GLN A  11 " =    1.877
peak=   -3.171 closest distance to " CA  ARG A 139 " =    0.956
peak=   -3.167 closest distance to " O   HOH Z 435 " =    2.407
peak=   -3.163 closest distance to " C   GLN A 240 " =    2.143
peak=   -3.163 closest distance to " CG  LEU A 228 " =    0.996
peak=   -3.163 closest distance to " O   HOH Z 377 " =    1.312
peak=   -3.158 closest distance to " CB  ASP A 124 " =    2.158
peak=   -3.148 closest distance to " O   HOH Z 227 " =    1.107
peak=   -3.145 closest distance to " OD1 ASP A 200 " =    1.340
peak=   -3.138 closest distance to " CD1 TRP A 179 " =    1.006
peak=   -3.138 closest distance to " N   GLN A 122 " =    1.611
peak=   -3.135 closest distance to " CA  ASP A 298 " =    1.059
peak=   -3.128 closest distance to " C   GLU A 236 " =    1.077
peak=   -3.124 closest distance to " O   HOH Z 105 " =    2.118
peak=   -3.123 closest distance to " CB  ALA A 227 " =    2.347
peak=   -3.117 closest distance to " O   HOH Z 252 " =    1.323
peak=   -3.115 closest distance to " CG  LEU A 281 " =    1.775
peak=   -3.112 closest distance to " C   LEU A 143 " =    1.316
peak=   -3.110 closest distance to " CD  ARG A  14 " =    2.930
peak=   -3.106 closest distance to " NE2 HIS A  86 " =    1.069
peak=   -3.105 closest distance to " C   LEU A 222 " =    0.918
peak=   -3.104 closest distance to " CZ3 TRP A  92 " =    1.109
peak=   -3.100 closest distance to " O   GLU A  44 " =    1.540
peak=   -3.095 closest distance to " N   GLY A  23 " =    2.045
peak=   -3.091 closest distance to " N   GLY A  17 " =    1.588
peak=   -3.086 closest distance to " N   ALA A 248 " =    1.751
peak=   -3.075 closest distance to " CZ  PHE A 130 " =    0.957
peak=   -3.068 closest distance to " O   HOH Z  97 " =    1.854
peak=   -3.059 closest distance to " CD1 ILE A 263 " =    2.415
peak=   -3.058 closest distance to " CB  PHE A  16 " =    2.511
peak=   -3.018 closest distance to " CB  ALA A 291 " =    2.220

================= 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    :  0.4671 0.4636   6.268025e+00   6.262643e+00
   1_bss:  0.4592 0.4530   6.267778e+00   6.257354e+00
   1_xyz:  0.3731 0.4096   6.136913e+00   6.190707e+00
   1_adp:  0.3273 0.3867   6.049452e+00   6.154700e+00
   1_occ:  0.3270 0.3872   6.048756e+00   6.154613e+00
   2_bss:  0.3244 0.3830   6.049251e+00   6.152311e+00
   2_xyz:  0.2408 0.3048   5.813195e+00   5.982388e+00
   2_adp:  0.2235 0.2846   5.749393e+00   5.929134e+00
   2_occ:  0.2233 0.2845   5.748419e+00   5.928982e+00
   3_bss:  0.2217 0.2814   5.747877e+00   5.926525e+00
   3_xyz:  0.1636 0.2158   5.474869e+00   5.692812e+00
   3_adp:  0.1482 0.1996   5.392856e+00   5.620554e+00
   3_occ:  0.1480 0.1994   5.392107e+00   5.619651e+00
   4_bss:  0.1479 0.1988   5.391277e+00   5.616806e+00
   4_xyz:  0.1257 0.1735   5.249229e+00   5.485065e+00
   4_adp:  0.1206 0.1694   5.220290e+00   5.460966e+00
   4_occ:  0.1204 0.1692   5.219860e+00   5.460721e+00
   5_bss:  0.1209 0.1693   5.221536e+00   5.461861e+00
   5_xyz:  0.1211 0.1679   5.224012e+00   5.457754e+00
   5_adp:  0.1211 0.1665   5.219579e+00   5.449854e+00
   5_occ:  0.1211 0.1663   5.219057e+00   5.449398e+00
