# Date 2008-01-16 Time 01:51:00 PST -0800 (1200477060.18 s)
#phil __OFF__

Command line arguments: "../587.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10326
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 587

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.8686, 85.9581, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9586 1.99051
Completeness in resolution range: 0.962746
Completeness with d_max=infinity: 0.959728

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9586
                             d_min =   1.9905

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9586 1.99051
Completeness in resolution range: 0.962746
Completeness with d_max=infinity: 0.959728

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9590 -  4.2585 [2137/2165]  1923   214  10.0%
  bin  2:  4.2585 -  3.3931 [2041/2064]  1837   204  10.0%
  bin  3:  3.3931 -  2.9680 [2030/2052]  1826   204  10.0%
  bin  4:  2.9680 -  2.6984 [2000/2019]  1804   196   9.8%
  bin  5:  2.6984 -  2.5059 [1999/2028]  1793   206  10.3%
  bin  6:  2.5059 -  2.3588 [1969/2010]  1777   192   9.8%
  bin  7:  2.3588 -  2.2410 [1974/2009]  1779   195   9.9%
  bin  8:  2.2410 -  2.1438 [1975/2014]  1772   203  10.3%
  bin  9:  2.1438 -  2.0615 [1948/1979]  1757   191   9.8%
  bin 10:  2.0615 -  1.9905 [1516/2007]  1362   154  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_587/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 26
        2.42 -     3.04: 2180
        3.04 -     3.66: 4661
        3.66 -     4.28: 8959
        4.28 -     4.90: 12362
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.937 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.973 3.040 -x+1/2,-y+1,z-1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.998 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.118 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28183 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_587/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_587/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.8686 85.95805 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: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4773   r_free= 0.4612   ksol= 0.00   Bsol= 0.00   scale= 0.792    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.279589                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.7494 0.99   1385  155 0.3900 0.3888      6.5809      6.5871|
|  2:  4.7494 -  3.7899 0.99   1338  146 0.4000 0.4211      6.7845      6.8391|
|  3:  3.7899 -  3.3168 0.99   1309  152 0.4346 0.3970      6.6845      6.6348|
|  4:  3.3168 -  3.0163 0.99   1301  133 0.4627 0.4030      6.5267      6.4345|
|  5:  3.0163 -  2.8016 0.98   1277  145 0.5125 0.4979      6.3921      6.4137|
|  6:  2.8016 -  2.6374 0.98   1295  144 0.5032 0.5099      6.2818      6.2176|
|  7:  2.6374 -  2.5059 0.99   1278  149 0.4921 0.4491      6.2481      6.1552|
|  8:  2.5059 -  2.3973 0.99   1278  136 0.5207 0.4822      6.1836       6.157|
|  9:  2.3973 -  2.3053 0.98   1287  146 0.5297 0.5286      6.1236      6.1477|
| 10:  2.3053 -  2.2261 0.97   1242  139 0.5340 0.5478      6.1188      6.1337|
| 11:  2.2261 -  2.1567 0.98   1259  143 0.5190 0.4784      6.0338      6.0637|
| 12:  2.1567 -  2.0952 0.99   1278  134 0.5300 0.5096      5.9871      6.0129|
| 13:  2.0952 -  2.0402 0.97   1248  134 0.5167 0.5238      5.8855      5.8817|
| 14:  2.0402 -  1.9905 0.67    855  103 0.5550 0.5143      5.8675       5.741|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9590 -  4.7494  1385   155  0.67  36.66   0.80     0.70      79182.26|
|  2:  4.7494 -  3.7899  1338   146  0.70  35.50   0.88     0.75     104130.24|
|  3:  3.7899 -  3.3168  1309   152  0.62  42.19   0.83     0.71     107326.58|
|  4:  3.3168 -  3.0163  1301   133  0.55  48.07   0.80     0.63      90213.86|
|  5:  3.0163 -  2.8016  1277   145  0.46  54.97   0.74     0.54      76945.76|
|  6:  2.8016 -  2.6374  1295   144  0.45  56.20   0.73     0.50      64973.95|
|  7:  2.6374 -  2.5059  1278   149  0.44  56.82   0.75     0.49      59635.53|
|  8:  2.5059 -  2.3973  1278   136  0.42  58.54   0.73     0.48      54511.65|
|  9:  2.3973 -  2.3053  1287   146  0.36  62.83   0.71     0.44      53287.33|
| 10:  2.3053 -  2.2261  1242   139  0.36  63.33   0.73     0.41      50340.48|
| 11:  2.2261 -  2.1567  1259   143  0.32  65.91   0.76     0.39      47393.43|
| 12:  2.1567 -  2.0952  1278   134  0.32  66.39   0.76     0.39      44170.09|
| 13:  2.0952 -  2.0402  1248   134  0.31  66.95   0.74     0.38      37759.34|
| 14:  2.0402 -  1.9905   855   103  0.32  65.96   0.71     0.36      29516.32|
|alpha:            min =        0.36 max =            0.75 mean =         0.52|
|beta:             min =    29516.32 max =       107326.58 mean =     65497.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.95 mean =        55.23|
|phase err.(test): min =        0.00 max =           89.97 mean =        55.20|
|-----------------------------------------------------------------------------|

