# Date 2008-01-16 Time 01:10:15 PST -0800 (1200474615.63 s)
#phil __OFF__

Command line arguments: "../317.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18146
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 317

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.1647, 88.1178, 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: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.906 1.97085
Completeness in resolution range: 0.935393
Completeness with d_max=infinity: 0.932543

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9060
                             d_min =   1.9708

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.906 1.97085
Completeness in resolution range: 0.935393
Completeness with d_max=infinity: 0.932543

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9064 -  4.2170 [2203/2231]  1982   221  10.0%
  bin  2:  4.2170 -  3.3598 [2108/2127]  1894   214  10.2%
  bin  3:  3.3598 -  2.9388 [2082/2102]  1880   202   9.7%
  bin  4:  2.9388 -  2.6718 [2064/2089]  1857   207  10.0%
  bin  5:  2.6718 -  2.4812 [2050/2070]  1840   210  10.2%
  bin  6:  2.4812 -  2.3355 [2030/2077]  1825   205  10.1%
  bin  7:  2.3355 -  2.2189 [2039/2072]  1847   192   9.4%
  bin  8:  2.2189 -  2.1226 [2030/2064]  1814   216  10.6%
  bin  9:  2.1226 -  2.0411 [2027/2057]  1830   197   9.7%
  bin 10:  2.0411 -  1.9708 [ 956/2053]   861    95   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_317/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: 0.13 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:
        1.47 -     2.16: 15
        2.16 -     2.84: 1054
        2.84 -     3.53: 4373
        3.53 -     4.21: 9244
        4.21 -     4.90: 13508
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.474 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.548 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.694 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.705 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.732 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28189 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_317/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_317/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.16465 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4735   r_free= 0.4574   ksol= 0.00   Bsol= 0.00   scale= 0.796    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.274575                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9064 -  4.7034 0.99   1430  158 0.3781 0.3663       6.577      6.5559|
|  2:  4.7034 -  3.7528 0.99   1375  153 0.3758 0.4265       6.729      6.8657|
|  3:  3.7528 -  3.2842 0.99   1343  151 0.4413 0.3867        6.66      6.6159|
|  4:  3.2842 -  2.9866 0.99   1351  142 0.4585 0.4566      6.4978      6.4711|
|  5:  2.9866 -  2.7740 0.99   1311  155 0.5029 0.4721      6.3542      6.3836|
|  6:  2.7740 -  2.6114 0.98   1333  144 0.5029 0.5414      6.2721      6.1998|
|  7:  2.6114 -  2.4812 0.99   1310  151 0.5029 0.4898      6.2202      6.1408|
|  8:  2.4812 -  2.3736 0.98   1323  141 0.5301 0.4408      6.1854      6.1538|
|  9:  2.3736 -  2.2826 0.98   1313  146 0.5330 0.5030      6.1328      6.1408|
| 10:  2.2826 -  2.2041 0.98   1296  143 0.5354 0.4881      6.1011      6.0907|
| 11:  2.2041 -  2.1354 0.99   1311  155 0.5175 0.5300      6.0144      6.0265|
| 12:  2.1354 -  2.0745 0.98   1297  140 0.5280 0.4838      5.9541      5.9433|
| 13:  2.0745 -  2.0200 0.93   1239  129 0.5339 0.5096      5.8893      5.8371|
| 14:  2.0200 -  1.9708 0.31    398   51 0.5161 0.3976      5.9144      5.6887|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9064 -  4.7034  1430   158  0.71  33.08   0.80     0.72      65932.11|
|  2:  4.7034 -  3.7528  1375   153  0.71  34.09   0.89     0.77      99893.16|
|  3:  3.7528 -  3.2842  1343   151  0.62  42.02   0.83     0.73     105276.29|
|  4:  3.2842 -  2.9866  1351   142  0.53  49.30   0.80     0.62      93201.71|
|  5:  2.9866 -  2.7740  1311   155  0.44  56.89   0.74     0.52      78136.76|
|  6:  2.7740 -  2.6114  1333   144  0.39  60.66   0.72     0.46      71778.90|
|  7:  2.6114 -  2.4812  1310   151  0.39  60.20   0.75     0.45      63552.20|
|  8:  2.4812 -  2.3736  1323   141  0.43  57.67   0.72     0.50      52920.85|
|  9:  2.3736 -  2.2826  1313   146  0.45  55.99   0.71     0.54      47047.46|
| 10:  2.2826 -  2.2041  1296   143  0.44  57.02   0.73     0.51      42327.23|
| 11:  2.2041 -  2.1354  1311   155  0.38  61.68   0.75     0.47      44663.85|
| 12:  2.1354 -  2.0745  1297   140  0.36  63.42   0.75     0.46      41069.75|
| 13:  2.0745 -  2.0200  1239   129  0.37  62.26   0.73     0.48      35463.94|
| 14:  2.0200 -  1.9708   398    51  0.48  54.01   0.77     0.48      24205.15|
|alpha:            min =        0.45 max =            0.77 mean =         0.56|
|beta:             min =    24205.15 max =       105276.29 mean =     64228.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.97 mean =        53.15|
|phase err.(test): min =        0.00 max =           89.93 mean =        53.49|
|-----------------------------------------------------------------------------|

