# Date 2008-01-16 Time 01:28:29 PST -0800 (1200475709.73 s)
#phil __OFF__

Command line arguments: "../442.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 = 31995
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 442

-------------------------------------------------------------------------------
  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: (69.5475, 47.3993, 85.0941, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.97128
Completeness in resolution range: 0.958929
Completeness with d_max=infinity: 0.955934

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8236
                             d_min =   1.9713

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: (69.5475, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.97128
Completeness in resolution range: 0.958929
Completeness with d_max=infinity: 0.955934

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8240 -  4.2174 [2148/2176]  1933   215  10.0%
  bin  2:  4.2174 -  3.3603 [2049/2072]  1845   204  10.0%
  bin  3:  3.3603 -  2.9393 [2039/2061]  1833   206  10.1%
  bin  4:  2.9393 -  2.6723 [2008/2027]  1814   194   9.7%
  bin  5:  2.6723 -  2.4817 [2013/2042]  1803   210  10.4%
  bin  6:  2.4817 -  2.3360 [1970/2011]  1780   190   9.6%
  bin  7:  2.3360 -  2.2194 [1982/2017]  1780   202  10.2%
  bin  8:  2.2194 -  2.1231 [1978/2017]  1778   200  10.1%
  bin  9:  2.1231 -  2.0416 [1952/1983]  1762   190   9.7%
  bin 10:  2.0416 -  1.9713 [1450/2022]  1302   148  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_442/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: 40
        2.42 -     3.04: 2209
        3.04 -     3.66: 4728
        3.66 -     4.28: 9089
        4.28 -     4.90: 12438
  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 178 " - " O   HOH Z 403 "  1.806 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.817 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.941 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.942 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28499 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_442/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_442/model_refine_001.geo

CPU time processing inputs: 9.31


============================ 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 = 69.5475 47.3993 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4624   r_free= 0.4549   ksol= 0.00   Bsol= 0.00   scale= 0.811    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.260523                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7036 0.99   1388  156 0.3774 0.3643      6.5506      6.5653|
|  2:  4.7036 -  3.7533 0.99   1348  146 0.3759 0.3785      6.7307      6.7383|
|  3:  3.7533 -  3.2848 0.99   1313  153 0.4069 0.3857      6.6313      6.6687|
|  4:  3.2848 -  2.9871 0.99   1312  137 0.4365 0.4167      6.4796      6.4377|
|  5:  2.9871 -  2.7745 0.98   1278  143 0.4834 0.4997      6.3677      6.3844|
|  6:  2.7745 -  2.6119 0.98   1292  144 0.4841 0.5489      6.2528      6.2233|
|  7:  2.6119 -  2.4817 0.99   1297  150 0.5041 0.4261      6.2477      6.1277|
|  8:  2.4817 -  2.3741 0.99   1279  134 0.5084 0.4907      6.1733      6.1656|
|  9:  2.3741 -  2.2831 0.98   1289  145 0.5210 0.5479      6.1141      6.1521|
| 10:  2.2831 -  2.2046 0.97   1249  144 0.5141 0.5152      6.1097      6.1077|
| 11:  2.2046 -  2.1358 0.98   1266  143 0.5168 0.4863       6.032      6.0397|
| 12:  2.1358 -  2.0749 0.99   1270  135 0.5320 0.5506      5.9873      6.0186|
| 13:  2.0749 -  2.0205 0.97   1259  137 0.5305 0.5381      5.8839      5.8743|
| 14:  2.0205 -  1.9713 0.62    790   92 0.5309 0.4682      5.8533      5.7354|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7036  1388   156  0.70  34.33   0.81     0.72      69379.12|
|  2:  4.7036 -  3.7533  1348   146  0.72  33.16   0.90     0.78      93590.15|
|  3:  3.7533 -  3.2848  1313   153  0.64  40.26   0.86     0.75      99090.41|
|  4:  3.2848 -  2.9871  1312   137  0.57  46.40   0.82     0.66      86536.95|
|  5:  2.9871 -  2.7745  1278   143  0.47  54.20   0.76     0.55      75633.22|
|  6:  2.7745 -  2.6119  1292   144  0.45  56.16   0.75     0.52      65022.09|
|  7:  2.6119 -  2.4817  1297   150  0.44  56.60   0.74     0.50      59275.53|
|  8:  2.4817 -  2.3741  1279   134  0.43  57.30   0.74     0.50      53166.78|
|  9:  2.3741 -  2.2831  1289   145  0.39  60.32   0.74     0.47      50202.69|
| 10:  2.2831 -  2.2046  1249   144  0.39  61.12   0.76     0.45      47779.81|
| 11:  2.2046 -  2.1358  1266   143  0.34  64.43   0.76     0.42      46228.96|
| 12:  2.1358 -  2.0749  1270   135  0.33  65.11   0.76     0.41      43579.13|
| 13:  2.0749 -  2.0205  1259   137  0.34  65.02   0.75     0.42      36573.45|
| 14:  2.0205 -  1.9713   790    92  0.41  59.03   0.73     0.47      27213.06|
|alpha:            min =        0.41 max =            0.78 mean =         0.55|
|beta:             min =    27213.06 max =        99090.41 mean =     62249.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.40|
|phase err.(test): min =        0.00 max =           89.72 mean =        53.44|
|-----------------------------------------------------------------------------|

============================== 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 = 10.970977             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.555   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.929597              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.004   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      708 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1525 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2668 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3948 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5109 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6606 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7779 |
|-----------------------------------------------------------------------------|
|-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 |       53.407 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.977 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    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 = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4690   r_free= 0.4630   ksol= 0.00   Bsol= 0.00   scale= 0.780    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.263202                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4539   r_free= 0.4470   ksol= 0.36   Bsol= 20.00   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.07,9.25,8.43,0.00,0.00,0.00); trace/3= 8.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.255347                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.030730             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.515   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.958521              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.645   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4539      final r-factor (work) = 0.3606          |
| start r-factor (free) = 0.4470      final r-factor (free) = 0.3827          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 84.8265 = 10.03 * 0.50 * 6.2646 + 1.00 * 53.4072                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.9550 = 10.03 * 0.50 * 6.1444 + 1.00 * 0.1384                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3606      final r-factor (work) = 0.3098          |
| start r-factor (free) = 0.3827      final r-factor (free) = 0.3497          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9039 = 0.96 * 1.00 * 6.1444 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7900 = 0.96 * 1.00 * 6.0253 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.31   12.06    None  None   None       |