============================== 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 = 12.681681             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.465   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.147843              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.079   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1511 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2605 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3906 |
| 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:     6548 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7654 |
|-----------------------------------------------------------------------------|
|-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 |       53.986 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.845 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.982)------------------------------------------|
|    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 = 11.982)------------------------------------------|
|    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: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4833   r_free= 0.4708   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.281274                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4696   r_free= 0.4566   ksol= 0.33   Bsol= 20.00   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.37,11.95,7.25,0.00,0.00,0.00); trace/3= 8.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.272114                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.452011             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.952   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.119580              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.238   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4696      final r-factor (work) = 0.3860          |
| start r-factor (free) = 0.4566      final r-factor (free) = 0.4008          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.0963 = 12.45 * 0.50 * 6.2818 + 1.00 * 53.9856                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.6571 = 12.45 * 0.50 * 6.1864 + 1.00 * 0.1405                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3860      final r-factor (work) = 0.3378          |
| start r-factor (free) = 0.4008      final r-factor (free) = 0.3784          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9409 = 1.12 * 1.00 * 6.1864 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8442 = 1.12 * 1.00 * 6.0978 + 1.00 * 0.0172                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.982)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.16   13.05    None  None   None       |
|    all(noH): 2823   0      0.00    82.16   13.05    None  None   None       |
|    Sol.    : 438    0      0.00    82.16   25.53    None  None   None       |
|    Mac.    : 2385   0      0.00    64.21   10.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.217: 1245   |   5:    41.082 -  49.299:   59        |
|      1:     8.217 -  16.433:  754   |   6:    49.299 -  57.515:   18        |
|      2:    16.433 -  24.649:  386   |   7:    57.515 -  65.732:    7        |
|      3:    24.649 -  32.866:  248   |   8:    65.732 -  73.948:    5        |
|      4:    32.866 -  41.082:  100   |   9:    73.948 -  82.165:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3378 r_free = 0.3784             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3372 r_free = 0.3777             target_work(ml) = 6.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3372   r_free= 0.3777   ksol= 0.33   Bsol= 20.00   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.37,11.95,7.25,0.00,0.00,0.00); trace/3= 8.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.073008                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3351   r_free= 0.3732   ksol= 0.31   Bsol= 35.44   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,7.67,4.30,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.074394                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.117100              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.630   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.449035              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.500  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3351      final r-factor (work) = 0.2707          |
| start r-factor (free) = 0.3732      final r-factor (free) = 0.3226          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7303 = 5.12 * 0.50 * 6.0935 + 1.00 * 0.1398                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3467 = 5.12 * 0.50 * 5.9636 + 1.00 * 0.0885                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2707      final r-factor (work) = 0.2562          |
| start r-factor (free) = 0.3226      final r-factor (free) = 0.3118          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6953 = 0.45 * 1.00 * 5.9636 + 1.00 * 0.0174                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6519 = 0.45 * 1.00 * 5.8785 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.982)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.27   12.90    None  None   None       |
|    all(noH): 2823   0      0.00    82.27   12.90    None  None   None       |
|    Sol.    : 438    0      0.00    82.27   28.90    None  None   None       |
|    Mac.    : 2385   0      0.00    73.42   9.97     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.228: 1316   |   5:    41.137 -  49.365:   71        |
|      1:     8.228 -  16.455:  769   |   6:    49.365 -  57.592:   32        |
|      2:    16.455 -  24.683:  336   |   7:    57.592 -  65.820:   10        |
|      3:    24.683 -  32.910:  169   |   8:    65.820 -  74.047:    9        |
|      4:    32.910 -  41.137:  110   |   9:    74.047 -  82.275:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2562 r_free = 0.3118             target_work(ml) = 5.868         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2560 r_free = 0.3118             target_work(ml) = 5.868         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2560   r_free= 0.3118   ksol= 0.31   Bsol= 35.44   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,7.67,4.30,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.867700                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2550   r_free= 0.3115   ksol= 0.30   Bsol= 45.38   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.84,5.06,3.11,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.867908                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.816504              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.055   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.303142              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.473  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2550      final r-factor (work) = 0.1967          |
| start r-factor (free) = 0.3115      final r-factor (free) = 0.2416          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3081 = 3.82 * 0.50 * 5.8795 + 1.00 * 0.0885                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0623 = 3.82 * 0.50 * 5.7585 + 1.00 * 0.0736                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1967      final r-factor (work) = 0.1812          |
| start r-factor (free) = 0.2416      final r-factor (free) = 0.2232          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7701 = 0.30 * 1.00 * 5.7585 + 1.00 * 0.0244                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7318 = 0.30 * 1.00 * 5.5793 + 1.00 * 0.0405                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.982)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.10   13.05    None  None   None       |
|    all(noH): 2823   0      0.00    77.10   13.05    None  None   None       |
|    Sol.    : 438    0      1.64    75.15   33.57    None  None   None       |
|    Mac.    : 2385   0      0.00    77.10   9.29     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 -   7.710: 1350   |   5:    38.551 -  46.261:   89        |
|      1:     7.710 -  15.420:  763   |   6:    46.261 -  53.971:   74        |
|      2:    15.420 -  23.130:  251   |   7:    53.971 -  61.681:   24        |
|      3:    23.130 -  30.841:  135   |   8:    61.681 -  69.391:   16        |
|      4:    30.841 -  38.551:  113   |   9:    69.391 -  77.101:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1812 r_free = 0.2232             target_work(ml) = 5.551         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1811 r_free = 0.2232             target_work(ml) = 5.550         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1811   r_free= 0.2232   ksol= 0.30   Bsol= 45.38   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.84,5.06,3.11,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.550408                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1808   r_free= 0.2226   ksol= 0.31   Bsol= 45.38   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.41,3.45,2.68,0.00,0.00,0.00); trace/3= 2.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.550134                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.134964              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.321   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.640864              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.128   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1808      final r-factor (work) = 0.1382          |
| start r-factor (free) = 0.2226      final r-factor (free) = 0.1786          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6123 = 4.13 * 0.50 * 5.5810 + 1.00 * 0.0736                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2946 = 4.13 * 0.50 * 5.4274 + 1.00 * 0.0735                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1382      final r-factor (work) = 0.1282          |