============================== 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 = 11.868531             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.369   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.949495              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.210   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      175 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      696 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1506 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2610 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3901 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5051 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6560 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7712 |
|-----------------------------------------------------------------------------|
|-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 |       53.864 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       2.044 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    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 = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4791   r_free= 0.4582   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.277662                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4629   r_free= 0.4485   ksol= 0.33   Bsol= 11.78   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.48,8.02,11.53,0.00,0.00,0.00); trace/3= 9.01                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.266464                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.776857             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.653   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.913974              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.971   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4629      final r-factor (work) = 0.3722          |
| start r-factor (free) = 0.4485      final r-factor (free) = 0.3947          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 87.6757 = 10.78 * 0.50 * 6.2748 + 1.00 * 53.8644                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.3523 = 10.78 * 0.50 * 6.1635 + 1.00 * 0.1406                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3722      final r-factor (work) = 0.3251          |
| start r-factor (free) = 0.3947      final r-factor (free) = 0.3715          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6477 = 0.91 * 1.00 * 6.1635 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5485 = 0.91 * 1.00 * 6.0551 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.98   12.65    None  None   None       |
|    all(noH): 2823   0      0.00    70.98   12.65    None  None   None       |
|    Sol.    : 438    0      0.00    70.98   26.52    None  None   None       |
|    Mac.    : 2385   0      0.00    61.64   10.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.098: 1095   |   5:    35.492 -  42.590:   67        |
|      1:     7.098 -  14.197:  794   |   6:    42.590 -  49.688:   54        |
|      2:    14.197 -  21.295:  428   |   7:    49.688 -  56.787:   22        |
|      3:    21.295 -  28.393:  227   |   8:    56.787 -  63.885:   10        |
|      4:    28.393 -  35.492:  124   |   9:    63.885 -  70.983:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3251 r_free = 0.3715             target_work(ml) = 6.029         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3247 r_free = 0.3723             target_work(ml) = 6.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3247   r_free= 0.3723   ksol= 0.33   Bsol= 11.78   scale= 1.111   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.48,8.02,11.53,0.00,0.00,0.00); trace/3= 9.01                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.028471                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3203   r_free= 0.3675   ksol= 0.32   Bsol= 39.79   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,3.94,7.34,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.028631                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.297950              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.383   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.434084              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.037  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3203      final r-factor (work) = 0.2367          |
| start r-factor (free) = 0.3675      final r-factor (free) = 0.2849          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1520 = 4.30 * 0.50 * 6.0547 + 1.00 * 0.1406                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7464 = 4.30 * 0.50 * 5.8970 + 1.00 * 0.0739                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2367      final r-factor (work) = 0.2170          |
| start r-factor (free) = 0.2849      final r-factor (free) = 0.2686          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5743 = 0.43 * 1.00 * 5.8970 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4988 = 0.43 * 1.00 * 5.7308 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.25   12.82    None  None   None       |
|    all(noH): 2823   0      0.00    69.25   12.82    None  None   None       |
|    Sol.    : 438    0      0.92    69.25   32.77    None  None   None       |
|    Mac.    : 2385   0      0.00    68.09   9.16     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.926: 1219   |   5:    34.627 -  41.553:  101        |
|      1:     6.926 -  13.851:  749   |   6:    41.553 -  48.478:   78        |
|      2:    13.851 -  20.777:  344   |   7:    48.478 -  55.404:   41        |
|      3:    20.777 -  27.702:  137   |   8:    55.404 -  62.329:   20        |
|      4:    27.702 -  34.627:  127   |   9:    62.329 -  69.255:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2170 r_free = 0.2686             target_work(ml) = 5.706         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2168 r_free = 0.2684             target_work(ml) = 5.706         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2168   r_free= 0.2684   ksol= 0.32   Bsol= 39.79   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,3.94,7.34,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.705560                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2148   r_free= 0.2681   ksol= 0.31   Bsol= 51.44   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,2.73,4.79,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.705926                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.748646              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.136  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.421225              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.871  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2148      final r-factor (work) = 0.1611          |
| start r-factor (free) = 0.2681      final r-factor (free) = 0.2091          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9593 = 2.75 * 0.50 * 5.7378 + 1.00 * 0.0737                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7372 = 2.75 * 0.50 * 5.5849 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1611      final r-factor (work) = 0.1504          |
| start r-factor (free) = 0.2091      final r-factor (free) = 0.1985          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3636 = 0.42 * 1.00 * 5.5849 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2930 = 0.42 * 1.00 * 5.4167 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.47   12.96    None  None   None       |
|    all(noH): 2823   0      0.00    72.47   12.96    None  None   None       |
|    Sol.    : 438    0      1.68    70.13   35.50    None  None   None       |
|    Mac.    : 2385   0      0.00    72.47   8.82     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:     0.000 -   7.248: 1318   |   5:    36.237 -  43.485:  105        |
|      1:     7.248 -  14.495:  776   |   6:    43.485 -  50.732:   94        |
|      2:    14.495 -  21.742:  245   |   7:    50.732 -  57.980:   50        |
|      3:    21.742 -  28.990:  103   |   8:    57.980 -  65.227:   20        |
|      4:    28.990 -  36.237:  106   |   9:    65.227 -  72.475:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1504 r_free = 0.1985             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1503 r_free = 0.1984             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1503   r_free= 0.1984   ksol= 0.31   Bsol= 51.44   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,2.73,4.79,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.390859                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1504   r_free= 0.1975   ksol= 0.33   Bsol= 56.65   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.12,2.14,3.88,0.00,0.00,0.00); trace/3= 2.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.390206                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.714543              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.634  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.846271              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.567  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1504      final r-factor (work) = 0.1330          |
| start r-factor (free) = 0.1975      final r-factor (free) = 0.1760          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7088 = 1.71 * 0.50 * 5.4207 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6320 = 1.71 * 0.50 * 5.3380 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1330      final r-factor (work) = 0.1293          |
| start r-factor (free) = 0.1760      final r-factor (free) = 0.1732          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5288 = 0.85 * 1.00 * 5.3380 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8753 = 0.85 * 1.00 * 5.2732 + 1.00 * 6.4127                              |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.74   13.02    None  None   None       |
|    all(noH): 2823   0      0.00    74.74   13.02    None  None   None       |