|    all(noH): 2823   0      0.00    73.31   12.06    None  None   None       |
|    Sol.    : 438    0      0.00    73.31   27.66    None  None   None       |
|    Mac.    : 2385   0      0.00    72.11   9.19     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 -   7.331: 1313   |   5:    36.656 -  43.987:   85        |
|      1:     7.331 -  14.662:  709   |   6:    43.987 -  51.318:   45        |
|      2:    14.662 -  21.993:  340   |   7:    51.318 -  58.649:   22        |
|      3:    21.993 -  29.324:  178   |   8:    58.649 -  65.980:   12        |
|      4:    29.324 -  36.656:  115   |   9:    65.980 -  73.311:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3098 r_free = 0.3497             target_work(ml) = 5.991         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3090 r_free = 0.3497             target_work(ml) = 5.990         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3090   r_free= 0.3497   ksol= 0.36   Bsol= 20.00   scale= 1.096   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.07,9.25,8.43,0.00,0.00,0.00); trace/3= 8.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.989900                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3056   r_free= 0.3456   ksol= 0.32   Bsol= 35.31   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.76,5.62,5.53,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.990335                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.232973              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.937   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.379114              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.244  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3056      final r-factor (work) = 0.2035          |
| start r-factor (free) = 0.3456      final r-factor (free) = 0.2455          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9095 = 6.23 * 0.50 * 6.0232 + 1.00 * 0.1384                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2299 = 6.23 * 0.50 * 5.8259 + 1.00 * 0.0735                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2035      final r-factor (work) = 0.1796          |
| start r-factor (free) = 0.2455      final r-factor (free) = 0.2257          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2234 = 0.38 * 1.00 * 5.8259 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1266 = 0.38 * 1.00 * 5.5804 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.95   12.20    None  None   None       |
|    all(noH): 2823   0      0.00    74.95   12.20    None  None   None       |
|    Sol.    : 438    0      1.31    68.01   32.60    None  None   None       |
|    Mac.    : 2385   0      0.00    74.95   8.45     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.495: 1457   |   5:    37.475 -  44.970:  100        |
|      1:     7.495 -  14.990:  699   |   6:    44.970 -  52.465:   64        |
|      2:    14.990 -  22.485:  213   |   7:    52.465 -  59.960:   31        |
|      3:    22.485 -  29.980:  119   |   8:    59.960 -  67.455:   15        |
|      4:    29.980 -  37.475:  121   |   9:    67.455 -  74.951:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1796 r_free = 0.2257             target_work(ml) = 5.531         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1794 r_free = 0.2254             target_work(ml) = 5.530         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1794   r_free= 0.2254   ksol= 0.32   Bsol= 35.31   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.76,5.62,5.53,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.530389                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1769   r_free= 0.2237   ksol= 0.33   Bsol= 35.31   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,3.53,3.60,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.529333                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.421425              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.320  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.270549              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.079  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1769      final r-factor (work) = 0.1367          |
| start r-factor (free) = 0.2237      final r-factor (free) = 0.1780          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8468 = 2.42 * 0.50 * 5.5945 + 1.00 * 0.0735                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6232 = 2.42 * 0.50 * 5.4225 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1367      final r-factor (work) = 0.1298          |
| start r-factor (free) = 0.1780      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4778 = 0.27 * 1.00 * 5.4225 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4390 = 0.27 * 1.00 * 5.2754 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.29   12.28    None  None   None       |
|    all(noH): 2823   0      0.00    76.29   12.28    None  None   None       |
|    Sol.    : 438    0      1.41    65.26   34.06    None  None   None       |
|    Mac.    : 2385   0      0.00    76.29   8.28     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 -   7.629: 1520   |   5:    38.144 -  45.773:  105        |
|      1:     7.629 -  15.258:  680   |   6:    45.773 -  53.402:   72        |
|      2:    15.258 -  22.887:  175   |   7:    53.402 -  61.031:   34        |
|      3:    22.887 -  30.515:  103   |   8:    61.031 -  68.659:    9        |
|      4:    30.515 -  38.144:  121   |   9:    68.659 -  76.288:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1298 r_free = 0.1686             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1296 r_free = 0.1687             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1687   ksol= 0.33   Bsol= 35.31   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,3.53,3.60,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.249474                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1300   r_free= 0.1690   ksol= 0.32   Bsol= 35.31   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,2.91,3.08,0.00,0.00,0.00); trace/3= 2.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.251097                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.272433              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.377  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.522157              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.808  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1300      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6942 = 3.27 * 0.50 * 5.2781 + 1.00 * 0.0581                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5738 = 3.27 * 0.50 * 5.1950 + 1.00 * 0.0737                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1145      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1579      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7240 = 0.52 * 1.00 * 5.1950 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6977 = 0.52 * 1.00 * 5.1453 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.45   12.37    None  None   None       |
|    all(noH): 2823   0      0.00    81.45   12.37    None  None   None       |
|    Sol.    : 438    0      1.24    69.81   34.92    None  None   None       |
|    Mac.    : 2385   0      0.00    81.45   8.23     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 -   8.145: 1630   |   5:    40.725 -  48.871:  104        |
|      1:     8.145 -  16.290:  612   |   6:    48.871 -  57.016:   65        |
|      2:    16.290 -  24.435:  157   |   7:    57.016 -  65.161:   25        |
|      3:    24.435 -  32.580:  111   |   8:    65.161 -  73.306:    6        |