| start r-factor (free) = 0.1786      final r-factor (free) = 0.1715          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5178 = 0.64 * 1.00 * 5.4274 + 1.00 * 0.0396                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3889 = 0.64 * 1.00 * 5.2686 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.982)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.58   13.57    None  None   None       |
|    all(noH): 2823   0      0.00    86.58   13.57    None  None   None       |
|    Sol.    : 438    0      1.75    79.64   37.80    None  None   None       |
|    Mac.    : 2385   0      0.00    86.58   9.12     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.658: 1537   |   5:    43.289 -  51.947:   95        |
|      1:     8.658 -  17.316:  690   |   6:    51.947 -  60.605:   66        |
|      2:    17.316 -  25.973:  172   |   7:    60.605 -  69.262:   35        |
|      3:    25.973 -  34.631:  105   |   8:    69.262 -  77.920:   15        |
|      4:    34.631 -  43.289:  101   |   9:    77.920 -  86.578:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1282 r_free = 0.1715             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1282 r_free = 0.1714             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1714   ksol= 0.31   Bsol= 45.38   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.41,3.45,2.68,0.00,0.00,0.00); trace/3= 2.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.250718                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1285   r_free= 0.1716   ksol= 0.32   Bsol= 53.25   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.28,2.73,2.65,0.00,0.00,0.00); trace/3= 2.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.251543                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.857436              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.245  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.769884              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.621  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1285      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1716      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6024 = 2.86 * 0.50 * 5.2697 + 1.00 * 0.0735                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5254 = 2.86 * 0.50 * 5.2178 + 1.00 * 0.0707                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1182      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0295 = 0.77 * 1.00 * 5.2178 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0063 = 0.77 * 1.00 * 5.1870 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.982)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.32   13.37    None  None   None       |
|    all(noH): 2823   0      0.00    89.32   13.37    None  None   None       |
|    Sol.    : 438    0      1.68    81.97   37.74    None  None   None       |
|    Mac.    : 2385   0      0.00    89.32   8.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.932: 1632   |   5:    44.662 -  53.594:   93        |
|      1:     8.932 -  17.865:  618   |   6:    53.594 -  62.527:   57        |
|      2:    17.865 -  26.797:  161   |   7:    62.527 -  71.459:   26        |
|      3:    26.797 -  35.730:  113   |   8:    71.459 -  80.391:   16        |
|      4:    35.730 -  44.662:  101   |   9:    80.391 -  89.324:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1164 r_free = 0.1636             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1637             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1637   ksol= 0.32   Bsol= 53.25   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.28,2.73,2.65,0.00,0.00,0.00); trace/3= 2.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.182887                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.7494 0.99   1385  155 0.0989 0.1319      5.3929      5.5479|
|  2:  4.7494 -  3.7899 0.99   1338  146 0.0864 0.1093      5.4517      5.6547|
|  3:  3.7899 -  3.3168 0.99   1309  152 0.1080 0.1553      5.4994      5.8784|
|  4:  3.3168 -  3.0163 0.99   1301  133 0.1284 0.1623      5.4873      5.6604|
|  5:  3.0163 -  2.8016 0.98   1277  145 0.1357 0.1691      5.3665      5.5164|
|  6:  2.8016 -  2.6374 0.98   1295  144 0.1346 0.2041      5.2861      5.5364|
|  7:  2.6374 -  2.5059 0.99   1278  149 0.1267 0.1754      5.1915      5.4244|
|  8:  2.5059 -  2.3973 0.99   1278  136 0.1239 0.1850      5.1384      5.3888|
|  9:  2.3973 -  2.3053 0.98   1287  146 0.1241 0.1931      5.0747      5.3784|
| 10:  2.3053 -  2.2261 0.97   1242  139 0.1222 0.1866      5.0335      5.2537|
| 11:  2.2261 -  2.1567 0.98   1259  143 0.1215 0.1710      4.9762      5.2689|
| 12:  2.1567 -  2.0952 0.99   1278  134 0.1152 0.1851      4.9011      5.2036|
| 13:  2.0952 -  2.0402 0.97   1248  134 0.1188 0.1740      4.8316      5.0713|
| 14:  2.0402 -  1.9905 0.67    855  103 0.1100 0.1797      4.7156      4.9574|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9590 -  4.7494  1385   155  0.94   9.45   0.97     0.95       7746.62|
|  2:  4.7494 -  3.7899  1338   146  0.95   8.56   1.01     0.99       9580.68|
|  3:  3.7899 -  3.3168  1309   152  0.93  11.58   1.02     1.01      11035.38|
|  4:  3.3168 -  3.0163  1301   133  0.91  14.32   1.01     0.98      10744.05|
|  5:  3.0163 -  2.8016  1277   145  0.90  16.43   1.00     0.97       8924.69|
|  6:  2.8016 -  2.6374  1295   144  0.89  17.11   0.98     0.95       7991.97|
|  7:  2.6374 -  2.5059  1278   149  0.90  16.16   0.99     0.96       6579.20|
|  8:  2.5059 -  2.3973  1278   136  0.90  16.30   0.99     0.96       6169.19|
|  9:  2.3973 -  2.3053  1287   146  0.89  17.02   1.00     0.97       5549.01|
| 10:  2.3053 -  2.2261  1242   139  0.89  16.86   0.99     0.95       5121.16|
| 11:  2.2261 -  2.1567  1259   143  0.90  16.52   0.99     0.95       4560.11|
| 12:  2.1567 -  2.0952  1278   134  0.91  15.76   1.00     0.98       4121.10|
| 13:  2.0952 -  2.0402  1248   134  0.90  16.64   0.99     0.98       3631.90|
| 14:  2.0402 -  1.9905   855   103  0.90  16.12   0.97     0.93       2875.27|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2875.27 max =        11035.38 mean =      6892.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.82|
|phase err.(test): min =        0.00 max =           89.74 mean =        14.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1637   ksol= 0.32   Bsol= 53.82   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.87,0.37,0.49,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.182918                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1637   ksol= 0.32   Bsol= 53.82   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.87,0.37,0.49,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.182918                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.7494 0.99   1385  155 0.0989 0.1320      5.3934      5.5483|
|  2:  4.7494 -  3.7899 0.99   1338  146 0.0863 0.1091       5.451      5.6532|
|  3:  3.7899 -  3.3168 0.99   1309  152 0.1080 0.1553      5.4993      5.8793|
|  4:  3.3168 -  3.0163 0.99   1301  133 0.1284 0.1621      5.4875        5.66|
|  5:  3.0163 -  2.8016 0.98   1277  145 0.1358 0.1692      5.3665      5.5164|
|  6:  2.8016 -  2.6374 0.98   1295  144 0.1346 0.2037      5.2859      5.5351|
|  7:  2.6374 -  2.5059 0.99   1278  149 0.1267 0.1754      5.1912      5.4244|
|  8:  2.5059 -  2.3973 0.99   1278  136 0.1239 0.1849      5.1388      5.3893|
|  9:  2.3973 -  2.3053 0.98   1287  146 0.1239 0.1930      5.0747      5.3789|
| 10:  2.3053 -  2.2261 0.97   1242  139 0.1222 0.1867       5.034       5.255|
| 11:  2.2261 -  2.1567 0.98   1259  143 0.1215 0.1710      4.9762      5.2689|
| 12:  2.1567 -  2.0952 0.99   1278  134 0.1152 0.1853      4.9012      5.2049|
| 13:  2.0952 -  2.0402 0.97   1248  134 0.1190 0.1741      4.8318      5.0714|
| 14:  2.0402 -  1.9905 0.67    855  103 0.1099 0.1795      4.7151       4.956|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9590 -  4.7494  1385   155  0.94   9.46   0.97     0.95       7757.09|
|  2:  4.7494 -  3.7899  1338   146  0.95   8.54   1.01     0.99       9571.77|
|  3:  3.7899 -  3.3168  1309   152  0.93  11.58   1.02     1.02      11023.31|
|  4:  3.3168 -  3.0163  1301   133  0.91  14.33   1.01     0.99      10748.20|
|  5:  3.0163 -  2.8016  1277   145  0.90  16.42   1.00     0.97       8913.43|
|  6:  2.8016 -  2.6374  1295   144  0.89  17.10   0.98     0.95       7983.40|
|  7:  2.6374 -  2.5059  1278   149  0.90  16.16   0.99     0.96       6574.82|
|  8:  2.5059 -  2.3973  1278   136  0.90  16.31   1.00     0.96       6175.60|
|  9:  2.3973 -  2.3053  1287   146  0.89  17.04   1.00     0.97       5557.54|
| 10:  2.3053 -  2.2261  1242   139  0.89  16.87   1.00     0.96       5125.59|
| 11:  2.2261 -  2.1567  1259   143  0.90  16.52   1.00     0.96       4562.17|
| 12:  2.1567 -  2.0952  1278   134  0.91  15.77   1.00     0.98       4125.79|
| 13:  2.0952 -  2.0402  1248   134  0.90  16.63   0.99     0.98       3630.05|
| 14:  2.0402 -  1.9905   855   103  0.90  16.10   0.97     0.94       2868.30|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2868.30 max =        11023.31 mean =      6891.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.86 mean =        14.82|
|phase err.(test): min =        0.00 max =           89.83 mean =        14.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.982)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.28    91.60   15.65    None  None   None       |
|    all(noH): 2823   0      2.28    91.60   15.65    None  None   None       |
|    Sol.    : 438    0      3.96    84.25   40.01    None  None   None       |
|    Mac.    : 2385   0      2.28    91.60   11.17    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:     2.278 -  11.210: 1632   |   5:    46.940 -  55.872:   93        |
|      1:    11.210 -  20.143:  618   |   6:    55.872 -  64.805:   57        |
|      2:    20.143 -  29.075:  161   |   7:    64.805 -  73.737:   26        |
|      3:    29.075 -  38.008:  113   |   8:    73.737 -  82.669:   16        |
|      4:    38.008 -  46.940:  101   |   9:    82.669 -  91.602:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 325         
Filter by distance & map next to the model:
   mapped sites are within: 0.301 - 5.152
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 325
   mapped sites are within: 0.721 - 5.152