|    Sol.    : 438    0      1.23    74.71   36.45    None  None   None       |
|    Mac.    : 2385   0      0.00    74.74   8.72     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.474: 1398   |   5:    37.368 -  44.842:  104        |
|      1:     7.474 -  14.947:  733   |   6:    44.842 -  52.315:   91        |
|      2:    14.947 -  22.421:  216   |   7:    52.315 -  59.789:   54        |
|      3:    22.421 -  29.895:   99   |   8:    59.789 -  67.263:   18        |
|      4:    29.895 -  37.368:  103   |   9:    67.263 -  74.736:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1293 r_free = 0.1732             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1292 r_free = 0.1732             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1292   r_free= 0.1732   ksol= 0.33   Bsol= 56.65   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.12,2.14,3.88,0.00,0.00,0.00); trace/3= 2.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.267075                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1292   r_free= 0.1732   ksol= 0.33   Bsol= 55.48   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.28,2.23,3.81,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.267168                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.499466              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.953  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 153.463428            wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.660   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1292      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1732      final r-factor (free) = 0.1679          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6460 = 2.50 * 0.50 * 5.2732 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6187 = 2.50 * 0.50 * 5.2373 + 1.00 * 0.0735                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1196          |
| start r-factor (free) = 0.1679      final r-factor (free) = 0.1685          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 803.7646 = 153.46 * 1.00 * 5.2373 + 1.00 * 0.0354                           |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 800.3832 = 153.46 * 1.00 * 5.2154 + 1.00 * 0.0176                           |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.87  13.66    None  None   None       |
|    all(noH): 2823   0      0.00    100.87  13.66    None  None   None       |
|    Sol.    : 438    0      1.08    100.87  39.94    None  None   None       |
|    Mac.    : 2385   0      0.00    93.31   8.83     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 -  10.087: 1779   |   5:    50.435 -  60.522:   79        |
|      1:    10.087 -  20.174:  510   |   6:    60.522 -  70.610:   53        |
|      2:    20.174 -  30.261:  154   |   7:    70.610 -  80.697:   23        |
|      3:    30.261 -  40.348:  114   |   8:    80.697 -  90.784:   11        |
|      4:    40.348 -  50.435:   97   |   9:    90.784 - 100.871:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1196 r_free = 0.1685             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1195 r_free = 0.1685             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1685   ksol= 0.33   Bsol= 55.48   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.28,2.23,3.81,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.218156                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9064 -  4.7034 0.99   1430  158 0.1013 0.1357      5.4335      5.6011|
|  2:  4.7034 -  3.7528 0.99   1375  153 0.0865 0.1101      5.4646      5.6598|
|  3:  3.7528 -  3.2842 0.99   1343  151 0.1145 0.1580      5.5313      5.8633|
|  4:  3.2842 -  2.9866 0.99   1351  142 0.1279 0.1741      5.4915      5.6993|
|  5:  2.9866 -  2.7740 0.99   1311  155 0.1408 0.1652      5.3964      5.5357|
|  6:  2.7740 -  2.6114 0.98   1333  144 0.1354 0.2334      5.2932      5.6233|
|  7:  2.6114 -  2.4812 0.99   1310  151 0.1375 0.1753      5.2526      5.3917|
|  8:  2.4812 -  2.3736 0.98   1323  141 0.1256 0.1775       5.162      5.3985|
|  9:  2.3736 -  2.2826 0.98   1313  146 0.1275 0.2081      5.0949      5.4337|
| 10:  2.2826 -  2.2041 0.98   1296  143 0.1227 0.1750      5.0253      5.2156|
| 11:  2.2041 -  2.1354 0.99   1311  155 0.1232 0.2025      4.9942      5.3673|
| 12:  2.1354 -  2.0745 0.98   1297  140 0.1221 0.1671      4.9403      5.1553|
| 13:  2.0745 -  2.0200 0.93   1239  129 0.1170 0.1797      4.8325      5.0593|
| 14:  2.0200 -  1.9708 0.31    398   51 0.1028 0.1859      4.7222      5.0017|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9064 -  4.7034  1430   158  0.93  10.18   0.97     0.95       8478.33|
|  2:  4.7034 -  3.7528  1375   153  0.95   8.62   1.01     1.00       9930.11|
|  3:  3.7528 -  3.2842  1343   151  0.93  12.28   1.03     1.03      11451.09|
|  4:  3.2842 -  2.9866  1351   142  0.92  14.31   1.01     1.00      11101.60|
|  5:  2.9866 -  2.7740  1311   155  0.89  17.35   0.99     0.96       9747.34|
|  6:  2.7740 -  2.6114  1333   144  0.88  18.54   0.97     0.94       8613.57|
|  7:  2.6114 -  2.4812  1310   151  0.89  17.58   0.98     0.93       7479.57|
|  8:  2.4812 -  2.3736  1323   141  0.89  17.30   0.99     0.95       6706.43|
|  9:  2.3736 -  2.2826  1313   146  0.89  17.67   0.99     0.96       5852.52|
| 10:  2.2826 -  2.2041  1296   143  0.89  17.64   0.98     0.94       5211.77|
| 11:  2.2041 -  2.1354  1311   155  0.89  17.91   0.98     0.93       5016.17|
| 12:  2.1354 -  2.0745  1297   140  0.89  17.52   0.99     0.98       4591.46|
| 13:  2.0745 -  2.0200  1239   129  0.89  17.54   0.98     0.95       3775.62|
| 14:  2.0200 -  1.9708   398    51  0.91  14.98   0.96     0.92       2862.01|
|alpha:            min =        0.92 max =            1.03 mean =         0.96|
|beta:             min =     2862.01 max =        11451.09 mean =      7480.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.63|
|phase err.(test): min =        0.00 max =           88.79 mean =        15.19|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1682   ksol= 0.33   Bsol= 61.23   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.11,-0.20,1.31,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.218336                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1682   ksol= 0.33   Bsol= 61.23   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.11,-0.20,1.31,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.218336                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9064 -  4.7034 0.99   1430  158 0.1014 0.1362       5.435      5.6048|
|  2:  4.7034 -  3.7528 0.99   1375  153 0.0868 0.1106      5.4673      5.6622|
|  3:  3.7528 -  3.2842 0.99   1343  151 0.1145 0.1582      5.5321      5.8637|
|  4:  3.2842 -  2.9866 0.99   1351  142 0.1278 0.1738      5.4906      5.6987|
|  5:  2.9866 -  2.7740 0.99   1311  155 0.1406 0.1648      5.3954       5.534|
|  6:  2.7740 -  2.6114 0.98   1333  144 0.1353 0.2332      5.2924      5.6227|
|  7:  2.6114 -  2.4812 0.99   1310  151 0.1374 0.1752      5.2522      5.3914|
|  8:  2.4812 -  2.3736 0.98   1323  141 0.1255 0.1776      5.1622      5.3986|
|  9:  2.3736 -  2.2826 0.98   1313  146 0.1275 0.2082      5.0951      5.4342|
| 10:  2.2826 -  2.2041 0.98   1296  143 0.1227 0.1751      5.0254      5.2153|
| 11:  2.2041 -  2.1354 0.99   1311  155 0.1233 0.2022       4.994      5.3667|
| 12:  2.1354 -  2.0745 0.98   1297  140 0.1221 0.1671      4.9401      5.1553|
| 13:  2.0745 -  2.0200 0.93   1239  129 0.1169 0.1797      4.8323      5.0586|
| 14:  2.0200 -  1.9708 0.31    398   51 0.1028 0.1859      4.7228      5.0017|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9064 -  4.7034  1430   158  0.93  10.21   0.97     0.95       8522.54|
|  2:  4.7034 -  3.7528  1375   153  0.95   8.65   1.02     1.00       9981.85|
|  3:  3.7528 -  3.2842  1343   151  0.93  12.31   1.04     1.03      11493.36|
|  4:  3.2842 -  2.9866  1351   142  0.92  14.31   1.02     1.01      11091.22|
|  5:  2.9866 -  2.7740  1311   155  0.89  17.34   1.00     0.97       9730.06|
|  6:  2.7740 -  2.6114  1333   144  0.88  18.53   0.98     0.95       8594.51|
|  7:  2.6114 -  2.4812  1310   151  0.89  17.58   0.99     0.95       7472.10|
|  8:  2.4812 -  2.3736  1323   141  0.89  17.31   1.00     0.96       6708.77|
|  9:  2.3736 -  2.2826  1313   146  0.89  17.68   1.01     0.97       5854.59|
| 10:  2.2826 -  2.2041  1296   143  0.89  17.64   1.00     0.95       5209.62|
| 11:  2.2041 -  2.1354  1311   155  0.89  17.90   1.00     0.95       5007.41|
| 12:  2.1354 -  2.0745  1297   140  0.89  17.52   1.01     1.00       4589.70|
| 13:  2.0745 -  2.0200  1239   129  0.89  17.53   0.99     0.96       3771.63|
| 14:  2.0200 -  1.9708   398    51  0.91  14.98   0.98     0.93       2858.00|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2858.00 max =        11493.36 mean =      7485.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.88 mean =        15.64|
|phase err.(test): min =        0.00 max =           88.72 mean =        15.19|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.73    103.60  16.39    None  None   None       |
|    all(noH): 2823   0      2.73    103.60  16.39    None  None   None       |
|    Sol.    : 438    0      3.81    103.60  42.67    None  None   None       |
|    Mac.    : 2385   0      2.73    96.04   11.56    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:     2.728 -  12.815: 1779   |   5:    53.164 -  63.251:   79        |
|      1:    12.815 -  22.902:  510   |   6:    63.251 -  73.338:   53        |
|      2:    22.902 -  32.990:  154   |   7:    73.338 -  83.425:   23        |
|      3:    32.990 -  43.077:  114   |   8:    83.425 -  93.512:   11        |
|      4:    43.077 -  53.164:   97   |   9:    93.512 - 103.599:    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)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.419 - 4.258
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 300 from: 307
   mapped sites are within: 0.722 - 4.258