|      4:    32.580 -  40.725:  108   |   9:    73.306 -  81.451:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1579             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1579             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1579   ksol= 0.32   Bsol= 35.31   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,2.91,3.08,0.00,0.00,0.00); trace/3= 2.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145171                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1579   ksol= 0.32   Bsol= 38.68   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.82,3.09,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144893                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.638762              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.143  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.181356              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.035  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1579      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2894 = 1.64 * 0.50 * 5.1449 + 1.00 * 0.0737                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2787 = 1.64 * 0.50 * 5.1541 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9457 = 0.18 * 1.00 * 5.1541 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9454 = 0.18 * 1.00 * 5.1593 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.10   12.29    None  None   None       |
|    all(noH): 2823   0      0.00    81.10   12.29    None  None   None       |
|    Sol.    : 438    0      1.35    69.43   34.47    None  None   None       |
|    Mac.    : 2385   0      0.00    81.10   8.21     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 -   8.110: 1637   |   5:    40.549 -  48.659:  105        |
|      1:     8.110 -  16.220:  611   |   6:    48.659 -  56.769:   63        |
|      2:    16.220 -  24.330:  159   |   7:    56.769 -  64.879:   25        |
|      3:    24.330 -  32.439:  103   |   8:    64.879 -  72.988:    5        |
|      4:    32.439 -  40.549:  109   |   9:    72.988 -  81.098:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1142 r_free = 0.1570             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1142 r_free = 0.1571             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1571   ksol= 0.32   Bsol= 38.68   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.82,3.09,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155350                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7036 0.99   1388  156 0.1018 0.1272      5.3881      5.5235|
|  2:  4.7036 -  3.7533 0.99   1348  146 0.0889 0.1126      5.4529      5.6428|
|  3:  3.7533 -  3.2848 0.99   1313  153 0.1059 0.1534      5.4748      5.8553|
|  4:  3.2848 -  2.9871 0.99   1312  137 0.1238 0.1524      5.4605      5.6244|
|  5:  2.9871 -  2.7745 0.98   1278  143 0.1343 0.1592      5.3435      5.4701|
|  6:  2.7745 -  2.6119 0.98   1292  144 0.1287 0.2017      5.2369      5.4936|
|  7:  2.6119 -  2.4817 0.99   1297  150 0.1217 0.1625      5.1617      5.3941|
|  8:  2.4817 -  2.3741 0.99   1279  134 0.1191 0.1764      5.0879      5.3373|
|  9:  2.3741 -  2.2831 0.98   1289  145 0.1215 0.1798      5.0422      5.3148|
| 10:  2.2831 -  2.2046 0.97   1249  144 0.1158 0.1684        4.98      5.1813|
| 11:  2.2046 -  2.1358 0.98   1266  143 0.1194 0.1690       4.931      5.2487|
| 12:  2.1358 -  2.0749 0.99   1270  135 0.1100 0.1669      4.8577      5.1276|
| 13:  2.0749 -  2.0205 0.97   1259  137 0.1172 0.1775       4.801      5.0743|
| 14:  2.0205 -  1.9713 0.62    790   92 0.1137 0.1703      4.7268      4.9058|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7036  1388   156  0.94   8.81   0.98     0.97       6995.03|
|  2:  4.7036 -  3.7533  1348   146  0.95   8.05   1.02     1.00       8961.92|
|  3:  3.7533 -  3.2848  1313   153  0.93  11.25   1.03     1.02      10422.99|
|  4:  3.2848 -  2.9871  1312   137  0.92  13.60   1.01     0.99      10224.52|
|  5:  2.9871 -  2.7745  1278   143  0.90  15.89   0.99     0.96       8310.11|
|  6:  2.7745 -  2.6119  1292   144  0.90  16.31   0.98     0.96       7286.91|
|  7:  2.6119 -  2.4817  1297   150  0.91  15.36   0.99     0.96       6099.27|
|  8:  2.4817 -  2.3741  1279   134  0.91  15.08   1.00     0.97       5498.79|
|  9:  2.3741 -  2.2831  1289   145  0.90  15.86   1.01     0.99       5036.80|
| 10:  2.2831 -  2.2046  1249   144  0.90  15.51   1.01     0.98       4482.83|
| 11:  2.2046 -  2.1358  1266   143  0.91  15.44   1.00     0.97       4021.12|
| 12:  2.1358 -  2.0749  1270   135  0.92  14.45   1.01     1.00       3672.11|
| 13:  2.0749 -  2.0205  1259   137  0.90  16.02   1.01     1.00       3376.92|
| 14:  2.0205 -  1.9713   790    92  0.91  15.61   0.99     0.96       2844.54|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2844.54 max =        10422.99 mean =      6364.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.98|
|phase err.(test): min =        0.00 max =           86.20 mean =        13.52|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1571   ksol= 0.32   Bsol= 43.60   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.72,0.22,0.51,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155160                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1571   ksol= 0.32   Bsol= 43.60   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.72,0.22,0.51,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155160                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7036 0.99   1388  156 0.1018 0.1275       5.388      5.5245|
|  2:  4.7036 -  3.7533 0.99   1348  146 0.0891 0.1129      5.4549      5.6456|
|  3:  3.7533 -  3.2848 0.99   1313  153 0.1060 0.1534      5.4759      5.8556|
|  4:  3.2848 -  2.9871 0.99   1312  137 0.1238 0.1524      5.4604      5.6241|
|  5:  2.9871 -  2.7745 0.98   1278  143 0.1342 0.1592      5.3427      5.4695|
|  6:  2.7745 -  2.6119 0.98   1292  144 0.1286 0.2015      5.2361      5.4928|
|  7:  2.6119 -  2.4817 0.99   1297  150 0.1216 0.1625      5.1608      5.3939|
|  8:  2.4817 -  2.3741 0.99   1279  134 0.1191 0.1761      5.0872      5.3357|
|  9:  2.3741 -  2.2831 0.98   1289  145 0.1214 0.1799      5.0417      5.3147|
| 10:  2.2831 -  2.2046 0.97   1249  144 0.1158 0.1684      4.9794      5.1806|
| 11:  2.2046 -  2.1358 0.98   1266  143 0.1194 0.1689      4.9306      5.2485|
| 12:  2.1358 -  2.0749 0.99   1270  135 0.1100 0.1670      4.8574      5.1276|
| 13:  2.0749 -  2.0205 0.97   1259  137 0.1172 0.1774      4.8006      5.0739|
| 14:  2.0205 -  1.9713 0.62    790   92 0.1137 0.1702       4.726      4.9047|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7036  1388   156  0.94   8.82   0.98     0.97       7001.19|
|  2:  4.7036 -  3.7533  1348   146  0.95   8.08   1.02     1.00       8989.24|
|  3:  3.7533 -  3.2848  1313   153  0.93  11.27   1.03     1.02      10458.41|
|  4:  3.2848 -  2.9871  1312   137  0.92  13.60   1.01     0.99      10222.00|
|  5:  2.9871 -  2.7745  1278   143  0.90  15.88   0.99     0.96       8300.63|
|  6:  2.7745 -  2.6119  1292   144  0.90  16.29   0.98     0.96       7276.55|
|  7:  2.6119 -  2.4817  1297   150  0.91  15.35   0.99     0.96       6091.22|
|  8:  2.4817 -  2.3741  1279   134  0.91  15.07   1.00     0.98       5490.64|
|  9:  2.3741 -  2.2831  1289   145  0.90  15.85   1.01     0.99       5030.14|
| 10:  2.2831 -  2.2046  1249   144  0.90  15.49   1.01     0.98       4478.03|
| 11:  2.2046 -  2.1358  1266   143  0.91  15.43   1.00     0.97       4017.14|
| 12:  2.1358 -  2.0749  1270   135  0.92  14.44   1.01     1.00       3669.20|
| 13:  2.0749 -  2.0205  1259   137  0.90  16.01   1.01     1.00       3372.93|
| 14:  2.0205 -  1.9713   790    92  0.91  15.59   1.00     0.96       2838.66|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2838.66 max =        10458.41 mean =      6365.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.98|