peak=    9.615 closest distance to " CG2 VAL A 230 " =    1.393
peak=    6.944 closest distance to " CD1AILE A 234 " =    1.368
peak=    6.456 closest distance to " CG2 VAL A 296 " =    1.077
peak=    6.397 closest distance to " CG  LEU A   5 " =    1.210
peak=    6.252 closest distance to " O   HOH Z 210 " =    1.210
peak=    5.602 closest distance to " NH2 ARG A  56 " =    2.346
peak=    5.495 closest distance to " CB  VAL A 296 " =    1.063
peak=    5.331 closest distance to " CB  SER A  63 " =    1.191
peak=    5.270 closest distance to " O   HOH Z 402 " =    1.640
peak=    5.095 closest distance to " CG  LEU A 228 " =    1.194
peak=    5.011 closest distance to " CB  GLN A 223 " =    1.385
peak=    4.958 closest distance to " O   HOH Z 433 " =    1.656
peak=    4.954 closest distance to " O   HOH Z 403 " =    1.777
peak=    4.936 closest distance to " CB  VAL A 230 " =    1.186
peak=    4.931 closest distance to " O   HOH Z  44 " =    2.386
peak=    4.901 closest distance to " CB  PRO A  54 " =    0.887
peak=    4.864 closest distance to " O   HOH Z 124 " =    1.461
peak=    4.707 closest distance to " C   PRO A 198 " =    1.473
peak=    4.686 closest distance to " CG  PRO A  54 " =    1.279
peak=    4.671 closest distance to " O   HOH Z 247 " =    1.473
peak=    4.637 closest distance to " CG  PRO A 213 " =    1.214
peak=    4.571 closest distance to " CB  ARG A 275 " =    0.862
peak=    4.546 closest distance to " CA  TYR A  30 " =    0.947
peak=    4.539 closest distance to " O   HOH Z  80 " =    1.951
peak=    4.504 closest distance to " CG  PRO A 280 " =    0.721
peak=    4.498 closest distance to " NE2 GLN A  11 " =    1.035
peak=    4.469 closest distance to " CB  GLN A 183 " =    1.338
peak=    4.454 closest distance to " CG  PRO A 198 " =    1.159
peak=    4.415 closest distance to " O   HOH Z 154 " =    1.513
peak=    4.383 closest distance to " O   HOH Z 232 " =    2.381
peak=    4.371 closest distance to " O   HOH Z 120 " =    1.055
peak=    4.356 closest distance to " O   HOH Z 134 " =    1.972
peak=    4.326 closest distance to " O   HOH Z  48 " =    1.877
peak=    4.316 closest distance to " O   GLY A  23 " =    2.398
peak=    4.273 closest distance to " O   HOH Z 357 " =    2.044
peak=    4.262 closest distance to " O   HOH Z 234 " =    3.634
peak=    4.257 closest distance to " O   SER A  87 " =    2.289
peak=    4.253 closest distance to " O   HOH Z 102 " =    1.338
peak=    4.245 closest distance to " CG1 ILE A  33 " =    1.248
peak=    4.208 closest distance to " O   HOH Z  49 " =    1.066
peak=    4.180 closest distance to " O   HOH Z 193 " =    1.740
peak=    4.179 closest distance to " CG  ARG A  66 " =    2.809
peak=    4.173 closest distance to " CG2 VAL A 296 " =    1.799
peak=    4.154 closest distance to " CB  SER A   3 " =    1.289
peak=    4.144 closest distance to " O   HOH Z 431 " =    1.213
peak=    4.114 closest distance to " O   HOH Z 154 " =    2.443
peak=    4.088 closest distance to " O   HOH Z  67 " =    1.962
peak=    4.078 closest distance to " O   HOH Z 126 " =    2.634
peak=    4.077 closest distance to " O   HOH Z 423 " =    1.780
peak=    4.068 closest distance to " CB  TRP A 179 " =    1.291
peak=    4.067 closest distance to " O   HOH Z 316 " =    2.820
peak=    4.064 closest distance to " O   HOH Z  54 " =    2.187
peak=    4.051 closest distance to " NH2 ARG A 156 " =    1.142
peak=    4.046 closest distance to " CA  ALA A  51 " =    1.075
peak=    4.037 closest distance to " CG2 THR A 221 " =    1.193
peak=    4.036 closest distance to " O   HOH Z 346 " =    1.551
peak=    4.021 closest distance to " O   HOH Z 130 " =    1.130
peak=    4.000 closest distance to " CB  GLU A 277 " =    3.646
peak=    3.978 closest distance to " O   HOH Z 142 " =    1.498
peak=    3.964 closest distance to " CB  GLU A 152 " =    1.103
peak=    3.963 closest distance to " O   HOH Z  97 " =    1.909
peak=    3.960 closest distance to " O   HOH Z  85 " =    1.271
peak=    3.960 closest distance to " O   HOH Z 412 " =    3.496
peak=    3.956 closest distance to " O   HOH Z 327 " =    1.639
peak=    3.949 closest distance to " CB  PRO A  54 " =    1.339
peak=    3.948 closest distance to " O   HOH Z 126 " =    1.642
peak=    3.939 closest distance to " O   HOH Z  40 " =    1.888
peak=    3.919 closest distance to " OE1 GLU A   2 " =    1.902
peak=    3.918 closest distance to " CB  ARG A 190 " =    1.714
peak=    3.912 closest distance to " O   HOH Z 345 " =    2.910
peak=    3.909 closest distance to " O   HOH Z 189 " =    2.470
peak=    3.902 closest distance to " OG1 THR A 294 " =    2.279
peak=    3.898 closest distance to " O   HOH Z 245 " =    1.384
peak=    3.896 closest distance to " O   HOH Z 383 " =    1.969
peak=    3.895 closest distance to " O   HOH Z 425 " =    1.371
peak=    3.893 closest distance to " O   HOH Z 128 " =    1.454
peak=    3.879 closest distance to " O   HOH Z  48 " =    1.611
peak=    3.877 closest distance to " O   HOH Z 414 " =    1.918
peak=    3.874 closest distance to " O   ASP A 124 " =    1.350
peak=    3.871 closest distance to " CB  TYR A 169 " =    0.839
peak=    3.870 closest distance to " O   HOH Z 126 " =    1.851
peak=    3.860 closest distance to " CA  VAL A  41 " =    0.849
peak=    3.860 closest distance to " OG BSER A 164 " =    2.189
peak=    3.856 closest distance to " CD2 LEU A 228 " =    1.191
peak=    3.854 closest distance to " O   HOH Z 303 " =    2.270
peak=    3.850 closest distance to " CB  ASN A 148 " =    1.296
peak=    3.836 closest distance to " O   HOH Z 263 " =    1.460
peak=    3.835 closest distance to " O   HOH Z  15 " =    2.186
peak=    3.822 closest distance to " O   HOH Z 257 " =    2.320
peak=    3.815 closest distance to " CE1 HIS A 108 " =    1.097
peak=    3.812 closest distance to " O   HOH Z 193 " =    2.085
peak=    3.801 closest distance to " O   ALA A 165 " =    1.260
peak=    3.793 closest distance to " NZ  LYS A 117 " =    3.073
peak=    3.788 closest distance to " CD  LYS A 166 " =    1.398
peak=    3.782 closest distance to " O   HOH Z  61 " =    1.510
peak=    3.780 closest distance to " CB BVAL A  41 " =    1.058
peak=    3.777 closest distance to " CG  ARG A  66 " =    0.956
peak=    3.758 closest distance to " CB  GLU A 128 " =    1.175
peak=    3.757 closest distance to " O   HOH Z 408 " =    1.728
peak=    3.744 closest distance to " O   HOH Z 272 " =    1.946
peak=    3.744 closest distance to " NH2BARG A 145 " =    2.131
peak=    3.744 closest distance to " O   HOH Z 369 " =    2.221
peak=    3.737 closest distance to " O   HOH Z 394 " =    1.599
peak=    3.736 closest distance to " CD  ARG A 159 " =    0.812
peak=    3.727 closest distance to " CA  ARG A 195 " =    1.176
peak=    3.721 closest distance to " O   HOH Z 368 " =    2.306
peak=    3.711 closest distance to " ND2 ASN A 249 " =    2.055
peak=    3.710 closest distance to " O   HOH Z  54 " =    1.373
peak=    3.706 closest distance to " O   HOH Z 298 " =    1.997
peak=    3.679 closest distance to " CA  ALA A  21 " =    1.256
peak=    3.674 closest distance to " CZ  PHE A 218 " =    1.189
peak=    3.673 closest distance to " CD2 TRP A 179 " =    1.398
peak=    3.671 closest distance to " CE  LYS A 119 " =    1.097
peak=    3.661 closest distance to " O   HOH Z  48 " =    2.299
peak=    3.656 closest distance to " CA  ALA A 295 " =    1.041
peak=    3.656 closest distance to " OD1 ASN A  69 " =    2.473
peak=    3.652 closest distance to " O   HOH Z 280 " =    3.030
peak=    3.635 closest distance to " CB  ALA A 100 " =    1.341
peak=    3.634 closest distance to " O   HOH Z 214 " =    2.775
peak=    3.634 closest distance to " O   HOH Z  44 " =    1.801
peak=    3.633 closest distance to " CB  ALA A   9 " =    1.621
peak=    3.630 closest distance to " O   ALA A 158 " =    1.234
peak=    3.630 closest distance to " CE1 TYR A 186 " =    1.272
peak=    3.625 closest distance to " O   HOH Z 403 " =    1.479
peak=    3.620 closest distance to " CD  ARG A 269 " =    1.079
peak=    3.606 closest distance to " O   HOH Z 371 " =    3.371
peak=    3.604 closest distance to " CA  ASP A 191 " =    1.023
peak=    3.598 closest distance to " CG2 VAL A 197 " =    1.123
peak=    3.587 closest distance to " O   HOH Z 203 " =    1.781
peak=    3.584 closest distance to " NH1 ARG A  14 " =    1.185
peak=    3.579 closest distance to " C   SER A  32 " =    1.095
peak=    3.577 closest distance to " CB  VAL A 202 " =    1.450
peak=    3.573 closest distance to " O   HOH Z 155 " =    1.513
peak=    3.572 closest distance to " CB  TRP A 266 " =    1.040
peak=    3.562 closest distance to " NZ  LYS A 117 " =    1.440
peak=    3.561 closest distance to " CB  ARG A  79 " =    1.126
peak=    3.555 closest distance to " O   HOH Z 406 " =    1.508
peak=    3.553 closest distance to " O   HOH Z 334 " =    1.391
peak=    3.552 closest distance to " O   HOH Z 417 " =    3.165
peak=    3.552 closest distance to " O   HOH Z 196 " =    1.079
peak=    3.551 closest distance to " O   HOH Z 261 " =    1.995
peak=    3.548 closest distance to " CB  SER A  26 " =    1.691
peak=    3.542 closest distance to " O   HOH Z  21 " =    1.837
peak=    3.540 closest distance to " O   HOH Z 163 " =    1.389
peak=    3.539 closest distance to " O   HOH Z 185 " =    1.623
peak=    3.522 closest distance to " CD  PRO A  54 " =    1.026
peak=    3.515 closest distance to " CZ  PHE A  38 " =    1.303
peak=    3.512 closest distance to " O   HOH Z 248 " =    1.670
peak=    3.504 closest distance to " O   HOH Z 128 " =    1.865
peak=    3.500 closest distance to " CB  ALA A  71 " =    1.288
peak=    3.500 closest distance to " O  BHOH Z  74 " =    1.378
peak=    3.499 closest distance to " O   HOH Z 287 " =    1.894
peak=    3.499 closest distance to " O   HOH Z 339 " =    1.184
peak=    3.496 closest distance to " O   HOH Z 344 " =    2.994
peak=    3.492 closest distance to " OG  SER A  62 " =    2.900
peak=    3.490 closest distance to " CD1 LEU A 300 " =    1.219
peak=    3.489 closest distance to " O   HOH Z 279 " =    2.033
peak=    3.483 closest distance to " O   HOH Z 332 " =    1.557
peak=    3.483 closest distance to " O   HOH Z 271 " =    2.414
peak=    3.482 closest distance to " CB  ASN A  39 " =    0.780
peak=    3.479 closest distance to " O   HOH Z 132 " =    2.595