peak=   10.457 closest distance to " CB  VAL A 230 " =    1.409
peak=    6.812 closest distance to " CG  ARG A 138 " =    1.121
peak=    6.111 closest distance to " CD2 LEU A   5 " =    1.202
peak=    5.596 closest distance to " CG  PRO A  54 " =    1.403
peak=    5.584 closest distance to " CG1 VAL A 296 " =    1.210
peak=    5.530 closest distance to " CD1AILE A 234 " =    1.045
peak=    5.463 closest distance to " NH2 ARG A  56 " =    2.175
peak=    5.451 closest distance to " CG  LEU A   5 " =    1.198
peak=    5.413 closest distance to " NH1 ARG A 138 " =    0.971
peak=    5.204 closest distance to " O   HOH Z 248 " =    1.311
peak=    5.140 closest distance to " NE2 GLN A  11 " =    1.034
peak=    5.139 closest distance to " O   HOH Z 402 " =    1.495
peak=    5.059 closest distance to " O   HOH Z 403 " =    1.750
peak=    5.020 closest distance to " CB  ARG A 275 " =    0.985
peak=    5.015 closest distance to " CG  LEU A 228 " =    1.220
peak=    4.881 closest distance to " CB  VAL A 296 " =    1.086
peak=    4.838 closest distance to " O   HOH Z 232 " =    2.288
peak=    4.772 closest distance to " CB  GLN A 223 " =    1.541
peak=    4.700 closest distance to " CB  VAL A 230 " =    1.236
peak=    4.580 closest distance to " CD2 LEU A 228 " =    1.210
peak=    4.575 closest distance to " CG  PRO A 280 " =    0.883
peak=    4.536 closest distance to " O   HOH Z 126 " =    1.629
peak=    4.526 closest distance to " O   HOH Z  76 " =    1.113
peak=    4.456 closest distance to " CG  PRO A 243 " =    1.149
peak=    4.445 closest distance to " O   HOH Z 369 " =    2.193
peak=    4.403 closest distance to " O   HOH Z 193 " =    1.780
peak=    4.392 closest distance to " O   HOH Z 142 " =    1.650
peak=    4.373 closest distance to " O   HOH Z  91 " =    2.451
peak=    4.365 closest distance to " O   HOH Z 188 " =    1.349
peak=    4.363 closest distance to " CD2 TRP A 179 " =    1.350
peak=    4.358 closest distance to " CG2 VAL A 296 " =    1.030
peak=    4.356 closest distance to " O   HOH Z 128 " =    1.381
peak=    4.353 closest distance to " O   HOH Z 126 " =    1.900
peak=    4.343 closest distance to " O   HOH Z 346 " =    1.548
peak=    4.329 closest distance to " O   HOH Z 425 " =    1.476
peak=    4.307 closest distance to " O   HOH Z 265 " =    2.103
peak=    4.287 closest distance to " CA  TYR A  30 " =    0.957
peak=    4.283 closest distance to " CG  GLN A  58 " =    0.943
peak=    4.278 closest distance to " O   HOH Z  85 " =    1.300
peak=    4.268 closest distance to " CZ  PHE A 218 " =    1.136
peak=    4.265 closest distance to " CB  ASN A 148 " =    1.382
peak=    4.261 closest distance to " O   HOH Z 251 " =    1.671
peak=    4.242 closest distance to " CG  PRO A 198 " =    1.187
peak=    4.233 closest distance to " O   HOH Z   4 " =    1.496
peak=    4.221 closest distance to " O   HOH Z 427 " =    2.939
peak=    4.218 closest distance to " CB  SER A  26 " =    1.818
peak=    4.196 closest distance to " O   HOH Z 248 " =    1.677
peak=    4.190 closest distance to " CZ3 TRP A 266 " =    1.099
peak=    4.188 closest distance to " O   HOH Z 130 " =    2.488
peak=    4.183 closest distance to " O   HOH Z 359 " =    1.727
peak=    4.177 closest distance to " O   HOH Z 124 " =    1.253
peak=    4.156 closest distance to " CB  ARG A  79 " =    1.481
peak=    4.151 closest distance to " O   HOH Z 303 " =    2.139
peak=    4.146 closest distance to " O  BHOH Z  74 " =    1.163
peak=    4.146 closest distance to " CA  ALA A  51 " =    0.985
peak=    4.121 closest distance to " O   HOH Z 368 " =    2.410
peak=    4.113 closest distance to " O   HOH Z 406 " =    1.516
peak=    4.096 closest distance to " O   PRO A 198 " =    1.552
peak=    4.089 closest distance to " CD  ARG A 159 " =    0.722
peak=    4.079 closest distance to " NH2AARG A 145 " =    1.125
peak=    4.060 closest distance to " O   HOH Z 412 " =    3.983
peak=    4.055 closest distance to " O   HOH Z 236 " =    1.600
peak=    4.031 closest distance to " O   HOH Z 130 " =    1.032
peak=    4.029 closest distance to " CB  GLU A 277 " =    3.731
peak=    4.012 closest distance to " O   HOH Z  80 " =    1.943
peak=    4.005 closest distance to " CA  ARG A 195 " =    1.199
peak=    4.001 closest distance to " CB  GLN A 183 " =    1.272
peak=    3.994 closest distance to " CB  ASN A 110 " =    1.197
peak=    3.991 closest distance to " CB  ASN A 142 " =    1.191
peak=    3.989 closest distance to " O   HOH Z  59 " =    2.249
peak=    3.978 closest distance to " O   HOH Z 247 " =    1.333
peak=    3.970 closest distance to " O   HOH Z 365 " =    2.684
peak=    3.964 closest distance to " CD2 LEU A 297 " =    0.951
peak=    3.959 closest distance to " CD  LYS A  76 " =    1.850
peak=    3.949 closest distance to " CG2AVAL A 121 " =    2.286
peak=    3.947 closest distance to " O   HOH Z 313 " =    1.944
peak=    3.932 closest distance to " O   HOH Z 316 " =    3.037
peak=    3.930 closest distance to " O   HOH Z 209 " =    2.302
peak=    3.929 closest distance to " O   HOH Z 287 " =    1.710
peak=    3.922 closest distance to " CB  SER A  63 " =    1.153
peak=    3.921 closest distance to " O   HOH Z  78 " =    1.685
peak=    3.921 closest distance to " CB  ARG A 190 " =    1.678
peak=    3.907 closest distance to " CG AARG A 275 " =    1.164
peak=    3.897 closest distance to " O   HOH Z 404 " =    1.383
peak=    3.884 closest distance to " O   HOH Z  63 " =    1.939
peak=    3.876 closest distance to " CG2 ILE A 234 " =    1.160
peak=    3.875 closest distance to " CA  ARG A  36 " =    0.957
peak=    3.869 closest distance to " O   HOH Z 394 " =    1.466
peak=    3.861 closest distance to " O   HOH Z  49 " =    1.153
peak=    3.859 closest distance to " O   HOH Z 261 " =    2.329
peak=    3.858 closest distance to " CB  ASN A 187 " =    1.453
peak=    3.853 closest distance to " O   HOH Z 422 " =    2.639
peak=    3.853 closest distance to " O   HOH Z 238 " =    1.125
peak=    3.837 closest distance to " O   HOH Z 272 " =    1.890
peak=    3.836 closest distance to " O   HOH Z 162 " =    1.587
peak=    3.826 closest distance to " O   HOH Z 207 " =    1.203
peak=    3.816 closest distance to " CD  LYS A 166 " =    1.413
peak=    3.789 closest distance to " O   HOH Z 214 " =    1.195
peak=    3.785 closest distance to " O   HOH Z  43 " =    2.184
peak=    3.780 closest distance to " CE1 TYR A 186 " =    1.283
peak=    3.778 closest distance to " CG  PRO A 213 " =    1.221
peak=    3.771 closest distance to " O   HOH Z 214 " =    3.037
peak=    3.770 closest distance to " CB AVAL A  41 " =    1.307
peak=    3.769 closest distance to " O   HOH Z 371 " =    2.813
peak=    3.760 closest distance to " O   HOH Z 337 " =    1.841
peak=    3.752 closest distance to " CB  TRP A 179 " =    1.432
peak=    3.745 closest distance to " CB  PRO A  54 " =    0.939
peak=    3.739 closest distance to " CA  VAL A 125 " =    1.173
peak=    3.737 closest distance to " O   HOH Z 438 " =    2.740
peak=    3.731 closest distance to " O  BHOH Z 338 " =    2.345
peak=    3.704 closest distance to " CZ  PHE A  38 " =    1.119
peak=    3.704 closest distance to " CB  ASN A  39 " =    0.895
peak=    3.703 closest distance to " CG  MET A 185 " =    1.188
peak=    3.698 closest distance to " CE  LYS A 119 " =    1.094
peak=    3.689 closest distance to " CA  ALA A 160 " =    0.920
peak=    3.679 closest distance to " O   HOH Z 132 " =    2.733
peak=    3.677 closest distance to " O   HOH Z 280 " =    2.975
peak=    3.676 closest distance to " OG BSER A 164 " =    2.256
peak=    3.675 closest distance to " O   HOH Z 368 " =    3.381
peak=    3.665 closest distance to " O   HOH Z 172 " =    3.730
peak=    3.664 closest distance to " O   HOH Z 298 " =    1.838
peak=    3.662 closest distance to " O   HOH Z 234 " =    3.673
peak=    3.643 closest distance to " O   HOH Z 188 " =    2.555
peak=    3.639 closest distance to " N   ASP A 162 " =    1.251
peak=    3.638 closest distance to " NZ  LYS A 117 " =    3.131
peak=    3.634 closest distance to " CG  LEU A 167 " =    1.210
peak=    3.629 closest distance to " ND2 ASN A 249 " =    0.907
peak=    3.627 closest distance to " O   HOH Z 372 " =    0.937
peak=    3.627 closest distance to " O   HOH Z  40 " =    1.759
peak=    3.620 closest distance to " CE  LYS A  76 " =    0.966
peak=    3.607 closest distance to " CB  LYS A 117 " =    1.158
peak=    3.595 closest distance to " O   HOH Z 263 " =    1.697
peak=    3.594 closest distance to " CG2 VAL A 257 " =    0.796
peak=    3.588 closest distance to " CB  THR A 235 " =    1.333
peak=    3.585 closest distance to " O   HOH Z 112 " =    0.991
peak=    3.570 closest distance to " CB  VAL A 202 " =    1.559
peak=    3.565 closest distance to " CB  TYR A 169 " =    0.837
peak=    3.559 closest distance to " CB  GLN A  89 " =    1.247
peak=    3.559 closest distance to " CB  SER A 288 " =    1.539
peak=    3.555 closest distance to " CA  ASP A 162 " =    1.041
peak=    3.552 closest distance to " CB  GLU A 175 " =    1.271
peak=    3.549 closest distance to " O   HOH Z 107 " =    1.046
peak=    3.547 closest distance to " O   HOH Z 361 " =    2.568
peak=    3.546 closest distance to " CA  ILE A 234 " =    0.974
peak=    3.545 closest distance to " CB  GLU A 128 " =    1.064
peak=    3.543 closest distance to " CG AARG A 102 " =    1.235
peak=    3.542 closest distance to " CB  VAL A 265 " =    1.261
peak=    3.527 closest distance to " O   HOH Z 299 " =    4.258
peak=    3.515 closest distance to " O   HOH Z  19 " =    1.937
peak=    3.507 closest distance to " N   ASN A  39 " =    1.302