|phase err.(test): min =        0.00 max =           85.84 mean =        13.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.59    83.69   14.88    None  None   None       |
|    all(noH): 2823   0      2.59    83.69   14.88    None  None   None       |
|    Sol.    : 438    0      3.95    72.03   37.07    None  None   None       |
|    Mac.    : 2385   0      2.59    83.69   10.81    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:     2.595 -  10.704: 1637   |   5:    43.144 -  51.253:  105        |
|      1:    10.704 -  18.814:  611   |   6:    51.253 -  59.363:   63        |
|      2:    18.814 -  26.924:  159   |   7:    59.363 -  67.473:   25        |
|      3:    26.924 -  35.034:  103   |   8:    67.473 -  75.583:    5        |
|      4:    35.034 -  43.144:  109   |   9:    75.583 -  83.693:    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)= 306         
Filter by distance & map next to the model:
   mapped sites are within: 0.413 - 4.464
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 306
   mapped sites are within: 0.710 - 4.464

peak=   10.992 closest distance to " CB  VAL A 230 " =    1.442
peak=    7.629 closest distance to " CG2 VAL A 296 " =    1.126
peak=    6.187 closest distance to " CG  LEU A   5 " =    1.281
peak=    5.847 closest distance to " NH2 ARG A  56 " =    2.197
peak=    5.503 closest distance to " CB  VAL A 296 " =    1.082
peak=    5.495 closest distance to " CB  ARG A 275 " =    0.933
peak=    5.335 closest distance to " CG  PRO A  54 " =    1.337
peak=    5.294 closest distance to " CD2 LEU A   5 " =    1.214
peak=    5.166 closest distance to " CB  GLN A 223 " =    1.384
peak=    5.006 closest distance to " CG  LEU A 228 " =    1.223
peak=    4.977 closest distance to " O   HOH Z 193 " =    1.779
peak=    4.946 closest distance to " CB  SER A  63 " =    1.191
peak=    4.900 closest distance to " CG  PRO A 213 " =    1.295
peak=    4.874 closest distance to " O   HOH Z 124 " =    1.574
peak=    4.801 closest distance to " O   HOH Z 402 " =    1.476
peak=    4.797 closest distance to " O   HOH Z 126 " =    1.904
peak=    4.750 closest distance to " C   PRO A 198 " =    1.518
peak=    4.648 closest distance to " CB  PRO A  54 " =    0.948
peak=    4.633 closest distance to " O   SER A  87 " =    2.174
peak=    4.613 closest distance to " O   HOH Z 234 " =    3.665
peak=    4.530 closest distance to " O   HOH Z 272 " =    1.926
peak=    4.517 closest distance to " O   HOH Z  44 " =    2.431
peak=    4.514 closest distance to " CB  SER A   3 " =    1.287
peak=    4.497 closest distance to " O   HOH Z  48 " =    1.702
peak=    4.483 closest distance to " CB  VAL A 230 " =    1.201
peak=    4.479 closest distance to " NE2 GLN A  11 " =    1.074
peak=    4.474 closest distance to " CG  PRO A 198 " =    1.235
peak=    4.427 closest distance to " O   HOH Z 232 " =    2.264
peak=    4.423 closest distance to " CD2 LEU A 228 " =    1.176
peak=    4.421 closest distance to " CB  GLN A 183 " =    1.287
peak=    4.419 closest distance to " O   HOH Z 423 " =    1.823
peak=    4.415 closest distance to " O   HOH Z 316 " =    2.856
peak=    4.403 closest distance to " O   HOH Z  59 " =    2.284
peak=    4.402 closest distance to " CB  GLU A 152 " =    1.137
peak=    4.394 closest distance to " CG  PRO A 280 " =    0.754
peak=    4.387 closest distance to " O   HOH Z 128 " =    2.146
peak=    4.385 closest distance to " O   HOH Z 278 " =    1.129
peak=    4.365 closest distance to " O   HOH Z  85 " =    1.459
peak=    4.346 closest distance to " CG  PRO A 243 " =    1.161
peak=    4.319 closest distance to " CA  TYR A  30 " =    0.967
peak=    4.300 closest distance to " O   HOH Z 403 " =    1.727
peak=    4.286 closest distance to " O   HOH Z 236 " =    1.826
peak=    4.260 closest distance to " O   HOH Z  97 " =    1.914
peak=    4.241 closest distance to " O   HOH Z 142 " =    1.623
peak=    4.221 closest distance to " O   HOH Z 298 " =    1.884
peak=    4.215 closest distance to " O   HOH Z  97 " =    2.517
peak=    4.212 closest distance to " CA  ALA A  21 " =    1.180
peak=    4.206 closest distance to " O   HOH Z 247 " =    1.321
peak=    4.200 closest distance to " CG1BVAL A  72 " =    1.649
peak=    4.182 closest distance to " O   HOH Z 368 " =    2.244
peak=    4.170 closest distance to " O   HOH Z  80 " =    1.688
peak=    4.154 closest distance to " CA  VAL A  41 " =    0.804
peak=    4.154 closest distance to " OD1 ASN A  69 " =    2.602
peak=    4.133 closest distance to " O   HOH Z 346 " =    1.494
peak=    4.117 closest distance to " CB  GLU A 128 " =    1.044
peak=    4.093 closest distance to " CB  ASN A 148 " =    1.329
peak=    4.081 closest distance to " ND2 ASN A 187 " =    1.626
peak=    4.057 closest distance to " O   HOH Z 345 " =    2.984
peak=    4.049 closest distance to " CB  TRP A 179 " =    1.233
peak=    4.041 closest distance to " O   HOH Z 102 " =    1.253
peak=    4.025 closest distance to " O   TRP A 274 " =    1.953
peak=    4.022 closest distance to " CB  TYR A 169 " =    0.730
peak=    3.998 closest distance to " O   HOH Z 389 " =    1.841
peak=    3.996 closest distance to " O   HOH Z 369 " =    2.166
peak=    3.993 closest distance to " O   HOH Z 130 " =    2.846
peak=    3.989 closest distance to " O   HOH Z 344 " =    2.739
peak=    3.982 closest distance to " CB  ASN A  39 " =    0.814
peak=    3.981 closest distance to " O   HOH Z  78 " =    1.625
peak=    3.978 closest distance to " O   HOH Z 411 " =    3.599
peak=    3.957 closest distance to " O   HOH Z 227 " =    1.616
peak=    3.957 closest distance to " O   HOH Z 303 " =    2.057
peak=    3.956 closest distance to " O   HOH Z 189 " =    2.510
peak=    3.948 closest distance to " O   HOH Z  48 " =    1.637
peak=    3.936 closest distance to " O   HOH Z 371 " =    3.199
peak=    3.935 closest distance to " CB  ALA A   9 " =    1.578
peak=    3.928 closest distance to " O   HOH Z 357 " =    1.959
peak=    3.905 closest distance to " O   HOH Z 426 " =    1.476
peak=    3.896 closest distance to " CB  GLU A 277 " =    3.552
peak=    3.889 closest distance to " O   HOH Z 284 " =    2.990
peak=    3.884 closest distance to " O   HOH Z 203 " =    1.696
peak=    3.884 closest distance to " N   ASN A  39 " =    1.148
peak=    3.867 closest distance to " O   HOH Z 414 " =    1.533
peak=    3.818 closest distance to " O   HOH Z 245 " =    1.437
peak=    3.813 closest distance to " O   HOH Z 197 " =    2.607
peak=    3.808 closest distance to " O   HOH Z  40 " =    1.669
peak=    3.797 closest distance to " O   HOH Z 263 " =    1.468
peak=    3.793 closest distance to " CG1 VAL A 296 " =    1.137
peak=    3.777 closest distance to " CG  ARG A  66 " =    0.976
peak=    3.775 closest distance to " CB  ARG A  79 " =    1.403
peak=    3.774 closest distance to " O   HOH Z 128 " =    1.947
peak=    3.773 closest distance to " O   HOH Z 134 " =    1.482
peak=    3.772 closest distance to " CD  ARG A 269 " =    1.045
peak=    3.751 closest distance to " CB  ARG A 139 " =    0.928
peak=    3.751 closest distance to " CG AARG A 275 " =    1.078
peak=    3.749 closest distance to " O   HOH Z  61 " =    1.592
peak=    3.743 closest distance to " NH2 ARG A 156 " =    1.105
peak=    3.737 closest distance to " O   HOH Z 416 " =    2.727
peak=    3.736 closest distance to " O   HOH Z  54 " =    1.493
peak=    3.732 closest distance to " NZ  LYS A 117 " =    3.019
peak=    3.729 closest distance to " CB  ALA A 248 " =    1.372
peak=    3.727 closest distance to " O   HOH Z 261 " =    2.041
peak=    3.726 closest distance to " CA  LYS A 117 " =    1.278
peak=    3.725 closest distance to " OD2 ASP A 286 " =    2.757
peak=    3.719 closest distance to " OG BSER A 164 " =    2.201