   5_bss:  0.1211 0.1663   5.218907e+00   5.449288e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   7.914   7.597   8.652   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.914   7.597   8.652   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.914   7.597   8.652   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.914   7.597   8.652   0.000   0.000   0.000
   2_bss:  0.308  36.767   4.647   4.348   5.985   0.000   0.000   0.000
   2_xyz:  0.308  36.767   4.647   4.348   5.985   0.000   0.000   0.000
   2_adp:  0.308  36.767   4.647   4.348   5.985   0.000   0.000   0.000
   2_occ:  0.308  36.767   4.647   4.348   5.985   0.000   0.000   0.000
   3_bss:  0.317  36.767   2.896   2.871   3.748   0.000   0.000   0.000
   3_xyz:  0.317  36.767   2.896   2.871   3.748   0.000   0.000   0.000
   3_adp:  0.317  36.767   2.896   2.871   3.748   0.000   0.000   0.000
   3_occ:  0.317  36.767   2.896   2.871   3.748   0.000   0.000   0.000
   4_bss:  0.317  36.767   2.259   2.290   2.715   0.000   0.000   0.000
   4_xyz:  0.317  36.767   2.259   2.290   2.715   0.000   0.000   0.000
   4_adp:  0.317  36.767   2.259   2.290   2.715   0.000   0.000   0.000
   4_occ:  0.317  36.767   2.259   2.290   2.715   0.000   0.000   0.000
   5_bss:  0.319  44.617   2.259   2.290   2.715   0.000   0.000   0.000
   5_xyz:  0.319  44.617   2.259   2.290   2.715   0.000   0.000   0.000
   5_adp:  0.319  44.617   2.259   2.290   2.715   0.000   0.000   0.000
   5_occ:  0.319  44.617   2.259   2.290   2.715   0.000   0.000   0.000
   5_bss:  0.319  46.892  -0.141  -0.079   0.220   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.142 0.4429  0.5181    66912.744
   1_bss:  56.902 0.4302  0.6265    64505.532
   1_xyz:  47.615 0.5472  0.7889    48672.801
   1_adp:  43.461 0.5991  0.8924    42685.654
   1_occ:  43.488 0.5987  0.8916    42774.316
   2_bss:  43.271 0.6013  0.8059    42444.001
   2_xyz:  32.238 0.7315  0.9550    25430.691
   2_adp:  29.206 0.7662  0.9918    21820.456
   2_occ:  29.181 0.7664  0.9920    21778.725
   3_bss:  29.032 0.7680  0.9304    21630.317
   3_xyz:  21.136 0.8501  0.9871    12092.740
   3_adp:  19.217 0.8692  0.9934    10428.742
   3_occ:  19.192 0.8695  0.9934    10402.002
   4_bss:  19.104 0.8703  0.9671    10322.482
   4_xyz:  16.246 0.8959  0.9809     7828.733
   4_adp:  15.682 0.9010  0.9788     7473.575
   4_occ:  15.670 0.9011  0.9788     7468.303
   5_bss:  15.688 0.9010  0.9789     7510.755
   5_xyz:  15.488 0.9029  0.9786     7321.653
   5_adp:  15.268 0.9049  0.9773     7209.565
   5_occ:  15.257 0.9050  0.9773     7204.663
   5_bss:  15.254 0.9051  0.9722     7203.514
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3703e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3703e+01
   1_xyz:   1.688  0.013  0.108 18.083  0.007  4.110   1.3948e-01
   1_adp:   1.688  0.013  0.108 18.083  0.007  4.110   1.3948e-01
   1_occ:   1.688  0.013  0.108 18.083  0.007  4.110   1.3948e-01
   2_bss:   1.688  0.013  0.108 18.083  0.007  4.110   1.3948e-01
   2_xyz:   1.080  0.008  0.073 15.974  0.004  4.115   7.2133e-02