peak=    3.478 closest distance to " O   HOH Z 336 " =    1.730
peak=    3.475 closest distance to " O   HOH Z 146 " =    1.418
peak=    3.471 closest distance to " O   HOH Z  43 " =    1.773
peak=    3.469 closest distance to " N   ASN A  39 " =    1.218
peak=    3.468 closest distance to " CB  ASN A 187 " =    1.277
peak=    3.467 closest distance to " O   HOH Z 423 " =    3.102
peak=    3.462 closest distance to " O   HOH Z 419 " =    1.904
peak=    3.461 closest distance to " CA  ASN A 176 " =    1.103
peak=    3.461 closest distance to " CD2 LEU A   5 " =    1.108
peak=    3.456 closest distance to " O   HOH Z  20 " =    1.406
peak=    3.452 closest distance to " O   HOH Z 123 " =    2.156
peak=    3.440 closest distance to " O   HOH Z 128 " =    1.901
peak=    3.436 closest distance to " CB  LEU A 228 " =    1.371
peak=    3.434 closest distance to " O   HOH Z 146 " =    1.306
peak=    3.433 closest distance to " CG AARG A 275 " =    1.171
peak=    3.432 closest distance to " O   HOH Z 155 " =    3.010
peak=    3.426 closest distance to " CB  PRO A 198 " =    1.059
peak=    3.426 closest distance to " O   HOH Z 395 " =    1.409
peak=    3.425 closest distance to " CB  TYR A 247 " =    1.009
peak=    3.423 closest distance to " CD1 LEU A 101 " =    1.214
peak=    3.422 closest distance to " O   HOH Z 126 " =    1.985
peak=    3.417 closest distance to " O   HOH Z  78 " =    1.586
peak=    3.416 closest distance to " CG  PRO A 243 " =    1.158
peak=    3.416 closest distance to " CB  ARG A 139 " =    0.930
peak=    3.413 closest distance to " O   HOH Z 136 " =    1.253
peak=    3.411 closest distance to " O   HOH Z 435 " =    1.927
peak=    3.407 closest distance to " CA  GLY A  80 " =    0.975
peak=    3.407 closest distance to " CB  SER A 273 " =    0.853
peak=    3.402 closest distance to " OG  SER A 276 " =    1.574
peak=    3.402 closest distance to " CB  SER A 141 " =    1.078
peak=    3.401 closest distance to " O   HOH Z 147 " =    1.837
peak=    3.400 closest distance to " O   GLY A  91 " =    1.206
peak=    3.396 closest distance to " O   HOH Z 250 " =    1.359
peak=    3.390 closest distance to " CZ3 TRP A  85 " =    0.946
peak=    3.389 closest distance to " OD2 ASP A 298 " =    3.834
peak=    3.371 closest distance to " CG  GLN A  58 " =    2.652
peak=    3.370 closest distance to " CB  ASP A 140 " =    0.777
peak=    3.369 closest distance to " CA  ASP A 162 " =    1.121
peak=    3.366 closest distance to " CD2 LEU A 297 " =    0.804
peak=    3.362 closest distance to " O   HOH Z 409 " =    4.061
peak=    3.361 closest distance to " CB  MET A  40 " =    0.758
peak=    3.360 closest distance to " O   HOH Z 345 " =    1.712
peak=    3.359 closest distance to " CB  PHE A 204 " =    1.127
peak=    3.358 closest distance to " O   HOH Z 197 " =    2.088
peak=    3.358 closest distance to " O   HOH Z 166 " =    1.527
peak=    3.358 closest distance to " O   HOH Z  35 " =    2.159
peak=    3.357 closest distance to " OG BSER A 134 " =    2.916
peak=    3.352 closest distance to " O   HOH Z 158 " =    2.922
peak=    3.351 closest distance to " OE1 GLN A  11 " =    1.876
peak=    3.340 closest distance to " O   ASN A  74 " =    1.672
peak=    3.337 closest distance to " O   HOH Z 420 " =    1.918
peak=    3.333 closest distance to " O   HOH Z  88 " =    3.008
peak=    3.330 closest distance to " CA  LYS A 117 " =    1.324
peak=    3.329 closest distance to " O   HOH Z 421 " =    1.794
peak=    3.327 closest distance to " CD  LYS A 119 " =    1.886
peak=    3.323 closest distance to " CB  THR A  52 " =    1.020
peak=    3.321 closest distance to " CG1BVAL A  72 " =    1.795
peak=    3.321 closest distance to " O   HOH Z 404 " =    2.194
peak=    3.320 closest distance to " CA  ILE A 106 " =    0.724
peak=    3.315 closest distance to " O   HOH Z 329 " =    3.792
peak=    3.314 closest distance to " O   HOH Z 112 " =    1.673
peak=    3.313 closest distance to " O   HOH Z 402 " =    2.794
peak=    3.312 closest distance to " OG  SER A 245 " =    1.477
peak=    3.311 closest distance to " O   HOH Z 227 " =    1.533
peak=    3.302 closest distance to " CA  ALA A 160 " =    0.894
peak=    3.300 closest distance to " CB  ALA A 248 " =    1.362
peak=    3.298 closest distance to " O   HOH Z 250 " =    1.583
peak=    3.298 closest distance to " O   HOH Z  90 " =    3.501
peak=    3.296 closest distance to " N   ASP A 231 " =    1.613
peak=    3.295 closest distance to " CB  ALA A 295 " =    1.328
peak=    3.294 closest distance to " O   TRP A 274 " =    1.903
peak=    3.293 closest distance to " O   HOH Z 281 " =    4.676
peak=    3.289 closest distance to " CG1 VAL A 153 " =    1.118
peak=    3.288 closest distance to " O   HOH Z 374 " =    2.697
peak=    3.287 closest distance to " O   HOH Z 438 " =    2.242
peak=    3.285 closest distance to " CG2 THR A 220 " =    0.752
peak=    3.284 closest distance to " NH2 ARG A  79 " =    1.272
peak=    3.284 closest distance to " O   HOH Z 189 " =    2.653
peak=    3.279 closest distance to " ND2 ASN A 187 " =    1.645
peak=    3.276 closest distance to " C   VAL A 265 " =    1.165
peak=    3.276 closest distance to " OH  TYR A 116 " =    1.171
peak=    3.276 closest distance to " CD1 LEU A   5 " =    1.385
peak=    3.275 closest distance to " ND1 HIS A  81 " =    1.630
peak=    3.274 closest distance to " OD2 ASP A 286 " =    2.753
peak=    3.274 closest distance to " CA  THR A  82 " =    1.505
peak=    3.272 closest distance to " NZ  LYS A 166 " =    3.033
peak=    3.272 closest distance to " CA  ALA A 291 " =    0.886
peak=    3.271 closest distance to " O   HOH Z 130 " =    2.517
peak=    3.270 closest distance to " O   HOH Z 426 " =    1.612
peak=    3.265 closest distance to " O   HOH Z 273 " =    2.872
peak=    3.261 closest distance to " O   HOH Z 368 " =    3.489
peak=    3.261 closest distance to " CD1 ILE A  33 " =    1.561
peak=    3.260 closest distance to " CB  SER A  62 " =    0.798
peak=    3.258 closest distance to " O   HOH Z 387 " =    2.733
peak=    3.256 closest distance to " O   HOH Z 366 " =    2.824
peak=    3.251 closest distance to " O   HOH Z 380 " =    1.934
peak=    3.245 closest distance to " O   HOH Z 427 " =    3.066
peak=    3.236 closest distance to " CG1 VAL A 296 " =    1.130
peak=    3.235 closest distance to " O   HOH Z  54 " =    1.270
peak=    3.231 closest distance to " CG1 ILE A  49 " =    1.644
peak=    3.231 closest distance to " CD BLYS A 290 " =    0.967
peak=    3.230 closest distance to " O   HOH Z 422 " =    2.499
peak=    3.228 closest distance to " CG  MET A 185 " =    1.141
peak=    3.226 closest distance to " CB  PHE A 283 " =    0.765
peak=    3.224 closest distance to " O   HOH Z 427 " =    2.851
peak=    3.222 closest distance to " O   HOH Z 162 " =    1.710
peak=    3.221 closest distance to " O   HOH Z 298 " =    5.152
peak=    3.221 closest distance to " CG2 ILE A  20 " =    1.418
peak=    3.209 closest distance to " O   HOH Z 133 " =    2.511
peak=    3.209 closest distance to " CD2 LEU A 255 " =    1.246
peak=    3.208 closest distance to " O   HOH Z 280 " =    2.654
peak=    3.204 closest distance to " CA  THR A 264 " =    0.786
peak=    3.202 closest distance to " O   HOH Z 418 " =    1.284
peak=    3.192 closest distance to " CD1 LEU A  96 " =    0.722
peak=    3.189 closest distance to " O   HOH Z  28 " =    1.433
peak=    3.185 closest distance to " O   HOH Z 214 " =    1.440
peak=    3.185 closest distance to " NH1BARG A 190 " =    2.255
peak=    3.183 closest distance to " O   HOH Z 145 " =    2.588
peak=    3.182 closest distance to " CB  ALA A 291 " =    1.357
peak=    3.180 closest distance to " O   HOH Z 151 " =    1.873
peak=    3.180 closest distance to " O   HOH Z 361 " =    2.845
peak=    3.180 closest distance to " CB  VAL A 265 " =    1.314
peak=    3.177 closest distance to " O   HOH Z 419 " =    2.459
peak=    3.175 closest distance to " O   HOH Z 355 " =    1.806
peak=    3.175 closest distance to " NH1AARG A 145 " =    1.219
peak=    3.170 closest distance to " O   HOH Z  66 " =    2.153
peak=    3.168 closest distance to " CG2AVAL A 121 " =    2.034
peak=    3.159 closest distance to " CG  ARG A  66 " =    2.917
peak=    3.158 closest distance to " CB  ASN A 215 " =    1.079
peak=    3.156 closest distance to " O   HOH Z 370 " =    1.855
peak=    3.153 closest distance to " CA  TYR A 116 " =    1.362
peak=    3.144 closest distance to " O   HOH Z 180 " =    2.226
peak=    3.142 closest distance to " C   ILE A 106 " =    1.823
peak=    3.141 closest distance to " O   HOH Z 227 " =    1.601
peak=    3.141 closest distance to " O   HOH Z 109 " =    2.101
peak=    3.140 closest distance to " CG2 ILE A 120 " =    1.211
peak=    3.139 closest distance to " O   HOH Z 313 " =    1.573
peak=    3.135 closest distance to " NE1 TRP A 274 " =    0.887
peak=    3.128 closest distance to " O   HOH Z 193 " =    1.513
peak=    3.127 closest distance to " CB  ALA A 242 " =    1.014
peak=    3.125 closest distance to " CA  VAL A 126 " =    0.877
peak=    3.124 closest distance to " OG1 THR A 157 " =    1.244
peak=    3.122 closest distance to " O   HOH Z 251 " =    1.311
peak=    3.115 closest distance to " CA  ALA A 158 " =    1.244
peak=    3.114 closest distance to " CG2 ILE A 234 " =    0.963
peak=    3.112 closest distance to " CB  LEU A 261 " =    1.187
peak=    3.107 closest distance to " CB  ALA A  34 " =    0.783
peak=    3.106 closest distance to " N   TYR A 247 " =    1.260
peak=    3.105 closest distance to " CA  ALA A 299 " =    0.956
peak=    3.105 closest distance to " CG  GLU A  37 " =    0.885
peak=    3.101 closest distance to " CB  ASN A 142 " =    1.179
peak=    3.099 closest distance to " O   HOH Z 291 " =    1.782
peak=    3.087 closest distance to " O   HOH Z 244 " =    1.597
peak=    3.086 closest distance to " CA  THR A 221 " =    1.588
peak=    3.080 closest distance to " CA  LYS A 290 " =    1.255
peak=    3.076 closest distance to " O   HOH Z 222 " =    3.052
peak=    3.068 closest distance to " CB  GLN A 278 " =    0.925
peak=    3.058 closest distance to " CA  ARG A  36 " =    1.041
peak=    3.054 closest distance to " O   HOH Z   9 " =    2.431
peak=    3.041 closest distance to " CB  ALA A 256 " =    1.018
peak=    3.032 closest distance to " CB  TRP A 179 " =    1.933