peak=    3.713 closest distance to " CB  PRO A 198 " =    1.000
peak=    3.711 closest distance to " CB  VAL A 265 " =    1.252
peak=    3.710 closest distance to " CA  ASP A 140 " =    1.192
peak=    3.709 closest distance to " CB  SER A  26 " =    1.674
peak=    3.702 closest distance to " CG  GLN A  77 " =    2.275
peak=    3.694 closest distance to " O   HOH Z  43 " =    2.288
peak=    3.691 closest distance to " CE1 TYR A 186 " =    1.257
peak=    3.686 closest distance to " CB  VAL A 202 " =    1.486
peak=    3.661 closest distance to " O   HOH Z 271 " =    2.526
peak=    3.656 closest distance to " CB  ALA A 295 " =    1.153
peak=    3.655 closest distance to " CD2 TRP A 179 " =    1.382
peak=    3.655 closest distance to " O   HOH Z 273 " =    2.731
peak=    3.649 closest distance to " CG1 ILE A  33 " =    1.364
peak=    3.645 closest distance to " O   HOH Z  63 " =    2.366
peak=    3.644 closest distance to " CA  ARG A  36 " =    1.076
peak=    3.643 closest distance to " CG2 THR A 221 " =    1.212
peak=    3.639 closest distance to " O   HOH Z 406 " =    1.576
peak=    3.637 closest distance to " O   HOH Z 193 " =    2.065
peak=    3.636 closest distance to " CE1 HIS A 108 " =    1.142
peak=    3.634 closest distance to " O   HOH Z 261 " =    2.097
peak=    3.621 closest distance to " CA  ASP A 191 " =    0.906
peak=    3.617 closest distance to " O   HOH Z 419 " =    1.674
peak=    3.612 closest distance to " CA  ALA A  51 " =    1.003
peak=    3.608 closest distance to " O   HOH Z 411 " =    1.800
peak=    3.606 closest distance to " OG1 THR A 294 " =    2.297
peak=    3.605 closest distance to " CG2 ILE A 120 " =    1.331
peak=    3.600 closest distance to " CD1 LEU A  96 " =    0.741
peak=    3.600 closest distance to " O   HOH Z  15 " =    2.058
peak=    3.600 closest distance to " O   HOH Z 366 " =    2.849
peak=    3.599 closest distance to " CD  LYS A 166 " =    1.325
peak=    3.588 closest distance to " O   HOH Z 421 " =    1.706
peak=    3.588 closest distance to " O   HOH Z 214 " =    2.492
peak=    3.582 closest distance to " O   HOH Z 130 " =    2.315
peak=    3.578 closest distance to " CB BVAL A  41 " =    1.027
peak=    3.577 closest distance to " CG2 ILE A  20 " =    1.447
peak=    3.577 closest distance to " OD2 ASP A 298 " =    3.972
peak=    3.571 closest distance to " CD2 HIS A  81 " =    1.112
peak=    3.565 closest distance to " CZ  PHE A 218 " =    1.069
peak=    3.563 closest distance to " O   HOH Z 367 " =    3.382
peak=    3.545 closest distance to " O   HOH Z 427 " =    2.777
peak=    3.542 closest distance to " O   HOH Z  54 " =    2.430
peak=    3.541 closest distance to " CA  ASN A 176 " =    1.046
peak=    3.537 closest distance to " OE1 GLU A   2 " =    2.107
peak=    3.536 closest distance to " NH1BARG A 190 " =    2.166
peak=    3.533 closest distance to " CB  TRP A 266 " =    0.986
peak=    3.528 closest distance to " N   ARG A 190 " =    1.018
peak=    3.526 closest distance to " CD  ARG A 159 " =    0.741
peak=    3.522 closest distance to " O   HOH Z 154 " =    1.374
peak=    3.516 closest distance to " CB  ARG A 190 " =    1.733
peak=    3.513 closest distance to " OE1 GLN A  11 " =    1.795
peak=    3.512 closest distance to " O   HOH Z 155 " =    2.901
peak=    3.510 closest distance to " NZ  LYS A  76 " =    1.271
peak=    3.508 closest distance to " O   HOH Z 420 " =    1.849
peak=    3.501 closest distance to " O   GLY A  91 " =    1.371
peak=    3.496 closest distance to " CB  SER A 273 " =    0.827
peak=    3.491 closest distance to " O   HOH Z 435 " =    1.920
peak=    3.472 closest distance to " O   HOH Z 417 " =    3.269
peak=    3.468 closest distance to " CB  ALA A 291 " =    1.304
peak=    3.466 closest distance to " O   HOH Z 280 " =    2.384
peak=    3.457 closest distance to " O   HOH Z  21 " =    1.781
peak=    3.452 closest distance to " O   HOH Z 383 " =    1.863
peak=    3.447 closest distance to " O   MET A 105 " =    1.810
peak=    3.446 closest distance to " O   HOH Z  49 " =    2.488
peak=    3.441 closest distance to " O   HOH Z 374 " =    2.545
peak=    3.440 closest distance to " O   HOH Z 313 " =    1.780
peak=    3.439 closest distance to " CA  ALA A 295 " =    1.037
peak=    3.433 closest distance to " O   ASP A 124 " =    1.247
peak=    3.432 closest distance to " CG BARG A 102 " =    1.840
peak=    3.427 closest distance to " CA  ASP A 162 " =    1.037
peak=    3.415 closest distance to " CD BLYS A 290 " =    1.091
peak=    3.412 closest distance to " NH2BARG A 145 " =    2.192
peak=    3.412 closest distance to " CA  GLN A 194 " =    1.113
peak=    3.412 closest distance to " O   HOH Z 209 " =    2.330
peak=    3.408 closest distance to " O   HOH Z 132 " =    2.850
peak=    3.407 closest distance to " CG1 VAL A 153 " =    0.990
peak=    3.399 closest distance to " O   HOH Z  68 " =    1.989
peak=    3.395 closest distance to " O   HOH Z 148 " =    3.154
peak=    3.394 closest distance to " O   HOH Z 123 " =    1.944
peak=    3.390 closest distance to " CB  ALA A   1 " =    1.275
peak=    3.385 closest distance to " CB  TYR A 169 " =    0.771
peak=    3.383 closest distance to " C   ALA A 299 " =    0.946
peak=    3.381 closest distance to " O   HOH Z 380 " =    1.949
peak=    3.380 closest distance to " CG  GLN A  58 " =    2.638
peak=    3.372 closest distance to " O   HOH Z 329 " =    3.731
peak=    3.371 closest distance to " O   HOH Z 422 " =    2.615
peak=    3.370 closest distance to " O   HOH Z 130 " =    1.142
peak=    3.370 closest distance to " O   HOH Z 327 " =    1.554
peak=    3.364 closest distance to " O   HOH Z  44 " =    1.847
peak=    3.363 closest distance to " CA  ASN A 215 " =    1.180
peak=    3.358 closest distance to " CA  ALA A 158 " =    1.205
peak=    3.357 closest distance to " O   HOH Z 250 " =    1.363
peak=    3.354 closest distance to " O   HOH Z 394 " =    1.481
peak=    3.351 closest distance to " CB  SER A 141 " =    1.008
peak=    3.345 closest distance to " CD2 LEU A 297 " =    0.941
peak=    3.344 closest distance to " OG  SER A  22 " =    2.692
peak=    3.342 closest distance to " O   HOH Z 128 " =    1.704
peak=    3.337 closest distance to " O   HOH Z  67 " =    1.701
peak=    3.337 closest distance to " O   HOH Z 251 " =    1.756
peak=    3.335 closest distance to " O   HOH Z 227 " =    2.204
peak=    3.330 closest distance to " O   HOH Z 112 " =    1.612
peak=    3.328 closest distance to " OD1 ASP A 286 " =    1.760
peak=    3.324 closest distance to " N   SER A 135 " =    1.348
peak=    3.322 closest distance to " CD  LYS A 119 " =    1.884
peak=    3.319 closest distance to " O   HOH Z 109 " =    2.503
peak=    3.318 closest distance to " CG2 ILE A 106 " =    0.795
peak=    3.317 closest distance to " CG1 ILE A  49 " =    1.532
peak=    3.315 closest distance to " O   HOH Z 423 " =    3.271
peak=    3.306 closest distance to " O   HOH Z 185 " =    1.656
peak=    3.305 closest distance to " CB  LEU A 143 " =    1.144
peak=    3.303 closest distance to " O   HOH Z  63 " =    1.631
peak=    3.298 closest distance to " O   HOH Z 250 " =    1.493
peak=    3.294 closest distance to " CB  THR A  31 " =    1.603
peak=    3.293 closest distance to " CA  THR A 264 " =    0.814
peak=    3.287 closest distance to " OG BSER A 258 " =    3.401
peak=    3.286 closest distance to " OG  SER A 276 " =    1.383
peak=    3.280 closest distance to " CG  MET A 185 " =    1.151
peak=    3.277 closest distance to " O   HOH Z  11 " =    1.329
peak=    3.275 closest distance to " O   HOH Z 261 " =    1.655
peak=    3.271 closest distance to " CB  PRO A 243 " =    1.217
peak=    3.271 closest distance to " CG2AVAL A 121 " =    2.176
peak=    3.267 closest distance to " NH1 ARG A 138 " =    1.283
peak=    3.265 closest distance to " CD1 ILE A  33 " =    1.642