   2_adp:   1.080  0.008  0.073 15.974  0.004  4.115   7.2133e-02
   2_occ:   1.080  0.008  0.073 15.974  0.004  4.115   7.2133e-02
   3_bss:   1.080  0.008  0.073 15.974  0.004  4.115   7.2133e-02
   3_xyz:   1.051  0.007  0.078 15.392  0.004  4.129   6.3733e-02
   3_adp:   1.051  0.007  0.078 15.392  0.004  4.129   6.3733e-02
   3_occ:   1.051  0.007  0.078 15.392  0.004  4.129   6.3733e-02
   4_bss:   1.051  0.007  0.078 15.392  0.004  4.129   6.3733e-02
   4_xyz:   1.108  0.008  0.085 15.694  0.004  4.125   7.0910e-02
   4_adp:   1.108  0.008  0.085 15.694  0.004  4.125   7.0910e-02
   4_occ:   1.108  0.008  0.085 15.694  0.004  4.125   7.0910e-02
   5_bss:   1.108  0.008  0.085 15.694  0.004  4.125   7.0910e-02
   5_xyz:   0.922  0.005  0.070 15.242  0.003  4.124   5.2691e-02
   5_adp:   0.922  0.005  0.070 15.242  0.003  4.124   5.2691e-02
   5_occ:   0.922  0.005  0.070 15.242  0.003  4.124   5.2691e-02
   5_bss:   0.922  0.005  0.070 15.242  0.003  4.124   5.2691e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9620e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9620e+00
   1_xyz:  14.747  0.165  0.475 84.874  0.053  2.182   9.9529e-02
   1_adp:  14.747  0.165  0.475 84.874  0.053  2.182   9.9529e-02
   1_occ:  14.747  0.165  0.475 84.874  0.053  2.182   9.9529e-02
   2_bss:  14.747  0.165  0.475 84.874  0.053  2.182   9.9529e-02
   2_xyz:   6.716  0.080  0.243 80.994  0.031  2.242   5.3695e-02
   2_adp:   6.716  0.080  0.243 80.994  0.031  2.242   5.3695e-02
   2_occ:   6.716  0.080  0.243 80.994  0.031  2.242   5.3695e-02
   3_bss:   6.716  0.080  0.243 80.994  0.031  2.242   5.3695e-02
   3_xyz:   7.485  0.052  0.363 88.186  0.044  2.395   5.0947e-02
   3_adp:   7.485  0.052  0.363 88.186  0.044  2.395   5.0947e-02
   3_occ:   7.485  0.052  0.363 88.186  0.044  2.395   5.0947e-02
   4_bss:   7.485  0.052  0.363 88.186  0.044  2.395   5.0947e-02
   4_xyz:   8.386  0.054  0.529 82.573  0.033  2.268   4.8695e-02
   4_adp:   8.386  0.054  0.529 82.573  0.033  2.268   4.8695e-02
   4_occ:   8.386  0.054  0.529 82.573  0.033  2.268   4.8695e-02
   5_bss:   8.386  0.054  0.529 82.573  0.033  2.268   4.8695e-02
   5_xyz:   7.577  0.045  0.374 84.100  0.032  2.429   2.8167e-02
   5_adp:   7.577  0.045  0.374 84.100  0.032  2.429   2.8167e-02
   5_occ:   7.577  0.045  0.374 84.100  0.032  2.429   2.8167e-02
   5_bss:   7.577  0.045  0.374 84.100  0.032  2.429   2.8167e-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:  82.08   0.00  12.44  78.58   0.00   9.59  82.08   0.00  27.95
   1_occ:  82.08   0.00  12.44  78.58   0.00   9.59  82.08   0.00  27.95
   2_bss:  82.08   0.00  12.44  78.58   0.00   9.59  82.08   0.00  27.95
   2_xyz:  82.08   0.00  12.44  78.58   0.00   9.59  82.08   0.00  27.95
   2_adp:  82.06   0.00  12.69  77.83   0.00   9.15  82.06   0.00  31.98
   2_occ:  82.06   0.00  12.69  77.83   0.00   9.15  82.06   0.00  31.98
   3_bss:  82.06   0.00  12.69  77.83   0.00   9.15  82.06   0.00  31.98
   3_xyz:  82.06   0.00  12.69  77.83   0.00   9.15  82.06   0.00  31.98
   3_adp:  89.47   0.00  13.52  89.47   0.00   8.98  82.35   1.81  38.29
   3_occ:  89.47   0.00  13.52  89.47   0.00   8.98  82.35   1.81  38.29