peak=    3.506 closest distance to " CG BARG A 102 " =    1.812
peak=    3.503 closest distance to " O   HOH Z 290 " =    1.073
peak=    3.497 closest distance to " CG1 ILE A  49 " =    1.658
peak=    3.493 closest distance to " CA  TYR A 116 " =    1.517
peak=    3.491 closest distance to " CB  PHE A 204 " =    0.938
peak=    3.486 closest distance to " O   HOH Z 199 " =    1.603
peak=    3.481 closest distance to " O   HOH Z 357 " =    2.088
peak=    3.478 closest distance to " O   HOH Z  68 " =    2.166
peak=    3.478 closest distance to " CA  ALA A  21 " =    1.097
peak=    3.474 closest distance to " CG  PHE A 204 " =    0.885
peak=    3.473 closest distance to " CD1 LEU A 101 " =    1.280
peak=    3.471 closest distance to " CE3 TRP A 274 " =    1.208
peak=    3.470 closest distance to " CB  ARG A 138 " =    1.026
peak=    3.467 closest distance to " CB  PRO A  90 " =    1.148
peak=    3.464 closest distance to " O   HOH Z  30 " =    1.214
peak=    3.460 closest distance to " O   HOH Z 329 " =    4.199
peak=    3.457 closest distance to " CB  THR A  31 " =    1.563
peak=    3.445 closest distance to " CA  ALA A 291 " =    0.862
peak=    3.429 closest distance to " O   ASP A 124 " =    1.227
peak=    3.429 closest distance to " O   HOH Z 353 " =    2.769
peak=    3.416 closest distance to " O   HOH Z  61 " =    1.811
peak=    3.413 closest distance to " CE3 TRP A 150 " =    1.142
peak=    3.409 closest distance to " CA  ALA A 295 " =    0.984
peak=    3.400 closest distance to " CB  TRP A 266 " =    1.138
peak=    3.397 closest distance to " CD1 ILE A  33 " =    1.704
peak=    3.394 closest distance to " CB  SER A   3 " =    1.374
peak=    3.393 closest distance to " CD  ARG A 138 " =    1.257
peak=    3.392 closest distance to " CB  PRO A 243 " =    1.221
peak=    3.388 closest distance to " CG2 VAL A 197 " =    1.061
peak=    3.386 closest distance to " O   HOH Z  85 " =    1.968
peak=    3.384 closest distance to " O   THR A 182 " =    1.481
peak=    3.383 closest distance to " CD  ARG A 269 " =    1.031
peak=    3.378 closest distance to " O   HOH Z 423 " =    1.793
peak=    3.375 closest distance to " CB  ALA A   9 " =    1.695
peak=    3.375 closest distance to " O   HOH Z 293 " =    2.012
peak=    3.369 closest distance to " CA  ASN A 217 " =    1.130
peak=    3.369 closest distance to " CD1BILE A 234 " =    0.976
peak=    3.360 closest distance to " O   HOH Z  97 " =    2.236
peak=    3.357 closest distance to " O   HOH Z 120 " =    2.694
peak=    3.347 closest distance to " CB  ASP A 124 " =    0.876
peak=    3.344 closest distance to " O   HOH Z 392 " =    2.698
peak=    3.341 closest distance to " CD2 TYR A 186 " =    1.143
peak=    3.340 closest distance to " O   HOH Z 421 " =    1.980
peak=    3.336 closest distance to " NE2 GLN A  77 " =    3.184
peak=    3.331 closest distance to " O   ALA A 165 " =    1.481
peak=    3.324 closest distance to " O   HOH Z 350 " =    1.569
peak=    3.322 closest distance to " CG2 ILE A  20 " =    1.459
peak=    3.321 closest distance to " O   HOH Z 156 " =    3.160
peak=    3.320 closest distance to " O   HOH Z  88 " =    3.687
peak=    3.310 closest distance to " O   HOH Z 193 " =    1.611
peak=    3.309 closest distance to " O   HOH Z 344 " =    2.890
peak=    3.308 closest distance to " O   HOH Z 389 " =    1.242
peak=    3.307 closest distance to " CB  ASN A 148 " =    1.948
peak=    3.301 closest distance to " CD  LYS A 119 " =    2.044
peak=    3.299 closest distance to " O   HOH Z 227 " =    1.506
peak=    3.296 closest distance to " O   HOH Z 145 " =    2.428
peak=    3.294 closest distance to " O   HOH Z 383 " =    1.974
peak=    3.290 closest distance to " O   HOH Z 154 " =    1.575
peak=    3.284 closest distance to " O   HOH Z 203 " =    1.678
peak=    3.280 closest distance to " CB  ASN A 215 " =    1.114
peak=    3.277 closest distance to " O   HOH Z 213 " =    1.812
peak=    3.277 closest distance to " CA  ARG A 139 " =    1.087
peak=    3.276 closest distance to " CB  ALA A 248 " =    1.367
peak=    3.275 closest distance to " O   HOH Z 189 " =    2.722
peak=    3.274 closest distance to " CB  SER A  62 " =    0.940
peak=    3.273 closest distance to " CD1 LEU A  96 " =    1.222
peak=    3.271 closest distance to " O   HOH Z 258 " =    1.044
peak=    3.271 closest distance to " O   HOH Z 200 " =    2.491
peak=    3.267 closest distance to " O   ASP A 200 " =    1.653
peak=    3.267 closest distance to " O   HOH Z 345 " =    3.326
peak=    3.267 closest distance to " NH2 ARG A 156 " =    1.120
peak=    3.265 closest distance to " CA  MET A 105 " =    1.079
peak=    3.260 closest distance to " O   HOH Z  35 " =    2.339
peak=    3.245 closest distance to " O   HOH Z 385 " =    3.889
peak=    3.238 closest distance to " CB  SER A 273 " =    0.883
peak=    3.237 closest distance to " CB  ALA A 295 " =    1.474
peak=    3.235 closest distance to " O   HOH Z 173 " =    2.083
peak=    3.230 closest distance to " OG BSER A 212 " =    2.680
peak=    3.229 closest distance to " CA  ALA A 154 " =    1.063
peak=    3.227 closest distance to " O   HOH Z 102 " =    1.271
peak=    3.226 closest distance to " O   HOH Z 258 " =    2.035
peak=    3.225 closest distance to " CB  GLU A 152 " =    1.159
peak=    3.225 closest distance to " CB  PRO A 198 " =    1.139
peak=    3.224 closest distance to " ND2 ASN A 187 " =    1.702
peak=    3.220 closest distance to " O   HOH Z  95 " =    0.964
peak=    3.220 closest distance to " O   HOH Z 141 " =    1.598
peak=    3.217 closest distance to " CD1 ILE A 199 " =    1.057
peak=    3.215 closest distance to " CA  LYS A 117 " =    1.277
peak=    3.212 closest distance to " O   HOH Z 410 " =    2.969
peak=    3.211 closest distance to " CA  GLY A 211 " =    1.396
peak=    3.210 closest distance to " CB  ALA A 114 " =    0.742
peak=    3.209 closest distance to " O   CYS A 168 " =    1.062
peak=    3.209 closest distance to " CD  PRO A  54 " =    0.833
peak=    3.204 closest distance to " CB  ASN A 173 " =    1.052
peak=    3.204 closest distance to " CB  THR A  52 " =    0.854
peak=    3.200 closest distance to " O   HOH Z 258 " =    1.496
peak=    3.200 closest distance to " CB  SER A  95 " =    0.939
peak=    3.195 closest distance to " CG2 THR A 221 " =    1.274
peak=    3.195 closest distance to " OE1 GLU A   2 " =    1.747
peak=    3.189 closest distance to " OD2 ASP A  50 " =    2.855
peak=    3.185 closest distance to " O   GLY A  91 " =    1.346
peak=    3.185 closest distance to " CA  GLN A  58 " =    0.909
peak=    3.180 closest distance to " NZ  LYS A  48 " =    1.076
peak=    3.175 closest distance to " CB  ASP A 191 " =    1.339
peak=    3.172 closest distance to " O   HOH Z 136 " =    0.916
peak=    3.170 closest distance to " O   HOH Z   3 " =    1.738
peak=    3.170 closest distance to " NH1AARG A 145 " =    1.256
peak=    3.169 closest distance to " CB  ASN A 285 " =    1.008
peak=    3.168 closest distance to " O   HOH Z 426 " =    1.349
peak=    3.166 closest distance to " CD2 LEU A  83 " =    1.401
peak=    3.162 closest distance to " O   HOH Z 368 " =    4.008
peak=    3.160 closest distance to " O   HOH Z 148 " =    3.437
peak=    3.157 closest distance to " O   HOH Z   9 " =    1.086
peak=    3.154 closest distance to " O   HOH Z  88 " =    2.976
peak=    3.149 closest distance to " O   HOH Z 298 " =    2.464
peak=    3.148 closest distance to " CB  ASP A 132 " =    1.053
peak=    3.147 closest distance to " CG  LYS A 119 " =    1.102
peak=    3.146 closest distance to " O   LEU A 228 " =    1.753
peak=    3.146 closest distance to " O   HOH Z 133 " =    2.815
peak=    3.145 closest distance to " O   HOH Z 151 " =    1.542
peak=    3.145 closest distance to " O   HOH Z 371 " =    1.215
peak=    3.140 closest distance to " CG2 ILE A 120 " =    1.382
peak=    3.140 closest distance to " O   HOH Z 222 " =    2.337
peak=    3.133 closest distance to " O   HOH Z 117 " =    2.016
peak=    3.132 closest distance to " O   HOH Z 301 " =    1.808
peak=    3.123 closest distance to " OE2 GLU A  53 " =    1.905
peak=    3.122 closest distance to " N   PHE A 130 " =    1.312
peak=    3.121 closest distance to " CA  LEU A 282 " =    1.279
peak=    3.112 closest distance to " CA  ARG A 102 " =    1.112
peak=    3.111 closest distance to " O   HOH Z  83 " =    1.445
peak=    3.110 closest distance to " NH2BARG A 190 " =    1.614
peak=    3.110 closest distance to " O   HOH Z 250 " =    1.247
peak=    3.107 closest distance to " O   HOH Z 156 " =    2.474
peak=    3.103 closest distance to " O   HOH Z 325 " =    2.043
peak=    3.100 closest distance to " O   GLU A   2 " =    1.547
peak=    3.099 closest distance to " O   HOH Z 420 " =    2.051
peak=    3.097 closest distance to " OG  SER A  62 " =    2.780
peak=    3.094 closest distance to " CA  LYS A 290 " =    1.212
peak=    3.092 closest distance to " O   HOH Z 180 " =    2.106
peak=    3.088 closest distance to " O   SER A 164 " =    1.236
peak=    3.086 closest distance to " N   TYR A 247 " =    1.415
peak=    3.082 closest distance to " O   HOH Z 408 " =    3.107
peak=    3.079 closest distance to " O   HOH Z 109 " =    1.258
peak=    3.079 closest distance to " CA  ASP A 149 " =    1.136
peak=    3.062 closest distance to " CB  SER A  99 " =    0.827
peak=    3.057 closest distance to " CG1 ILE A 151 " =    1.195
peak=    3.052 closest distance to " O   HOH Z 285 " =    2.054
peak=    3.042 closest distance to " O   HOH Z  80 " =    1.929
peak=    3.032 closest distance to " CD  ARG A  66 " =    2.217
peak=    3.031 closest distance to " O   HOH Z 124 " =    1.746