                           ----------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: 0.746 - 5.257
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 208
   mapped sites are within: 0.746 - 5.257

peak=   -4.980 closest distance to " CG2 VAL A 230 " =    0.821
peak=   -4.654 closest distance to " O   PRO A 163 " =    2.113
peak=   -4.538 closest distance to " O   HOH Z 166 " =    1.648
peak=   -4.471 closest distance to " CG2BVAL A  41 " =    2.720
peak=   -4.377 closest distance to " O   HOH Z 266 " =    4.793
peak=   -4.289 closest distance to " O   HOH Z  13 " =    1.730
peak=   -4.252 closest distance to " OXT GLY A 302 " =    2.834
peak=   -4.186 closest distance to " CD  ARG A 156 " =    2.085
peak=   -4.116 closest distance to " CG  MET A  93 " =    2.518
peak=   -4.113 closest distance to " CG1 VAL A 250 " =    2.683
peak=   -4.087 closest distance to " O   HOH Z 196 " =    2.508
peak=   -4.008 closest distance to " O   HOH Z 426 " =    1.699
peak=   -3.987 closest distance to " O   HOH Z 290 " =    0.948
peak=   -3.982 closest distance to " SG  CYS A 254 " =    3.244
peak=   -3.962 closest distance to " O   HOH Z 165 " =    1.988
peak=   -3.947 closest distance to " O   HOH Z  37 " =    1.913
peak=   -3.932 closest distance to " CD  GLN A  58 " =    1.173
peak=   -3.915 closest distance to " O   HOH Z 351 " =    1.498
peak=   -3.910 closest distance to " CE2 TYR A  30 " =    2.736
peak=   -3.893 closest distance to " O   HOH Z 136 " =    2.442
peak=   -3.875 closest distance to " C   HIS A 108 " =    1.186
peak=   -3.850 closest distance to " CG  ASP A 231 " =    0.886
peak=   -3.848 closest distance to " O   VAL A  67 " =    2.725
peak=   -3.844 closest distance to " NH2 ARG A  66 " =    1.284
peak=   -3.842 closest distance to " N   ALA A 226 " =    2.048
peak=   -3.839 closest distance to " CD1 PHE A  59 " =    1.982
peak=   -3.835 closest distance to " C   THR A 279 " =    1.179
peak=   -3.819 closest distance to " OG BSER A 134 " =    1.289
peak=   -3.810 closest distance to " CD2 LEU A 300 " =    2.728
peak=   -3.779 closest distance to " OG  SER A  97 " =    2.312
peak=   -3.775 closest distance to " O   ALA A   1 " =    1.960
peak=   -3.766 closest distance to " CB  PHE A 208 " =    2.342
peak=   -3.721 closest distance to " O   HOH Z 234 " =    4.153
peak=   -3.683 closest distance to " CB  ALA A 161 " =    2.553
peak=   -3.681 closest distance to " CG2 THR A 182 " =    2.315
peak=   -3.673 closest distance to " O   ALA A 256 " =    1.589
peak=   -3.672 closest distance to " O   HOH Z 196 " =    2.221
peak=   -3.665 closest distance to " OG1 THR A  82 " =    1.373
peak=   -3.664 closest distance to " OD1 ASN A 148 " =    1.526
peak=   -3.658 closest distance to " CA  ASP A 298 " =    1.001
peak=   -3.655 closest distance to " OG BSER A 210 " =    1.233
peak=   -3.651 closest distance to " O   HOH Z 407 " =    3.089
peak=   -3.634 closest distance to " CA  SER A 276 " =    1.494
peak=   -3.629 closest distance to " O   HOH Z  10 " =    1.536
peak=   -3.627 closest distance to " O   HOH Z 174 " =    2.023
peak=   -3.620 closest distance to " OE1 GLN A 223 " =    2.429
peak=   -3.619 closest distance to " O   HOH Z 377 " =    1.216
peak=   -3.614 closest distance to " O   HOH Z 171 " =    2.376
peak=   -3.606 closest distance to " N   THR A 235 " =    1.336
peak=   -3.604 closest distance to " O   HOH Z 210 " =    0.746
peak=   -3.601 closest distance to " CH2 TRP A 179 " =    1.237
peak=   -3.594 closest distance to " O   HOH Z 126 " =    1.795
peak=   -3.565 closest distance to " O   HOH Z 353 " =    2.256
peak=   -3.562 closest distance to " CA  GLY A 133 " =    2.402
peak=   -3.560 closest distance to " O   HOH Z 150 " =    1.833
peak=   -3.558 closest distance to " O   PRO A 198 " =    1.293
peak=   -3.555 closest distance to " CB  PRO A 243 " =    2.724
peak=   -3.554 closest distance to " O   HOH Z 283 " =    1.956
peak=   -3.554 closest distance to " CD  ARG A 139 " =    1.615
peak=   -3.553 closest distance to " O   TRP A  92 " =    1.989
peak=   -3.547 closest distance to " CE3 TRP A 150 " =    2.381
peak=   -3.545 closest distance to " O   HOH Z 423 " =    2.209
peak=   -3.543 closest distance to " O   HOH Z 197 " =    2.063
peak=   -3.543 closest distance to " CE BMET A  47 " =    1.603
peak=   -3.542 closest distance to " O   HOH Z  11 " =    1.866
peak=   -3.536 closest distance to " O   HOH Z 407 " =    1.528
peak=   -3.530 closest distance to " O   SER A  95 " =    1.780
peak=   -3.528 closest distance to " OD1 ASN A  39 " =    2.193
peak=   -3.524 closest distance to " O   HOH Z 231 " =    2.204
peak=   -3.524 closest distance to " O   HOH Z 151 " =    1.157
peak=   -3.517 closest distance to " CZ  TYR A 169 " =    1.829
peak=   -3.517 closest distance to " CB  ALA A 248 " =    2.121
peak=   -3.502 closest distance to " CA  GLY A 203 " =    2.259
peak=   -3.494 closest distance to " CG2 VAL A 189 " =    2.018
peak=   -3.492 closest distance to " O   HOH Z  60 " =    2.218
peak=   -3.487 closest distance to " OD1 ASN A 187 " =    1.756
peak=   -3.487 closest distance to " O   HOH Z  71 " =    1.611
peak=   -3.483 closest distance to " ND2 ASN A  69 " =    1.652
peak=   -3.483 closest distance to " O   HOH Z   6 " =    2.077
peak=   -3.482 closest distance to " CG1 VAL A 112 " =    2.521
peak=   -3.479 closest distance to " C   ALA A 158 " =    1.264
peak=   -3.477 closest distance to " OG  SER A  26 " =    1.301
peak=   -3.475 closest distance to " O   SER A 271 " =    1.828
peak=   -3.471 closest distance to " CG  ASP A  50 " =    2.138
peak=   -3.469 closest distance to " ND2 ASN A 187 " =    1.741
peak=   -3.455 closest distance to " CD1 LEU A  25 " =    2.517
peak=   -3.447 closest distance to " O   HOH Z  52 " =    1.979
peak=   -3.444 closest distance to " OG ASER A 134 " =    1.209
peak=   -3.439 closest distance to " CB  ASP A 162 " =    2.494
peak=   -3.432 closest distance to " CB  ALA A  51 " =    1.901
peak=   -3.430 closest distance to " O   HOH Z  19 " =    2.378
peak=   -3.423 closest distance to " CG  PRO A 243 " =    1.705
peak=   -3.411 closest distance to " NE1 TRP A 266 " =    2.413
peak=   -3.407 closest distance to " NH1 ARG A 195 " =    2.571
peak=   -3.405 closest distance to " CD2 LEU A 167 " =    1.732
peak=   -3.400 closest distance to " O   ALA A 161 " =    1.846
peak=   -3.398 closest distance to " CG  MET A 105 " =    0.890
peak=   -3.397 closest distance to " O   HOH Z 252 " =    3.918
peak=   -3.395 closest distance to " O   HOH Z 275 " =    1.475
peak=   -3.389 closest distance to " CB  ALA A 291 " =    2.329
peak=   -3.383 closest distance to " O   HOH Z 388 " =    1.945
peak=   -3.380 closest distance to " O   HOH Z 193 " =    1.588