   4_bss:  89.47   0.00  13.52  89.47   0.00   8.98  82.35   1.81  38.29
   4_xyz:  89.47   0.00  13.52  89.47   0.00   8.98  82.35   1.81  38.29
   4_adp: 100.94   0.00  13.48 100.94   0.00   8.86  87.86   1.75  38.60
   4_occ: 100.94   0.00  13.48 100.94   0.00   8.86  87.86   1.75  38.60
   5_bss: 100.94   0.00  13.48 100.94   0.00   8.86  87.86   1.75  38.60
   5_xyz: 100.94   0.00  13.48 100.94   0.00   8.86  87.86   1.75  38.60
   5_adp: 100.48   0.00  13.09 100.48   0.00   8.70  84.90   1.57  37.03
   5_occ: 100.48   0.00  13.09 100.48   0.00   8.70  84.90   1.57  37.03
   5_bss: 102.75   2.27  15.37 102.75   2.27  10.97  87.18   3.84  39.30
------------------------------------------------------------------------
 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:    1.223    0.012    0.412
   1_adp:    1.223    0.012    0.412
   1_occ:    1.223    0.012    0.412
   2_bss:    1.223    0.012    0.412
   2_xyz:    1.670    0.049    0.550
   2_adp:    1.670    0.049    0.550
   2_occ:    1.670    0.049    0.550
   3_bss:    1.670    0.049    0.550
   3_xyz:    1.627    0.047    0.627
   3_adp:    1.627    0.047    0.627
   3_occ:    1.627    0.047    0.627
   4_bss:    1.627    0.047    0.627
   4_xyz:    1.648    0.059    0.673
   4_adp:    1.648    0.059    0.673
   4_occ:    1.648    0.059    0.673
   5_bss:    1.648    0.059    0.673
   5_xyz:    1.693    0.053    0.680
   5_adp:    1.693    0.053    0.680
   5_occ:    1.693    0.053    0.680
   5_bss:    1.693    0.053    0.680
------------------------------------------------------------------------

CPU time actual refinement: 358.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1035/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_1035/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1035/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1035/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1035/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 358.56 
  Macro-tasks:
    bulk solvent and scale       = 40.80  
    individual site refinement   = 157.39 
    weights calculation          = 32.46  
    collect and process          = 6.50   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 237.26 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 114.72 
    alpha_beta                      = 8.17   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 126.44 
    fmodel                         = 7.16   
    r_factors                      = 0.21   
    phase_errors                   = 10.54  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 271.14 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.960 micro seconds
Total CPU time: 6.20 minutes
from_scatterers_fft:    653 calls, 114.29 s
gradients_fft:          597 calls, 112.47 s

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

# Date 2008-01-16 Time 03:02:47 PST -0800 (1200481367.54 s)
Start R-work = 0.4671, R-free = 0.4636 (no bulk solvent and anisotropic scale)
Final R-work = 0.1370, R-free = 0.1836 (no bulk solvent and anisotropic scale)

Start R-work = 0.4592, R-free = 0.4530
Final R-work = 0.1211, R-free = 0.1663