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.813 - 5.790
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 208
   mapped sites are within: 0.813 - 5.790

peak=   -4.715 closest distance to " CG  GLN A  58 " =    1.017
peak=   -4.538 closest distance to " CD  ARG A  14 " =    3.253
peak=   -4.437 closest distance to " OE1 GLN A 223 " =    2.470
peak=   -4.418 closest distance to " O   HOH Z 166 " =    1.622
peak=   -4.409 closest distance to " C   HIS A 108 " =    1.171
peak=   -4.357 closest distance to " CG1 VAL A 296 " =    1.030
peak=   -4.324 closest distance to " OG BSER A 134 " =    1.357
peak=   -4.314 closest distance to " O   HOH Z 193 " =    0.899
peak=   -4.313 closest distance to " CG2BVAL A  41 " =    2.724
peak=   -4.313 closest distance to " CZ2 TRP A  92 " =    2.880
peak=   -4.270 closest distance to " O   PRO A 198 " =    1.314
peak=   -4.259 closest distance to " O   HOH Z 107 " =    0.892
peak=   -4.200 closest distance to " CG1 VAL A 250 " =    2.688
peak=   -4.184 closest distance to " O   PRO A 163 " =    2.159
peak=   -4.165 closest distance to " CE3 TRP A 150 " =    2.234
peak=   -4.124 closest distance to " CD  ARG A 156 " =    2.109
peak=   -4.111 closest distance to " CD2 TYR A 293 " =    1.961
peak=   -4.064 closest distance to " NE2 GLN A  11 " =    1.646
peak=   -4.032 closest distance to " CD1 LEU A 101 " =    2.360
peak=   -4.007 closest distance to " O   HOH Z 131 " =    4.110
peak=   -3.997 closest distance to " CG2 VAL A 189 " =    2.003
peak=   -3.982 closest distance to " CG2 VAL A 230 " =    0.813
peak=   -3.956 closest distance to " CD  ARG A 138 " =    1.262
peak=   -3.947 closest distance to " NE2 GLN A  88 " =    1.208
peak=   -3.931 closest distance to " CB  PRO A 243 " =    2.800
peak=   -3.907 closest distance to " CE2 TYR A  30 " =    2.740
peak=   -3.893 closest distance to " OXT GLY A 302 " =    2.954
peak=   -3.861 closest distance to " O   HOH Z 128 " =    0.993
peak=   -3.854 closest distance to " CE  MET A 105 " =    2.450
peak=   -3.849 closest distance to " CA  ASP A 298 " =    1.044
peak=   -3.848 closest distance to " O   HOH Z 252 " =    3.709
peak=   -3.832 closest distance to " O   HOH Z 100 " =    0.921
peak=   -3.820 closest distance to " CG1 VAL A 112 " =    2.589
peak=   -3.819 closest distance to " CD1 ILE A 199 " =    2.386
peak=   -3.808 closest distance to " O   HOH Z 267 " =    5.699
peak=   -3.801 closest distance to " O   SER A 271 " =    1.891
peak=   -3.783 closest distance to " O   HOH Z 431 " =    2.003
peak=   -3.783 closest distance to " CG  ARG A 269 " =    2.203
peak=   -3.772 closest distance to " O   HOH Z 359 " =    2.816
peak=   -3.768 closest distance to " O   ASN A 252 " =    1.346
peak=   -3.768 closest distance to " O   HOH Z 211 " =    1.232
peak=   -3.764 closest distance to " O   HOH Z 394 " =    1.870
peak=   -3.751 closest distance to " O   HOH Z 216 " =    1.103
peak=   -3.744 closest distance to " O   HOH Z  13 " =    1.840
peak=   -3.728 closest distance to " CE2 TRP A  70 " =    2.238
peak=   -3.722 closest distance to " O   HOH Z 201 " =    2.175
peak=   -3.710 closest distance to " O   HOH Z 116 " =    1.441
peak=   -3.705 closest distance to " CB  VAL A 230 " =    1.095
peak=   -3.698 closest distance to " O   HOH Z 285 " =    1.914
peak=   -3.694 closest distance to " CG  TRP A 266 " =    1.815
peak=   -3.690 closest distance to " O   HOH Z 154 " =    1.557
peak=   -3.690 closest distance to " CB  ALA A  43 " =    2.538
peak=   -3.686 closest distance to " O   HOH Z 133 " =    1.174
peak=   -3.683 closest distance to " O   HOH Z 111 " =    1.597
peak=   -3.656 closest distance to " O   HOH Z 119 " =    2.217
peak=   -3.650 closest distance to " O   ILE A 106 " =    1.740
peak=   -3.611 closest distance to " OH  TYR A 172 " =    1.828
peak=   -3.610 closest distance to " O   HOH Z 371 " =    2.464
peak=   -3.609 closest distance to " O   HOH Z 231 " =    2.198
peak=   -3.608 closest distance to " O   HOH Z 275 " =    1.836
peak=   -3.607 closest distance to " CB  HIS A  86 " =    1.219
peak=   -3.605 closest distance to " CG  PRO A 243 " =    1.551
peak=   -3.602 closest distance to " O   HOH Z  69 " =    1.728
peak=   -3.578 closest distance to " O   HOH Z 214 " =    2.452
peak=   -3.578 closest distance to " N   THR A  52 " =    1.695
peak=   -3.574 closest distance to " CA  GLY A 241 " =    2.346
peak=   -3.570 closest distance to " O   HOH Z 166 " =    2.149
peak=   -3.562 closest distance to " O   HOH Z   6 " =    1.612
peak=   -3.560 closest distance to " CG2 VAL A 296 " =    1.277
peak=   -3.558 closest distance to " CB  PRO A 213 " =    2.253
peak=   -3.550 closest distance to " OG  SER A  97 " =    2.287
peak=   -3.550 closest distance to " CD2 PHE A 225 " =    1.104
peak=   -3.549 closest distance to " CG2 ILE A  20 " =    2.984
peak=   -3.543 closest distance to " CG2 THR A 178 " =    2.446
peak=   -3.542 closest distance to " CB  PRO A 280 " =    2.178
peak=   -3.535 closest distance to " CB  PHE A 192 " =    2.045
peak=   -3.534 closest distance to " O   HOH Z 191 " =    5.570
peak=   -3.529 closest distance to " O   ASN A  45 " =    1.926
peak=   -3.524 closest distance to " CD2 HIS A 207 " =    2.420
peak=   -3.520 closest distance to " O   HOH Z 165 " =    1.982
peak=   -3.517 closest distance to " O   HOH Z 372 " =    0.970
peak=   -3.513 closest distance to " O   HOH Z 307 " =    2.025
peak=   -3.513 closest distance to " ND2 ASN A  45 " =    1.171
peak=   -3.511 closest distance to " O   HOH Z 423 " =    2.393
peak=   -3.491 closest distance to " NE  ARG A  66 " =    4.291
peak=   -3.490 closest distance to " N   ALA A 226 " =    1.949
peak=   -3.488 closest distance to " O   PHE A 218 " =    1.457
peak=   -3.486 closest distance to " O   HOH Z  68 " =    1.315
peak=   -3.484 closest distance to " O   HOH Z 236 " =    1.783
peak=   -3.480 closest distance to " CG  ARG A 138 " =    0.927
peak=   -3.458 closest distance to " O   HOH Z 127 " =    1.099
peak=   -3.456 closest distance to " CB  ASN A  45 " =    2.025
peak=   -3.451 closest distance to " CE1 PHE A 192 " =    1.897
peak=   -3.444 closest distance to " O   HOH Z 137 " =    1.796
peak=   -3.430 closest distance to " CB  PRO A 163 " =    2.487
peak=   -3.422 closest distance to " O   MET A  40 " =    2.864
peak=   -3.418 closest distance to " OD2 ASP A 191 " =    1.426
peak=   -3.417 closest distance to " OD1 ASN A 249 " =    2.512
peak=   -3.406 closest distance to " CE BMET A  47 " =    1.292
peak=   -3.394 closest distance to " C   MET A 188 " =    1.437
peak=   -3.384 closest distance to " O   VAL A 174 " =    2.196
peak=   -3.382 closest distance to " OXT GLY A 302 " =    3.408