peak=    3.265 closest distance to " CB  GLN A 278 " =    0.821
peak=    3.262 closest distance to " CE  LYS A 119 " =    1.008
peak=    3.262 closest distance to " CD1 LEU A 300 " =    1.163
peak=    3.261 closest distance to " OG  SER A  97 " =    2.562
peak=    3.261 closest distance to " O   HOH Z 408 " =    1.499
peak=    3.258 closest distance to " CD AARG A 102 " =    2.390
peak=    3.255 closest distance to " O   HOH Z 281 " =    4.464
peak=    3.255 closest distance to " O   HOH Z 171 " =    2.693
peak=    3.252 closest distance to " CB  GLN A 103 " =    0.846
peak=    3.250 closest distance to " O   HOH Z 345 " =    1.616
peak=    3.250 closest distance to " CZ2 TRP A 274 " =    1.606
peak=    3.242 closest distance to " O   HOH Z 244 " =    1.628
peak=    3.241 closest distance to " O   HOH Z 158 " =    3.055
peak=    3.240 closest distance to " O   HOH Z 303 " =    1.668
peak=    3.239 closest distance to " CB  ASP A 140 " =    0.753
peak=    3.238 closest distance to " O   GLN A 278 " =    1.356
peak=    3.237 closest distance to " O   HOH Z 404 " =    2.148
peak=    3.228 closest distance to " O   HOH Z 409 " =    3.621
peak=    3.226 closest distance to " CD2 TYR A  30 " =    0.828
peak=    3.225 closest distance to " CG2 VAL A 197 " =    0.996
peak=    3.224 closest distance to " O   HOH Z 362 " =    3.509
peak=    3.218 closest distance to " CA  THR A 221 " =    0.821
peak=    3.217 closest distance to " NH1 ARG A  14 " =    1.110
peak=    3.216 closest distance to " NH2 ARG A  79 " =    1.263
peak=    3.215 closest distance to " O   HOH Z  88 " =    3.061
peak=    3.208 closest distance to " NZ  LYS A 166 " =    2.912
peak=    3.204 closest distance to " CG2 VAL A 202 " =    1.148
peak=    3.203 closest distance to " O   HOH Z 337 " =    3.717
peak=    3.202 closest distance to " CB  MET A  40 " =    0.771
peak=    3.201 closest distance to " CD  GLN A 194 " =    1.554
peak=    3.194 closest distance to " CB  GLN A 205 " =    1.167
peak=    3.191 closest distance to " O   HOH Z 284 " =    1.506
peak=    3.189 closest distance to " CB  ALA A  71 " =    1.230
peak=    3.181 closest distance to " OH  TYR A 116 " =    1.071
peak=    3.179 closest distance to " O   HOH Z 248 " =    1.668
peak=    3.175 closest distance to " O   HOH Z 155 " =    1.500
peak=    3.173 closest distance to " O   HOH Z 141 " =    1.488
peak=    3.173 closest distance to " CA  ASN A 217 " =    1.393
peak=    3.172 closest distance to " O   HOH Z 299 " =    4.336
peak=    3.170 closest distance to " CB  ARG A 259 " =    1.914
peak=    3.164 closest distance to " O   HOH Z 353 " =    2.793
peak=    3.161 closest distance to " O   HOH Z 197 " =    1.896
peak=    3.157 closest distance to " CB  GLU A  46 " =    1.043
peak=    3.155 closest distance to " CG2 VAL A 257 " =    0.856
peak=    3.151 closest distance to " O   HOH Z 359 " =    1.429
peak=    3.150 closest distance to " O   ALA A 158 " =    1.324
peak=    3.144 closest distance to " CA  VAL A 126 " =    0.913
peak=    3.144 closest distance to " CG  LEU A 167 " =    1.125
peak=    3.143 closest distance to " O   HOH Z 236 " =    1.629
peak=    3.143 closest distance to " CB  SER A 216 " =    0.710
peak=    3.139 closest distance to " O   HOH Z 438 " =    2.114
peak=    3.139 closest distance to " O   HOH Z 180 " =    2.155
peak=    3.129 closest distance to " CB  MET A  47 " =    1.059
peak=    3.126 closest distance to " C   ALA A   1 " =    1.758
peak=    3.119 closest distance to " CB  ILE A 120 " =    1.451
peak=    3.119 closest distance to " OD1 ASN A  45 " =    1.406
peak=    3.116 closest distance to " O   HOH Z   9 " =    2.104
peak=    3.111 closest distance to " O   HOH Z 151 " =    1.737
peak=    3.105 closest distance to " CB  ALA A 242 " =    0.901
peak=    3.097 closest distance to " O   HOH Z 147 " =    1.742
peak=    3.096 closest distance to " O   HOH Z 292 " =    1.577
peak=    3.091 closest distance to " O   HOH Z 162 " =    2.023
peak=    3.089 closest distance to " CA  LYS A 290 " =    1.188
peak=    3.085 closest distance to " O   HOH Z 271 " =    1.530
peak=    3.083 closest distance to " O   HOH Z 132 " =    0.834
peak=    3.075 closest distance to " O   HOH Z  46 " =    1.482
peak=    3.073 closest distance to " O   HOH Z 291 " =    1.650
peak=    3.067 closest distance to " O   HOH Z 163 " =    1.328
peak=    3.064 closest distance to " OD2 ASP A 200 " =    1.409
peak=    3.057 closest distance to " CB  ALA A  84 " =    1.248
peak=    3.056 closest distance to " CB  ASN A 215 " =    1.080
peak=    3.053 closest distance to " N   ARG A 156 " =    1.353
peak=    3.052 closest distance to " CG  GLN A  89 " =    1.523
peak=    3.049 closest distance to " CH2 TRP A 274 " =    2.041
peak=    3.049 closest distance to " O   HOH Z  43 " =    2.783
peak=    3.042 closest distance to " O   HOH Z  59 " =    2.298

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.562 - 5.335
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 202
   mapped sites are within: 0.711 - 5.335

peak=   -5.538 closest distance to " CG2 VAL A 230 " =    0.711
peak=   -4.577 closest distance to " CD  ARG A 156 " =    2.036
peak=   -4.492 closest distance to " O   HOH Z 290 " =    1.010
peak=   -4.352 closest distance to " O   PRO A 163 " =    2.077
peak=   -4.322 closest distance to " O   HOH Z 166 " =    1.808
peak=   -4.321 closest distance to " SG  CYS A 254 " =    3.206
peak=   -4.274 closest distance to " O   HOH Z 351 " =    1.460
peak=   -4.272 closest distance to " CG2BVAL A  41 " =    2.684
peak=   -4.263 closest distance to " C   HIS A 108 " =    1.201
peak=   -4.209 closest distance to " O   HOH Z 266 " =    4.538
peak=   -4.198 closest distance to " CD1 LEU A 101 " =    2.502
peak=   -4.159 closest distance to " CG  ASP A 231 " =    0.858
peak=   -4.151 closest distance to " CB  ALA A 161 " =    2.504
peak=   -4.125 closest distance to " CE2 TYR A  30 " =    2.821
peak=   -4.105 closest distance to " O   HOH Z  13 " =    1.507
peak=   -4.073 closest distance to " OXT GLY A 302 " =    2.737
peak=   -4.010 closest distance to " ND2 ASN A  45 " =    0.980
peak=   -3.918 closest distance to " O   HOH Z  11 " =    1.892
peak=   -3.899 closest distance to " C   THR A 279 " =    1.223
peak=   -3.823 closest distance to " OE1 GLN A 223 " =    2.314
peak=   -3.793 closest distance to " CD  LYS A 289 " =    2.554
peak=   -3.778 closest distance to " N   ALA A 226 " =    1.924
peak=   -3.777 closest distance to " OG ASER A 134 " =    1.299
peak=   -3.767 closest distance to " N   GLN A  58 " =    1.919
peak=   -3.767 closest distance to " O   HOH Z 196 " =    2.144
peak=   -3.762 closest distance to " O   PRO A 198 " =    1.194
peak=   -3.759 closest distance to " OG BSER A 134 " =    1.278
peak=   -3.759 closest distance to " O   HOH Z  37 " =    1.928
peak=   -3.757 closest distance to " O   HOH Z 231 " =    2.102
peak=   -3.729 closest distance to " NH2 ARG A  66 " =    1.525
peak=   -3.698 closest distance to " N   THR A 157 " =    1.555
peak=   -3.696 closest distance to " NH2AARG A 275 " =    4.881
peak=   -3.683 closest distance to " O   ALA A 161 " =    1.656
peak=   -3.683 closest distance to " O   HOH Z  71 " =    1.105
peak=   -3.678 closest distance to " O   HOH Z 423 " =    2.227
peak=   -3.659 closest distance to " O   HOH Z 407 " =    2.937
peak=   -3.656 closest distance to " O   HOH Z  17 " =    1.231
peak=   -3.653 closest distance to " CD  GLN A  58 " =    1.277
peak=   -3.650 closest distance to " CB  PRO A 243 " =    2.642
peak=   -3.649 closest distance to " C   MET A 188 " =    1.591
peak=   -3.643 closest distance to " CB  ALA A 248 " =    1.957
peak=   -3.641 closest distance to " CD2 LEU A 300 " =    2.735
peak=   -3.630 closest distance to " CB  TYR A  15 " =    2.223