peak=   -3.379 closest distance to " N   THR A 157 " =    1.542
peak=   -3.376 closest distance to " O   PHE A 218 " =    1.514
peak=   -3.375 closest distance to " ND2 ASN A  45 " =    1.144
peak=   -3.364 closest distance to " CG  GLU A  53 " =    1.468
peak=   -3.350 closest distance to " OG BSER A 210 " =    2.325
peak=   -3.350 closest distance to " N   GLN A  58 " =    1.492
peak=   -3.349 closest distance to " NE2 GLN A  88 " =    1.118
peak=   -3.333 closest distance to " O   HOH Z 166 " =    1.519
peak=   -3.333 closest distance to " CG2 ILE A  49 " =    2.762
peak=   -3.327 closest distance to " CB  PHE A 192 " =    2.100
peak=   -3.323 closest distance to " C   LEU A 143 " =    1.041
peak=   -3.322 closest distance to " ND2 ASN A  39 " =    1.210
peak=   -3.322 closest distance to " N   ALA A 242 " =    1.970
peak=   -3.319 closest distance to " NE2 GLN A 103 " =    1.700
peak=   -3.318 closest distance to " O   HOH Z  15 " =    1.505
peak=   -3.318 closest distance to " O   HOH Z  20 " =    1.102
peak=   -3.315 closest distance to " O   SER A 210 " =    1.756
peak=   -3.314 closest distance to " CA  VAL A 197 " =    0.973
peak=   -3.311 closest distance to " NH2AARG A 275 " =    4.889
peak=   -3.310 closest distance to " N   LEU A 281 " =    1.884
peak=   -3.308 closest distance to " CG1 VAL A  78 " =    2.797
peak=   -3.308 closest distance to " CB  PRO A 163 " =    2.731
peak=   -3.307 closest distance to " O   HOH Z 285 " =    1.526
peak=   -3.305 closest distance to " CG  ARG A 269 " =    2.293
peak=   -3.304 closest distance to " ND2BASN A 224 " =    1.837
peak=   -3.303 closest distance to " CE2 PHE A  38 " =    2.014
peak=   -3.301 closest distance to " CE  MET A 105 " =    2.235
peak=   -3.301 closest distance to " O   HOH Z 292 " =    4.392
peak=   -3.298 closest distance to " O   GLY A  80 " =    2.460
peak=   -3.298 closest distance to " CD  GLN A 223 " =    1.522
peak=   -3.294 closest distance to " NH2 ARG A  79 " =    1.992
peak=   -3.294 closest distance to " C   ASN A 285 " =    2.396
peak=   -3.294 closest distance to " O   ALA A  10 " =    1.786
peak=   -3.292 closest distance to " C   VAL A 265 " =    0.901
peak=   -3.291 closest distance to " O   TYR A  15 " =    1.669
peak=   -3.290 closest distance to " O   GLY A 196 " =    1.049
peak=   -3.289 closest distance to " CD1 TYR A 247 " =    2.329
peak=   -3.283 closest distance to " O   HOH Z 422 " =    1.611
peak=   -3.280 closest distance to " CG2 VAL A 112 " =    2.545
peak=   -3.279 closest distance to " CD2 LEU A 237 " =    2.797
peak=   -3.268 closest distance to " C   SER A 206 " =    1.617
peak=   -3.266 closest distance to " O   HOH Z 427 " =    1.394
peak=   -3.265 closest distance to " O   HOH Z 222 " =    1.417
peak=   -3.264 closest distance to " CG2 VAL A 296 " =    0.930
peak=   -3.262 closest distance to " O   HOH Z 372 " =    2.523
peak=   -3.262 closest distance to " CG1 VAL A 112 " =    2.587
peak=   -3.262 closest distance to " O   HOH Z 360 " =    2.487
peak=   -3.261 closest distance to " CD  ARG A  36 " =    1.909
peak=   -3.260 closest distance to " CD1 TRP A 179 " =    1.136
peak=   -3.260 closest distance to " O   ASN A 187 " =    1.575
peak=   -3.255 closest distance to " ND2 ASN A  45 " =    1.992
peak=   -3.252 closest distance to " CG  GLU A 277 " =    1.122
peak=   -3.251 closest distance to " O   HOH Z 311 " =    3.658
peak=   -3.250 closest distance to " O  BHOH Z 338 " =    1.326
peak=   -3.239 closest distance to " CB  SER A 210 " =    1.222
peak=   -3.235 closest distance to " CG  TRP A 266 " =    1.894
peak=   -3.232 closest distance to " O   HOH Z 131 " =    4.175
peak=   -3.227 closest distance to " O   HOH Z  78 " =    1.741
peak=   -3.221 closest distance to " CD2 TYR A 293 " =    1.910
peak=   -3.214 closest distance to " CB  MET A 188 " =    1.846
peak=   -3.214 closest distance to " CG1 VAL A 296 " =    1.309
peak=   -3.212 closest distance to " CD1 LEU A 167 " =    2.172
peak=   -3.209 closest distance to " CD  LYS A 289 " =    2.496
peak=   -3.209 closest distance to " O   HOH Z 377 " =    2.199
peak=   -3.207 closest distance to " SG  CYS A 260 " =    2.609
peak=   -3.207 closest distance to " CD1 LEU A 228 " =    2.245
peak=   -3.204 closest distance to " NE2 GLN A 194 " =    1.791
peak=   -3.203 closest distance to " O   HOH Z 139 " =    3.277
peak=   -3.203 closest distance to " CB  ALA A  10 " =    2.148
peak=   -3.202 closest distance to " ND2 ASN A  60 " =    1.652
peak=   -3.201 closest distance to " O   ASP A  27 " =    2.106
peak=   -3.201 closest distance to " O   HOH Z  56 " =    1.535
peak=   -3.188 closest distance to " O   ALA A 100 " =    2.084
peak=   -3.185 closest distance to " CG  ARG A 219 " =    2.626
peak=   -3.182 closest distance to " O   GLY A  80 " =    2.413
peak=   -3.181 closest distance to " O   HOH Z 185 " =    2.327
peak=   -3.179 closest distance to " O   HOH Z  17 " =    1.233
peak=   -3.178 closest distance to " NH1 ARG A 195 " =    2.288
peak=   -3.172 closest distance to " CD  PRO A 213 " =    2.152
peak=   -3.169 closest distance to " O   HOH Z 414 " =    2.256
peak=   -3.169 closest distance to " CG1 VAL A  78 " =    2.476
peak=   -3.162 closest distance to " ND2 ASN A  60 " =    1.546
peak=   -3.153 closest distance to " NE2 GLN A  88 " =    2.063
peak=   -3.132 closest distance to " O   HOH Z 350 " =    1.801
peak=   -3.123 closest distance to " O   HOH Z 200 " =    1.356
peak=   -3.123 closest distance to " O   HOH Z 385 " =    3.755
peak=   -3.121 closest distance to " OH  TYR A 169 " =    0.988
peak=   -3.104 closest distance to " O   HOH Z 123 " =    2.278
peak=   -3.097 closest distance to " CD2 PHE A  61 " =    2.049
peak=   -3.094 closest distance to " O   HOH Z 412 " =    5.257
peak=   -3.091 closest distance to " CE3 TRP A 274 " =    2.414
peak=   -3.088 closest distance to " O   HOH Z 236 " =    1.660
peak=   -3.086 closest distance to " CB  ASP A 132 " =    2.406
peak=   -3.085 closest distance to " CG  GLN A  11 " =    1.891
peak=   -3.064 closest distance to " OG BSER A 134 " =    1.760
peak=   -3.064 closest distance to " N   SER A   3 " =    2.339
peak=   -3.061 closest distance to " CZ  TYR A  68 " =    1.158
peak=   -3.053 closest distance to " CB  TRP A  85 " =    2.519
peak=   -3.051 closest distance to " O   ALA A  34 " =    2.419
peak=   -3.048 closest distance to " O   HOH Z  90 " =    1.648
peak=   -3.043 closest distance to " CB  CYS A 254 " =    2.395
peak=   -3.036 closest distance to " O   HOH Z 371 " =    1.984
peak=   -3.034 closest distance to " O   HOH Z  44 " =    2.089
peak=   -3.033 closest distance to " CG2 VAL A 189 " =    2.009
peak=   -3.028 closest distance to " OXT GLY A 302 " =    3.452