peak=   -3.378 closest distance to " O   ARG A  24 " =    2.104
peak=   -3.375 closest distance to " CB  TYR A  15 " =    2.145
peak=   -3.368 closest distance to " CG  LEU A   5 " =    1.021
peak=   -3.363 closest distance to " ND2 ASN A  69 " =    1.991
peak=   -3.356 closest distance to " CD  GLN A 223 " =    1.760
peak=   -3.353 closest distance to " OE1 GLN A  88 " =    0.960
peak=   -3.349 closest distance to " O   HOH Z 215 " =    2.050
peak=   -3.346 closest distance to " CD  PRO A 243 " =    1.881
peak=   -3.345 closest distance to " O   HOH Z 106 " =    1.710
peak=   -3.342 closest distance to " O   HOH Z   9 " =    1.661
peak=   -3.333 closest distance to " OG  SER A  87 " =    1.570
peak=   -3.331 closest distance to " O   HOH Z 411 " =    1.399
peak=   -3.323 closest distance to " O   HOH Z 102 " =    1.532
peak=   -3.322 closest distance to " O   HOH Z 128 " =    2.328
peak=   -3.319 closest distance to " N   SER A 276 " =    1.393
peak=   -3.317 closest distance to " CB  ALA A 248 " =    2.239
peak=   -3.317 closest distance to " O   HOH Z 421 " =    3.320
peak=   -3.317 closest distance to " CB  SER A 245 " =    2.240
peak=   -3.315 closest distance to " CB  ALA A 248 " =    2.140
peak=   -3.315 closest distance to " O   HOH Z 407 " =    2.700
peak=   -3.311 closest distance to " O   SER A 210 " =    1.654
peak=   -3.300 closest distance to " CG1 VAL A 112 " =    2.730
peak=   -3.295 closest distance to " O   HOH Z 110 " =    1.510
peak=   -3.295 closest distance to " CH2 TRP A 150 " =    1.095
peak=   -3.293 closest distance to " N   ALA A 248 " =    1.668
peak=   -3.287 closest distance to " OE2 GLU A 152 " =    1.451
peak=   -3.282 closest distance to " CA  GLY A 203 " =    2.494
peak=   -3.281 closest distance to " CB  ALA A  10 " =    2.258
peak=   -3.281 closest distance to " CB  GLN A  55 " =    1.157
peak=   -3.280 closest distance to " O   TRP A  70 " =    1.602
peak=   -3.275 closest distance to " CB  ASN A  39 " =    2.341
peak=   -3.274 closest distance to " CD1 LEU A 255 " =    2.744
peak=   -3.271 closest distance to " CB  ALA A 161 " =    2.535
peak=   -3.269 closest distance to " O   HOH Z  19 " =    2.250
peak=   -3.254 closest distance to " CA  GLN A  58 " =    1.097
peak=   -3.248 closest distance to " O   HOH Z 295 " =    1.614
peak=   -3.244 closest distance to " O   HOH Z 281 " =    2.871
peak=   -3.244 closest distance to " O   HOH Z 123 " =    2.619
peak=   -3.240 closest distance to " SG  CYS A 260 " =    1.734
peak=   -3.239 closest distance to " O   HOH Z 275 " =    1.493
peak=   -3.233 closest distance to " C   ASN A 285 " =    2.258
peak=   -3.226 closest distance to " N   THR A 157 " =    1.425
peak=   -3.223 closest distance to " CD  LYS A 289 " =    2.394
peak=   -3.214 closest distance to " CB  TRP A  85 " =    2.579
peak=   -3.209 closest distance to " O   HOH Z 251 " =    4.992
peak=   -3.207 closest distance to " C   ALA A 158 " =    1.213
peak=   -3.207 closest distance to " O   HOH Z  43 " =    1.946
peak=   -3.203 closest distance to " O   HOH Z  78 " =    1.899
peak=   -3.200 closest distance to " CZ3 TRP A 274 " =    2.130
peak=   -3.200 closest distance to " CE1 TYR A 247 " =    2.522
peak=   -3.198 closest distance to " O   HOH Z 109 " =    1.158
peak=   -3.198 closest distance to " CA  GLY A 133 " =    2.209
peak=   -3.198 closest distance to " O   TRP A  92 " =    1.896
peak=   -3.198 closest distance to " O   HOH Z 351 " =    1.561
peak=   -3.197 closest distance to " OG  SER A  87 " =    1.309
peak=   -3.196 closest distance to " N   MET A 188 " =    2.017
peak=   -3.190 closest distance to " O   HOH Z 260 " =    1.737
peak=   -3.189 closest distance to " NH2 ARG A  66 " =    5.790
peak=   -3.187 closest distance to " O   HOH Z  35 " =    2.472
peak=   -3.186 closest distance to " O   HOH Z 437 " =    1.443
peak=   -3.184 closest distance to " ND2BASN A 224 " =    1.915
peak=   -3.182 closest distance to " OG1 THR A  82 " =    1.456
peak=   -3.182 closest distance to " CZ  TYR A 169 " =    1.777
peak=   -3.180 closest distance to " O   HOH Z 162 " =    3.058
peak=   -3.178 closest distance to " O   HOH Z 136 " =    1.396
peak=   -3.177 closest distance to " O   HOH Z 136 " =    2.670
peak=   -3.177 closest distance to " O   HOH Z  52 " =    1.765
peak=   -3.173 closest distance to " CD1 PHE A  59 " =    2.015
peak=   -3.172 closest distance to " CB  SER A 210 " =    1.080
peak=   -3.170 closest distance to " CG1 VAL A  78 " =    2.446
peak=   -3.166 closest distance to " CB  ALA A   9 " =    2.345
peak=   -3.166 closest distance to " O   HOH Z 392 " =    1.788
peak=   -3.163 closest distance to " O   HOH Z 429 " =    1.629
peak=   -3.158 closest distance to " SG BCYS A 201 " =    2.423
peak=   -3.156 closest distance to " NH2 ARG A 159 " =    2.344
peak=   -3.150 closest distance to " O   HOH Z 113 " =    2.031
peak=   -3.150 closest distance to " O   HOH Z  64 " =    1.591
peak=   -3.147 closest distance to " O   HOH Z 177 " =    1.908
peak=   -3.146 closest distance to " NE2 GLN A 194 " =    2.022
peak=   -3.146 closest distance to " O   HOH Z 210 " =    1.022
peak=   -3.144 closest distance to " CB  PHE A 208 " =    2.313
peak=   -3.139 closest distance to " O   SER A 276 " =    1.734
peak=   -3.139 closest distance to " NH2 ARG A 219 " =    1.780
peak=   -3.136 closest distance to " O   ILE A 263 " =    2.252
peak=   -3.134 closest distance to " O   GLY A  80 " =    2.656
peak=   -3.134 closest distance to " O   TYR A 186 " =    1.640
peak=   -3.133 closest distance to " O   HOH Z   6 " =    1.963
peak=   -3.129 closest distance to " ND2 ASN A  39 " =    1.231
peak=   -3.126 closest distance to " CA  GLU A   2 " =    2.463
peak=   -3.126 closest distance to " CZ  PHE A  38 " =    2.132
peak=   -3.121 closest distance to " NH1 ARG A  66 " =    1.254
peak=   -3.119 closest distance to " O   LEU A 282 " =    2.127
peak=   -3.115 closest distance to " O   HOH Z 250 " =    1.675
peak=   -3.111 closest distance to " O   HOH Z 357 " =    2.156
peak=   -3.105 closest distance to " CE3 TRP A  70 " =    1.635
peak=   -3.103 closest distance to " CG  ASP A 132 " =    2.234
peak=   -3.100 closest distance to " O   HOH Z 150 " =    1.927
peak=   -3.096 closest distance to " O   HOH Z 111 " =    4.407
peak=   -3.094 closest distance to " CD2 TYR A 247 " =    2.383
peak=   -3.071 closest distance to " O   HOH Z 290 " =    1.281
peak=   -3.069 closest distance to " O   ARG A 195 " =    1.762
peak=   -3.066 closest distance to " O   ASN A 187 " =    1.650
peak=   -3.051 closest distance to " O   HOH Z 145 " =    2.661
peak=   -3.039 closest distance to " CD2 TYR A 172 " =    2.171
peak=   -3.026 closest distance to " OD1 ASN A 173 " =    1.460