peak=   -3.627 closest distance to " NH2 ARG A  79 " =    1.934
peak=   -3.624 closest distance to " O   VAL A  67 " =    2.507
peak=   -3.622 closest distance to " O   SER A 210 " =    1.944
peak=   -3.615 closest distance to " OG  SER A  97 " =    2.316
peak=   -3.607 closest distance to " O   ALA A 256 " =    1.505
peak=   -3.603 closest distance to " N   ALA A 248 " =    1.736
peak=   -3.601 closest distance to " ND2 ASN A 187 " =    1.627
peak=   -3.567 closest distance to " CG  GLU A 277 " =    1.133
peak=   -3.556 closest distance to " CB  GLN A  11 " =    1.745
peak=   -3.548 closest distance to " O   HOH Z  52 " =    1.642
peak=   -3.542 closest distance to " O   HOH Z 426 " =    1.781
peak=   -3.542 closest distance to " CB  ASN A  39 " =    2.133
peak=   -3.538 closest distance to " CE  MET A 105 " =    2.147
peak=   -3.537 closest distance to " CG2 VAL A 296 " =    0.928
peak=   -3.536 closest distance to " O   GLY A 196 " =    1.061
peak=   -3.536 closest distance to " CG  GLU A  53 " =    1.448
peak=   -3.525 closest distance to " C   ALA A 158 " =    1.242
peak=   -3.517 closest distance to " O   HOH Z 165 " =    1.971
peak=   -3.511 closest distance to " OG  SER A  62 " =    1.386
peak=   -3.507 closest distance to " O   MET A  40 " =    2.727
peak=   -3.507 closest distance to " O   HOH Z  63 " =    1.011
peak=   -3.500 closest distance to " CD  GLN A  88 " =    1.078
peak=   -3.498 closest distance to " O   HOH Z 118 " =    3.047
peak=   -3.495 closest distance to " N   SER A 276 " =    1.292
peak=   -3.493 closest distance to " OG BSER A 134 " =    1.682
peak=   -3.490 closest distance to " CH2 TRP A 179 " =    1.317
peak=   -3.489 closest distance to " O   HOH Z  92 " =    1.592
peak=   -3.488 closest distance to " CD1 PHE A  59 " =    2.201
peak=   -3.479 closest distance to " O   HOH Z 123 " =    2.391
peak=   -3.469 closest distance to " O   HOH Z 151 " =    1.443
peak=   -3.465 closest distance to " CZ  TYR A 169 " =    1.820
peak=   -3.461 closest distance to " O   HOH Z  44 " =    2.161
peak=   -3.458 closest distance to " CG  ASP A  50 " =    2.448
peak=   -3.454 closest distance to " CG  LYS A 193 " =    2.280
peak=   -3.453 closest distance to " O   ASN A  45 " =    1.864
peak=   -3.451 closest distance to " O   HOH Z 150 " =    1.781
peak=   -3.451 closest distance to " O   HOH Z 353 " =    2.162
peak=   -3.448 closest distance to " CD2 LEU A 237 " =    2.673
peak=   -3.448 closest distance to " N   THR A 235 " =    1.268
peak=   -3.440 closest distance to " O   HOH Z 292 " =    4.311
peak=   -3.429 closest distance to " O   HOH Z 174 " =    4.355
peak=   -3.428 closest distance to " O   HOH Z 234 " =    4.123
peak=   -3.426 closest distance to " CB  PRO A 163 " =    2.753
peak=   -3.424 closest distance to " O   GLY A  80 " =    2.399
peak=   -3.424 closest distance to " O   HOH Z 431 " =    1.892
peak=   -3.423 closest distance to " CA  ASP A 298 " =    1.054
peak=   -3.423 closest distance to " CG1 VAL A 296 " =    1.197
peak=   -3.422 closest distance to " O   HOH Z 377 " =    2.153
peak=   -3.421 closest distance to " O   HOH Z 311 " =    3.483
peak=   -3.409 closest distance to " CD  ARG A 139 " =    1.631
peak=   -3.405 closest distance to " OXT GLY A 302 " =    3.425
peak=   -3.403 closest distance to " CD2 TYR A 293 " =    2.081
peak=   -3.401 closest distance to " CD1 PHE A  59 " =    1.919
peak=   -3.395 closest distance to " CG1 VAL A 112 " =    2.664
peak=   -3.393 closest distance to " OG  SER A   3 " =    1.613
peak=   -3.392 closest distance to " CB  ASP A 162 " =    2.479
peak=   -3.390 closest distance to " CE2 PHE A 218 " =    2.705
peak=   -3.387 closest distance to " O   SER A  95 " =    1.568
peak=   -3.387 closest distance to " O   HOH Z  43 " =    1.812
peak=   -3.386 closest distance to " NE2 GLN A  88 " =    2.057
peak=   -3.382 closest distance to " CB  PHE A 192 " =    1.989
peak=   -3.380 closest distance to " O  BHOH Z 338 " =    1.356
peak=   -3.375 closest distance to " CB  ALA A 291 " =    2.328
peak=   -3.366 closest distance to " CE  LYS A 166 " =    3.051
peak=   -3.365 closest distance to " O   ASN A 187 " =    1.499
peak=   -3.365 closest distance to " CD1 LEU A 228 " =    2.214
peak=   -3.361 closest distance to " O   HOH Z 411 " =    1.537
peak=   -3.358 closest distance to " O   HOH Z 136 " =    2.103
peak=   -3.352 closest distance to " O   HOH Z 222 " =    1.404
peak=   -3.349 closest distance to " CE3 TRP A 150 " =    1.867
peak=   -3.346 closest distance to " O   HOH Z 185 " =    2.399
peak=   -3.344 closest distance to " C   ASP A 231 " =    2.491
peak=   -3.343 closest distance to " CG2 ILE A 263 " =    2.275
peak=   -3.334 closest distance to " N   ALA A 248 " =    2.465
peak=   -3.332 closest distance to " O   HOH Z  11 " =    1.732
peak=   -3.315 closest distance to " N   HIS A 115 " =    2.097
peak=   -3.312 closest distance to " O   VAL A 125 " =    2.238
peak=   -3.309 closest distance to " O   HOH Z 193 " =    1.646
peak=   -3.308 closest distance to " CA  GLY A 133 " =    2.245
peak=   -3.307 closest distance to " N   LEU A 281 " =    1.892
peak=   -3.300 closest distance to " CA  GLY A 133 " =    1.979
peak=   -3.300 closest distance to " CG1 VAL A 112 " =    2.631
peak=   -3.296 closest distance to " CG  TRP A 266 " =    1.930
peak=   -3.292 closest distance to " OG BSER A 210 " =    2.187
peak=   -3.281 closest distance to " ND2 ASN A  69 " =    1.554
peak=   -3.279 closest distance to " CD1 LEU A  25 " =    2.497
peak=   -3.276 closest distance to " CG  ARG A 219 " =    2.725
peak=   -3.271 closest distance to " OG1 THR A  82 " =    1.284
peak=   -3.271 closest distance to " CB  ALA A 248 " =    2.290
peak=   -3.270 closest distance to " CA  VAL A 296 " =    0.928
peak=   -3.269 closest distance to " O   HOH Z 427 " =    1.408
peak=   -3.266 closest distance to " O   SER A 146 " =    0.919
peak=   -3.263 closest distance to " O   HOH Z 250 " =    1.400
peak=   -3.263 closest distance to " O   ALA A  51 " =    1.485
peak=   -3.262 closest distance to " O   HOH Z 166 " =    1.851
peak=   -3.256 closest distance to " N   VAL A 230 " =    1.099
peak=   -3.256 closest distance to " O   VAL A 197 " =    1.276
peak=   -3.254 closest distance to " N   GLN A  77 " =    1.376
peak=   -3.244 closest distance to " CG  GLU A   2 " =    1.753
peak=   -3.244 closest distance to " CB  ALA A 291 " =    2.201
peak=   -3.243 closest distance to " ND2 ASN A  39 " =    1.179
peak=   -3.241 closest distance to " CG  MET A 105 " =    0.856
peak=   -3.241 closest distance to " CG  LEU A 228 " =    0.961
peak=   -3.235 closest distance to " O   PHE A 218 " =    1.683
peak=   -3.232 closest distance to " NZ  LYS A 119 " =    3.455
peak=   -3.232 closest distance to " CE BMET A  47 " =    1.636
peak=   -3.229 closest distance to " CZ  PHE A 130 " =    0.935
peak=   -3.226 closest distance to " CB  ASN A  69 " =    1.063
peak=   -3.226 closest distance to " OD1 ASN A 249 " =    1.268
peak=   -3.224 closest distance to " O   HOH Z  97 " =    1.369
peak=   -3.222 closest distance to " CD2 LEU A 167 " =    1.713
peak=   -3.221 closest distance to " O   HOH Z 252 " =    4.101
peak=   -3.217 closest distance to " C   VAL A 265 " =    0.785
peak=   -3.216 closest distance to " CG  PHE A 283 " =    2.694
peak=   -3.215 closest distance to " O   HOH Z 313 " =    1.148
peak=   -3.211 closest distance to " O   HOH Z 265 " =    2.030
peak=   -3.200 closest distance to " O   HOH Z  47 " =    1.499
peak=   -3.200 closest distance to " OG  SER A  26 " =    1.282
peak=   -3.193 closest distance to " CB  ALA A  10 " =    2.226
peak=   -3.190 closest distance to " O   HOH Z 191 " =    5.335
peak=   -3.186 closest distance to " CB  PHE A 208 " =    2.291
peak=   -3.185 closest distance to " OD2 ASP A 171 " =    2.294