================= 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    :  0.4773 0.4612   6.279589e+00   6.261374e+00
   1_bss:  0.4696 0.4566   6.272114e+00   6.253742e+00
   1_xyz:  0.3860 0.4008   6.163279e+00   6.182749e+00
   1_adp:  0.3378 0.3784   6.074025e+00   6.149133e+00
   1_occ:  0.3372 0.3777   6.073008e+00   6.148939e+00
   2_bss:  0.3351 0.3732   6.074394e+00   6.147794e+00
   2_xyz:  0.2707 0.3226   5.901777e+00   6.033814e+00
   2_adp:  0.2562 0.3118   5.867981e+00   6.007740e+00
   2_occ:  0.2560 0.3118   5.867700e+00   6.008315e+00
   3_bss:  0.2550 0.3115   5.867908e+00   6.007314e+00
   3_xyz:  0.1967 0.2416   5.620501e+00   5.781460e+00
   3_adp:  0.1812 0.2232   5.550878e+00   5.716170e+00
   3_occ:  0.1811 0.2232   5.550408e+00   5.716616e+00
   4_bss:  0.1808 0.2226   5.550134e+00   5.714762e+00
   4_xyz:  0.1382 0.1786   5.305012e+00   5.509535e+00
   4_adp:  0.1282 0.1715   5.251023e+00   5.473792e+00
   4_occ:  0.1282 0.1714   5.250718e+00   5.473599e+00
   5_bss:  0.1285 0.1716   5.251543e+00   5.473465e+00
   5_xyz:  0.1182 0.1645   5.194337e+00   5.431659e+00
   5_adp:  0.1164 0.1636   5.182916e+00   5.424239e+00
   5_occ:  0.1163 0.1637   5.182887e+00   5.424457e+00
   5_bss:  0.1163 0.1637   5.182918e+00   5.424511e+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:  0.333  20.000   6.368  11.954   7.246   0.000   0.000   0.000
   1_xyz:  0.333  20.000   6.368  11.954   7.246   0.000   0.000   0.000
   1_adp:  0.333  20.000   6.368  11.954   7.246   0.000   0.000   0.000
   1_occ:  0.333  20.000   6.368  11.954   7.246   0.000   0.000   0.000
   2_bss:  0.313  35.444   3.001   7.666   4.300   0.000   0.000   0.000
   2_xyz:  0.313  35.444   3.001   7.666   4.300   0.000   0.000   0.000
   2_adp:  0.313  35.444   3.001   7.666   4.300   0.000   0.000   0.000
   2_occ:  0.313  35.444   3.001   7.666   4.300   0.000   0.000   0.000
   3_bss:  0.300  45.378   1.838   5.060   3.108   0.000   0.000   0.000
   3_xyz:  0.300  45.378   1.838   5.060   3.108   0.000   0.000   0.000
   3_adp:  0.300  45.378   1.838   5.060   3.108   0.000   0.000   0.000
   3_occ:  0.300  45.378   1.838   5.060   3.108   0.000   0.000   0.000
   4_bss:  0.313  45.378   1.414   3.451   2.679   0.000   0.000   0.000
   4_xyz:  0.313  45.378   1.414   3.451   2.679   0.000   0.000   0.000
   4_adp:  0.313  45.378   1.414   3.451   2.679   0.000   0.000   0.000
   4_occ:  0.313  45.378   1.414   3.451   2.679   0.000   0.000   0.000
   5_bss:  0.323  53.245   1.278   2.735   2.649   0.000   0.000   0.000
   5_xyz:  0.323  53.245   1.278   2.735   2.649   0.000   0.000   0.000
   5_adp:  0.323  53.245   1.278   2.735   2.649   0.000   0.000   0.000
   5_occ:  0.323  53.245   1.278   2.735   2.649   0.000   0.000   0.000
   5_bss:  0.323  53.825  -0.866   0.375   0.491   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.229 0.4557  0.5177    65490.290
   1_bss:  55.471 0.4508  0.6552    63668.689
   1_xyz:  46.280 0.5654  0.8065    47038.925
   1_adp:  41.450 0.6255  0.9331    40604.000
   1_occ:  41.357 0.6266  0.9335    40474.696
   2_bss:  41.074 0.6301  0.8301    40122.278
   2_xyz:  34.599 0.7056  0.9199    29021.600
   2_adp:  33.269 0.7211  0.9312    27165.683
   2_occ:  33.288 0.7209  0.9307    27182.645
   3_bss:  33.134 0.7227  0.8805    27056.806
   3_xyz:  23.973 0.8222  0.9668    15041.864
   3_adp:  21.811 0.8447  0.9790    13008.761
   3_occ:  21.811 0.8447  0.9791    13020.972
   4_bss:  21.728 0.8455  0.9525    12934.939
   4_xyz:  16.767 0.8911  0.9820     8116.679
   4_adp:  15.911 0.8990  0.9810     7600.289
   4_occ:  15.906 0.8990  0.9811     7599.007
   5_bss:  15.910 0.8990  0.9711     7608.520
   5_xyz:  14.976 0.9071  0.9731     6982.126
   5_adp:  14.762 0.9091  0.9675     6887.326
   5_occ:  14.763 0.9091  0.9674     6891.133
   5_bss:  14.762 0.9091  0.9696     6890.332
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3986e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3986e+01
   1_xyz:   1.683  0.013  0.108 17.997  0.007  4.121   1.4055e-01
   1_adp:   1.683  0.013  0.108 17.997  0.007  4.121   1.4055e-01
   1_occ:   1.683  0.013  0.108 17.997  0.007  4.121   1.4055e-01
   2_bss:   1.683  0.013  0.108 17.997  0.007  4.121   1.4055e-01
   2_xyz:   1.214  0.009  0.077 16.094  0.005  4.125   8.8546e-02
   2_adp:   1.214  0.009  0.077 16.094  0.005  4.125   8.8546e-02
   2_occ:   1.214  0.009  0.077 16.094  0.005  4.125   8.8546e-02
   3_bss:   1.214  0.009  0.077 16.094  0.005  4.125   8.8546e-02
   3_xyz:   1.163  0.008  0.081 15.599  0.004  4.112   7.3605e-02
   3_adp:   1.163  0.008  0.081 15.599  0.004  4.112   7.3605e-02
   3_occ:   1.163  0.008  0.081 15.599  0.004  4.112   7.3605e-02
   4_bss:   1.163  0.008  0.081 15.599  0.004  4.112   7.3605e-02
   4_xyz:   1.122  0.009  0.085 15.500  0.004  4.125   7.3520e-02
   4_adp:   1.122  0.009  0.085 15.500  0.004  4.125   7.3520e-02
   4_occ:   1.122  0.009  0.085 15.500  0.004  4.125   7.3520e-02
   5_bss:   1.122  0.009  0.085 15.500  0.004  4.125   7.3520e-02
   5_xyz:   1.105  0.009  0.088 15.487  0.004  4.125   7.0743e-02
   5_adp:   1.105  0.009  0.088 15.487  0.004  4.125   7.0743e-02
   5_occ:   1.105  0.009  0.088 15.487  0.004  4.125   7.0743e-02
   5_bss:   1.105  0.009  0.088 15.487  0.004  4.125   7.0743e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9985e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9985e+00
   1_xyz:  15.301  0.158  0.518 88.015  0.045  2.304   1.0247e-01
   1_adp:  15.301  0.158  0.518 88.015  0.045  2.304   1.0247e-01
   1_occ:  15.301  0.158  0.518 88.015  0.045  2.304   1.0247e-01
   2_bss:  15.301  0.158  0.518 88.015  0.045  2.304   1.0247e-01
   2_xyz:   8.348  0.104  0.259 85.143  0.040  2.133   1.7130e-01
   2_adp:   8.348  0.104  0.259 85.143  0.040  2.133   1.7130e-01
   2_occ:   8.348  0.104  0.259 85.143  0.040  2.133   1.7130e-01
   3_bss:   8.348  0.104  0.259 85.143  0.040  2.133   1.7130e-01
   3_xyz:   8.154  0.084  0.293 87.500  0.045  2.230   7.0496e-02
   3_adp:   8.154  0.084  0.293 87.500  0.045  2.230   7.0496e-02
   3_occ:   8.154  0.084  0.293 87.500  0.045  2.230   7.0496e-02
   4_bss:   8.154  0.084  0.293 87.500  0.045  2.230   7.0496e-02
   4_xyz:   7.915  0.066  0.556 81.096  0.033  2.215   5.0129e-02
   4_adp:   7.915  0.066  0.556 81.096  0.033  2.215   5.0129e-02
   4_occ:   7.915  0.066  0.556 81.096  0.033  2.215   5.0129e-02
   5_bss:   7.915  0.066  0.556 81.096  0.033  2.215   5.0129e-02
   5_xyz:   7.767  0.048  0.630 82.412  0.031  2.321   5.0153e-02
   5_adp:   7.767  0.048  0.630 82.412  0.031  2.321   5.0153e-02
   5_occ:   7.767  0.048  0.630 82.412  0.031  2.321   5.0153e-02
   5_bss:   7.767  0.048  0.630 82.412  0.031  2.321   5.0153e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  82.16   0.00  13.05  64.21   0.00  10.76  82.16   0.00  25.53
   1_occ:  82.16   0.00  13.05  64.21   0.00  10.76  82.16   0.00  25.53
   2_bss:  82.16   0.00  13.05  64.21   0.00  10.76  82.16   0.00  25.53
   2_xyz:  82.16   0.00  13.05  64.21   0.00  10.76  82.16   0.00  25.53
   2_adp:  82.27   0.00  12.90  73.42   0.00   9.97  82.27   0.00  28.90
   2_occ:  82.27   0.00  12.90  73.42   0.00   9.97  82.27   0.00  28.90
   3_bss:  82.27   0.00  12.90  73.42   0.00   9.97  82.27   0.00  28.90
   3_xyz:  82.27   0.00  12.90  73.42   0.00   9.97  82.27   0.00  28.90
   3_adp:  77.10   0.00  13.05  77.10   0.00   9.29  75.15   1.64  33.57
   3_occ:  77.10   0.00  13.05  77.10   0.00   9.29  75.15   1.64  33.57
   4_bss:  77.10   0.00  13.05  77.10   0.00   9.29  75.15   1.64  33.57
   4_xyz:  77.10   0.00  13.05  77.10   0.00   9.29  75.15   1.64  33.57
   4_adp:  86.58   0.00  13.57  86.58   0.00   9.12  79.64   1.75  37.80
   4_occ:  86.58   0.00  13.57  86.58   0.00   9.12  79.64   1.75  37.80
   5_bss:  86.58   0.00  13.57  86.58   0.00   9.12  79.64   1.75  37.80
   5_xyz:  86.58   0.00  13.57  86.58   0.00   9.12  79.64   1.75  37.80
   5_adp:  89.32   0.00  13.37  89.32   0.00   8.89  81.97   1.68  37.74
   5_occ:  89.32   0.00  13.37  89.32   0.00   8.89  81.97   1.68  37.74
   5_bss:  91.60   2.28  15.65  91.60   2.28  11.17  84.25   3.96  40.01
------------------------------------------------------------------------
 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:    1.130    0.021    0.411
   1_adp:    1.130    0.021    0.411
   1_occ:    1.130    0.021    0.411
   2_bss:    1.130    0.021    0.411
   2_xyz:    1.653    0.013    0.555
   2_adp:    1.653    0.013    0.555
   2_occ:    1.653    0.013    0.555
   3_bss:    1.653    0.013    0.555
   3_xyz:    1.668    0.040    0.650
   3_adp:    1.668    0.040    0.650
   3_occ:    1.668    0.040    0.650
   4_bss:    1.668    0.040    0.650
   4_xyz:    1.790    0.057    0.739
   4_adp:    1.790    0.057    0.739
   4_occ:    1.790    0.057    0.739
   5_bss:    1.790    0.057    0.739
   5_xyz:    1.864    0.047    0.763
   5_adp:    1.864    0.047    0.763
   5_occ:    1.864    0.047    0.763
   5_bss:    1.864    0.047    0.763
------------------------------------------------------------------------

CPU time actual refinement: 343.53


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_587/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_587/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_587/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_587/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_587/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.38 
  Macro-tasks:
    bulk solvent and scale       = 41.39  
    individual site refinement   = 144.05 
    weights calculation          = 32.44  
    collect and process          = 6.60   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 224.61 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 107.06 
    alpha_beta                      = 8.28   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 118.03 
    fmodel                         = 7.22   
    r_factors                      = 0.24   
    phase_errors                   = 10.53  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 255.26 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.765 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    662 calls, 106.75 s
gradients_fft:          606 calls, 104.11 s

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

# Date 2008-01-16 Time 01:56:56 PST -0800 (1200477416.43 s)
Start R-work = 0.4773, R-free = 0.4612 (no bulk solvent and anisotropic scale)
Final R-work = 0.1332, R-free = 0.1789 (no bulk solvent and anisotropic scale)

Start R-work = 0.4696, R-free = 0.4566
Final R-work = 0.1163, R-free = 0.1637