================= 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    :  0.4735 0.4574   6.274575e+00   6.257373e+00
   1_bss:  0.4629 0.4485   6.266464e+00   6.249263e+00
   1_xyz:  0.3722 0.3947   6.128828e+00   6.166430e+00
   1_adp:  0.3251 0.3715   6.029187e+00   6.117995e+00
   1_occ:  0.3247 0.3723   6.028471e+00   6.119083e+00
   2_bss:  0.3203 0.3675   6.028631e+00   6.118740e+00
   2_xyz:  0.2367 0.2849   5.774496e+00   5.922880e+00
   2_adp:  0.2170 0.2686   5.706194e+00   5.873315e+00
   2_occ:  0.2168 0.2684   5.705560e+00   5.873290e+00
   3_bss:  0.2148 0.2681   5.705926e+00   5.873613e+00
   3_xyz:  0.1611 0.2091   5.450500e+00   5.648987e+00
   3_adp:  0.1504 0.1985   5.391412e+00   5.598092e+00
   3_occ:  0.1503 0.1984   5.390859e+00   5.597841e+00
   4_bss:  0.1504 0.1975   5.390206e+00   5.595217e+00
   4_xyz:  0.1330 0.1760   5.286466e+00   5.495861e+00
   4_adp:  0.1293 0.1732   5.267276e+00   5.481193e+00
   4_occ:  0.1292 0.1732   5.267075e+00   5.481228e+00
   5_bss:  0.1292 0.1732   5.267168e+00   5.481480e+00
   5_xyz:  0.1211 0.1679   5.222109e+00   5.454697e+00
   5_adp:  0.1196 0.1685   5.218217e+00   5.456433e+00
   5_occ:  0.1195 0.1685   5.218156e+00   5.456497e+00
   5_bss:  0.1194 0.1682   5.218336e+00   5.456698e+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:  0.332  11.779   7.485   8.020  11.534   0.000   0.000   0.000
   1_xyz:  0.332  11.779   7.485   8.020  11.534   0.000   0.000   0.000
   1_adp:  0.332  11.779   7.485   8.020  11.534   0.000   0.000   0.000
   1_occ:  0.332  11.779   7.485   8.020  11.534   0.000   0.000   0.000
   2_bss:  0.319  39.790   3.436   3.944   7.335   0.000   0.000   0.000
   2_xyz:  0.319  39.790   3.436   3.944   7.335   0.000   0.000   0.000
   2_adp:  0.319  39.790   3.436   3.944   7.335   0.000   0.000   0.000
   2_occ:  0.319  39.790   3.436   3.944   7.335   0.000   0.000   0.000
   3_bss:  0.314  51.442   1.694   2.725   4.786   0.000   0.000   0.000
   3_xyz:  0.314  51.442   1.694   2.725   4.786   0.000   0.000   0.000
   3_adp:  0.314  51.442   1.694   2.725   4.786   0.000   0.000   0.000
   3_occ:  0.314  51.442   1.694   2.725   4.786   0.000   0.000   0.000
   4_bss:  0.328  56.649   1.117   2.142   3.876   0.000   0.000   0.000
   4_xyz:  0.328  56.649   1.117   2.142   3.876   0.000   0.000   0.000
   4_adp:  0.328  56.649   1.117   2.142   3.876   0.000   0.000   0.000
   4_occ:  0.328  56.649   1.117   2.142   3.876   0.000   0.000   0.000
   5_bss:  0.327  55.477   1.276   2.230   3.810   0.000   0.000   0.000
   5_xyz:  0.327  55.477   1.276   2.230   3.810   0.000   0.000   0.000
   5_adp:  0.327  55.477   1.276   2.230   3.810   0.000   0.000   0.000
   5_occ:  0.327  55.477   1.276   2.230   3.810   0.000   0.000   0.000
   5_bss:  0.327  61.234  -1.108  -0.205   1.313   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.180 0.4818  0.5576    64224.312
   1_bss:  52.812 0.4852  0.7371    62398.989
   1_xyz:  43.860 0.5954  0.8732    43927.012
   1_adp:  39.526 0.6485  0.9818    37812.573
   1_occ:  39.592 0.6477  0.9793    37901.122
   2_bss:  39.301 0.6512  0.8539    37679.590
   2_xyz:  29.012 0.7686  0.9755    21332.727
   2_adp:  26.753 0.7935  0.9991    18874.268
   2_occ:  26.728 0.7938  0.9992    18861.748
   3_bss:  26.646 0.7948  0.9362    18848.055
   3_xyz:  20.130 0.8606  0.9813    11231.460
   3_adp:  18.768 0.8738  0.9845    10158.792
   3_occ:  18.764 0.8739  0.9847    10144.450
   4_bss:  18.669 0.8746  0.9616    10046.287
   4_xyz:  16.479 0.8942  0.9700     8127.739
   4_adp:  16.116 0.8976  0.9643     7893.560
   4_occ:  16.117 0.8976  0.9642     7895.916
   5_bss:  16.119 0.8976  0.9664     7899.435
   5_xyz:  15.583 0.9021  0.9696     7468.045
   5_adp:  15.590 0.9022  0.9621     7479.947
   5_occ:  15.589 0.9022  0.9620     7479.576
   5_bss:  15.593 0.9021  0.9719     7485.356
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3864e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3864e+01
   1_xyz:   1.695  0.013  0.107 18.061  0.007  4.110   1.4055e-01
   1_adp:   1.695  0.013  0.107 18.061  0.007  4.110   1.4055e-01
   1_occ:   1.695  0.013  0.107 18.061  0.007  4.110   1.4055e-01
   2_bss:   1.695  0.013  0.107 18.061  0.007  4.110   1.4055e-01
   2_xyz:   1.132  0.008  0.076 15.953  0.004  4.125   7.3870e-02
   2_adp:   1.132  0.008  0.076 15.953  0.004  4.125   7.3870e-02
   2_occ:   1.132  0.008  0.076 15.953  0.004  4.125   7.3870e-02
   3_bss:   1.132  0.008  0.076 15.953  0.004  4.125   7.3870e-02
   3_xyz:   1.021  0.007  0.078 15.500  0.004  4.127   6.1805e-02
   3_adp:   1.021  0.007  0.078 15.500  0.004  4.127   6.1805e-02
   3_occ:   1.021  0.007  0.078 15.500  0.004  4.127   6.1805e-02
   4_bss:   1.021  0.007  0.078 15.500  0.004  4.127   6.1805e-02
   4_xyz:   0.949  0.006  0.073 15.394  0.003  4.134   5.5814e-02
   4_adp:   0.949  0.006  0.073 15.394  0.003  4.134   5.5814e-02
   4_occ:   0.949  0.006  0.073 15.394  0.003  4.134   5.5814e-02
   5_bss:   0.949  0.006  0.073 15.394  0.003  4.134   5.5814e-02
   5_xyz:   1.134  0.009  0.087 15.563  0.004  4.112   7.3540e-02
   5_adp:   1.134  0.009  0.087 15.563  0.004  4.112   7.3540e-02
   5_occ:   1.134  0.009  0.087 15.563  0.004  4.112   7.3540e-02
   5_bss:   1.134  0.009  0.087 15.563  0.004  4.112   7.3540e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9810e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9810e+00
   1_xyz:  14.459  0.166  0.457 85.759  0.055  2.186   1.0447e-01
   1_adp:  14.459  0.166  0.457 85.759  0.055  2.186   1.0447e-01
   1_occ:  14.459  0.166  0.457 85.759  0.055  2.186   1.0447e-01
   2_bss:  14.459  0.166  0.457 85.759  0.055  2.186   1.0447e-01
   2_xyz:   7.306  0.083  0.258 80.983  0.042  2.296   5.3729e-02
   2_adp:   7.306  0.083  0.258 80.983  0.042  2.296   5.3729e-02
   2_occ:   7.306  0.083  0.258 80.983  0.042  2.296   5.3729e-02
   3_bss:   7.306  0.083  0.258 80.983  0.042  2.296   5.3729e-02
   3_xyz:   6.312  0.066  0.286 82.607  0.042  2.290   4.6926e-02
   3_adp:   6.312  0.066  0.286 82.607  0.042  2.290   4.6926e-02
   3_occ:   6.312  0.066  0.286 82.607  0.042  2.290   4.6926e-02
   4_bss:   6.312  0.066  0.286 82.607  0.042  2.290   4.6926e-02
   4_xyz:   6.840  0.038  0.280 82.439  0.028  2.373   3.3556e-02
   4_adp:   6.840  0.038  0.280 82.439  0.028  2.373   3.3556e-02
   4_occ:   6.840  0.038  0.280 82.439  0.028  2.373   3.3556e-02
   5_bss:   6.840  0.038  0.280 82.439  0.028  2.373   3.3556e-02
   5_xyz:   8.516  0.051  0.414 82.704  0.033  2.332   4.7804e-02
   5_adp:   8.516  0.051  0.414 82.704  0.033  2.332   4.7804e-02
   5_occ:   8.516  0.051  0.414 82.704  0.033  2.332   4.7804e-02
   5_bss:   8.516  0.051  0.414 82.704  0.033  2.332   4.7804e-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:  70.98   0.00  12.65  61.64   0.00  10.10  70.98   0.00  26.52
   1_occ:  70.98   0.00  12.65  61.64   0.00  10.10  70.98   0.00  26.52
   2_bss:  70.98   0.00  12.65  61.64   0.00  10.10  70.98   0.00  26.52
   2_xyz:  70.98   0.00  12.65  61.64   0.00  10.10  70.98   0.00  26.52
   2_adp:  69.25   0.00  12.82  68.09   0.00   9.16  69.25   0.92  32.77
   2_occ:  69.25   0.00  12.82  68.09   0.00   9.16  69.25   0.92  32.77
   3_bss:  69.25   0.00  12.82  68.09   0.00   9.16  69.25   0.92  32.77
   3_xyz:  69.25   0.00  12.82  68.09   0.00   9.16  69.25   0.92  32.77
   3_adp:  72.47   0.00  12.96  72.47   0.00   8.82  70.13   1.68  35.50
   3_occ:  72.47   0.00  12.96  72.47   0.00   8.82  70.13   1.68  35.50
   4_bss:  72.47   0.00  12.96  72.47   0.00   8.82  70.13   1.68  35.50
   4_xyz:  72.47   0.00  12.96  72.47   0.00   8.82  70.13   1.68  35.50
   4_adp:  74.74   0.00  13.02  74.74   0.00   8.72  74.71   1.23  36.45
   4_occ:  74.74   0.00  13.02  74.74   0.00   8.72  74.71   1.23  36.45
   5_bss:  74.74   0.00  13.02  74.74   0.00   8.72  74.71   1.23  36.45
   5_xyz:  74.74   0.00  13.02  74.74   0.00   8.72  74.71   1.23  36.45
   5_adp: 100.87   0.00  13.66  93.31   0.00   8.83 100.87   1.08  39.94
   5_occ: 100.87   0.00  13.66  93.31   0.00   8.83 100.87   1.08  39.94
   5_bss: 103.60   2.73  16.39  96.04   2.73  11.56 103.60   3.81  42.67
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.291    0.018    0.413
   1_adp:    1.291    0.018    0.413
   1_occ:    1.291    0.018    0.413
   2_bss:    1.291    0.018    0.413
   2_xyz:    1.880    0.025    0.548
   2_adp:    1.880    0.025    0.548
   2_occ:    1.880    0.025    0.548
   3_bss:    1.880    0.025    0.548
   3_xyz:    1.771    0.031    0.615
   3_adp:    1.771    0.031    0.615
   3_occ:    1.771    0.031    0.615
   4_bss:    1.771    0.031    0.615
   4_xyz:    1.910    0.059    0.654
   4_adp:    1.910    0.059    0.654
   4_occ:    1.910    0.059    0.654
   5_bss:    1.910    0.059    0.654
   5_xyz:    1.881    0.060    0.661
   5_adp:    1.881    0.060    0.661
   5_occ:    1.881    0.060    0.661
   5_bss:    1.881    0.060    0.661
------------------------------------------------------------------------

CPU time actual refinement: 334.43


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_317/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_317/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_317/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_317/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_317/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.29 
  Macro-tasks:
    bulk solvent and scale       = 46.16  
    individual site refinement   = 127.39 
    weights calculation          = 32.27  
    collect and process          = 6.73   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 212.65 
  Micro-tasks:
    mask                            = 1.67   
    f_calc                          = 103.06 
    alpha_beta                      = 8.58   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 107.17 
    fmodel                         = 7.32   
    r_factors                      = 0.20   
    phase_errors                   = 11.54  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 240.97 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.751 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    656 calls, 102.47 s
gradients_fft:          600 calls,  96.21 s

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

# Date 2008-01-16 Time 01:16:04 PST -0800 (1200474964.40 s)
Start R-work = 0.4735, R-free = 0.4574 (no bulk solvent and anisotropic scale)
Final R-work = 0.1368, R-free = 0.1835 (no bulk solvent and anisotropic scale)

Start R-work = 0.4629, R-free = 0.4485
Final R-work = 0.1194, R-free = 0.1682