peak=   -3.176 closest distance to " O   HOH Z 414 " =    1.892
peak=   -3.174 closest distance to " O   HOH Z 422 " =    1.523
peak=   -3.167 closest distance to " O   HOH Z 435 " =    2.703
peak=   -3.166 closest distance to " O   ALA A 160 " =    1.480
peak=   -3.163 closest distance to " CD1 ILE A 199 " =    2.478
peak=   -3.156 closest distance to " O   LYS A 117 " =    1.603
peak=   -3.156 closest distance to " N   GLY A  23 " =    2.036
peak=   -3.151 closest distance to " N   SER A 206 " =    1.880
peak=   -3.148 closest distance to " CG  ARG A 269 " =    2.227
peak=   -3.145 closest distance to " O   TRP A  92 " =    1.841
peak=   -3.140 closest distance to " N   SER A 271 " =    1.407
peak=   -3.140 closest distance to " O   HOH Z 297 " =    2.745
peak=   -3.139 closest distance to " CB  CYS A 254 " =    2.534
peak=   -3.136 closest distance to " CB  VAL A 296 " =    1.108
peak=   -3.135 closest distance to " O   HOH Z 389 " =    1.689
peak=   -3.128 closest distance to " O   HOH Z  19 " =    2.108
peak=   -3.125 closest distance to " O   PRO A 198 " =    1.236
peak=   -3.121 closest distance to " O   LEU A 167 " =    1.557
peak=   -3.118 closest distance to " O   HOH Z 283 " =    1.783
peak=   -3.118 closest distance to " CB  SER A 210 " =    1.292
peak=   -3.115 closest distance to " O   HOH Z 360 " =    2.563
peak=   -3.114 closest distance to " O   HOH Z 339 " =    1.804
peak=   -3.103 closest distance to " O   HOH Z 377 " =    1.760
peak=   -3.101 closest distance to " CG2 VAL A 189 " =    2.009
peak=   -3.093 closest distance to " O   ASP A 107 " =    1.414
peak=   -3.091 closest distance to " O   VAL A 174 " =    1.987
peak=   -3.079 closest distance to " CD  ARG A 195 " =    5.097
peak=   -3.068 closest distance to " OD1 ASP A 200 " =    1.289
peak=   -3.052 closest distance to " NE1 TRP A 266 " =    2.322
peak=   -3.045 closest distance to " O   HOH Z 198 " =    2.079
peak=   -3.045 closest distance to " O   HOH Z 429 " =    2.145
peak=   -3.042 closest distance to " OG  SER A  63 " =    1.124
peak=   -3.016 closest distance to " CG  GLN A  11 " =    1.257

================= 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    :  0.4624 0.4549   6.260523e+00   6.250596e+00
   1_bss:  0.4539 0.4470   6.255347e+00   6.238762e+00
   1_xyz:  0.3606 0.3827   6.105167e+00   6.146731e+00
   1_adp:  0.3098 0.3497   5.990948e+00   6.086566e+00
   1_occ:  0.3090 0.3497   5.989900e+00   6.086309e+00
   2_bss:  0.3056 0.3456   5.990335e+00   6.083880e+00
   2_xyz:  0.2035 0.2455   5.644148e+00   5.811901e+00
   2_adp:  0.1796 0.2257   5.531304e+00   5.718929e+00
   2_occ:  0.1794 0.2254   5.530389e+00   5.718371e+00
   3_bss:  0.1769 0.2237   5.529333e+00   5.715414e+00
   3_xyz:  0.1367 0.1780   5.300000e+00   5.507444e+00
   3_adp:  0.1298 0.1686   5.250302e+00   5.458499e+00
   3_occ:  0.1296 0.1687   5.249474e+00   5.458103e+00
   4_bss:  0.1300 0.1690   5.251097e+00   5.457894e+00
   4_xyz:  0.1145 0.1579   5.156983e+00   5.391517e+00
   4_adp:  0.1119 0.1579   5.145424e+00   5.390418e+00
   4_occ:  0.1118 0.1579   5.145171e+00   5.390458e+00
   5_bss:  0.1118 0.1579   5.144893e+00   5.390321e+00
   5_xyz:  0.1134 0.1580   5.156280e+00   5.394348e+00
   5_adp:  0.1142 0.1570   5.155307e+00   5.387892e+00
   5_occ:  0.1142 0.1571   5.155350e+00   5.388265e+00
   5_bss:  0.1142 0.1571   5.155160e+00   5.388166e+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:  0.359  20.001   7.067   9.246   8.428   0.000   0.000   0.000
   1_xyz:  0.359  20.001   7.067   9.246   8.428   0.000   0.000   0.000
   1_adp:  0.359  20.001   7.067   9.246   8.428   0.000   0.000   0.000
   1_occ:  0.359  20.001   7.067   9.246   8.428   0.000   0.000   0.000
   2_bss:  0.318  35.306   3.756   5.622   5.527   0.000   0.000   0.000
   2_xyz:  0.318  35.306   3.756   5.622   5.527   0.000   0.000   0.000
   2_adp:  0.318  35.306   3.756   5.622   5.527   0.000   0.000   0.000
   2_occ:  0.318  35.306   3.756   5.622   5.527   0.000   0.000   0.000
   3_bss:  0.326  35.306   2.151   3.534   3.604   0.000   0.000   0.000
   3_xyz:  0.326  35.306   2.151   3.534   3.604   0.000   0.000   0.000
   3_adp:  0.326  35.306   2.151   3.534   3.604   0.000   0.000   0.000
   3_occ:  0.326  35.306   2.151   3.534   3.604   0.000   0.000   0.000
   4_bss:  0.318  35.306   1.828   2.906   3.083   0.000   0.000   0.000
   4_xyz:  0.318  35.306   1.828   2.906   3.083   0.000   0.000   0.000
   4_adp:  0.318  35.306   1.828   2.906   3.083   0.000   0.000   0.000
   4_occ:  0.318  35.306   1.828   2.906   3.083   0.000   0.000   0.000
   5_bss:  0.322  38.682   1.867   2.817   3.090   0.000   0.000   0.000
   5_xyz:  0.322  38.682   1.867   2.817   3.090   0.000   0.000   0.000
   5_adp:  0.322  38.682   1.867   2.817   3.090   0.000   0.000   0.000
   5_occ:  0.322  38.682   1.867   2.817   3.090   0.000   0.000   0.000
   5_bss:  0.322  43.599  -0.725   0.218   0.506   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.405 0.4786  0.5496    62245.045
   1_bss:  53.456 0.4754  0.6922    59490.415
   1_xyz:  43.486 0.5987  0.8588    41645.114
   1_adp:  37.695 0.6695  0.9742    33697.506
   1_occ:  37.674 0.6697  0.9732    33646.752
   2_bss:  37.440 0.6724  0.8691    33328.260
   2_xyz:  25.173 0.8086  1.0076    15997.343
   2_adp:  21.912 0.8429  1.0342    12984.205
   2_occ:  21.887 0.8432  1.0341    12961.126
   3_bss:  21.805 0.8439  0.9663    12876.869
   3_xyz:  16.646 0.8923  0.9939     8050.542
   3_adp:  15.462 0.9030  0.9985     7329.231
   3_occ:  15.452 0.9031  0.9985     7328.043
   4_bss:  15.465 0.9030  0.9806     7341.866
   4_xyz:  14.133 0.9139  0.9842     6432.642
   4_adp:  14.060 0.9147  0.9814     6415.974
   4_occ:  14.055 0.9147  0.9812     6418.621
   5_bss:  14.050 0.9148  0.9810     6422.108
   5_xyz:  14.075 0.9147  0.9803     6432.236
   5_adp:  13.932 0.9159  0.9809     6357.826
   5_occ:  13.935 0.9158  0.9807     6364.207
   5_bss:  13.932 0.9159  0.9810     6364.738
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3407e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3407e+01
   1_xyz:   1.686  0.013  0.109 18.010  0.007  4.110   1.3839e-01
   1_adp:   1.686  0.013  0.109 18.010  0.007  4.110   1.3839e-01
   1_occ:   1.686  0.013  0.109 18.010  0.007  4.110   1.3839e-01
   2_bss:   1.686  0.013  0.109 18.010  0.007  4.110   1.3839e-01
   2_xyz:   1.107  0.008  0.079 16.275  0.004  4.125   7.3481e-02
   2_adp:   1.107  0.008  0.079 16.275  0.004  4.125   7.3481e-02
   2_occ:   1.107  0.008  0.079 16.275  0.004  4.125   7.3481e-02
   3_bss:   1.107  0.008  0.079 16.275  0.004  4.125   7.3481e-02
   3_xyz:   0.983  0.006  0.074 15.337  0.003  4.110   5.8102e-02
   3_adp:   0.983  0.006  0.074 15.337  0.003  4.110   5.8102e-02
   3_occ:   0.983  0.006  0.074 15.337  0.003  4.110   5.8102e-02
   4_bss:   0.983  0.006  0.074 15.337  0.003  4.110   5.8102e-02
   4_xyz:   1.135  0.008  0.090 15.733  0.004  4.112   7.3704e-02
   4_adp:   1.135  0.008  0.090 15.733  0.004  4.112   7.3704e-02
   4_occ:   1.135  0.008  0.090 15.733  0.004  4.112   7.3704e-02
   5_bss:   1.135  0.008  0.090 15.733  0.004  4.112   7.3704e-02
   5_xyz:   0.951  0.006  0.075 15.131  0.003  4.112   5.5568e-02
   5_adp:   0.951  0.006  0.075 15.131  0.003  4.112   5.5568e-02
   5_occ:   0.951  0.006  0.075 15.131  0.003  4.112   5.5568e-02
   5_bss:   0.951  0.006  0.075 15.131  0.003  4.112   5.5568e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9225e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9225e+00
   1_xyz:  15.300  0.164  0.528 86.645  0.051  2.240   1.0143e-01
   1_adp:  15.300  0.164  0.528 86.645  0.051  2.240   1.0143e-01
   1_occ:  15.300  0.164  0.528 86.645  0.051  2.240   1.0143e-01
   2_bss:  15.300  0.164  0.528 86.645  0.051  2.240   1.0143e-01
   2_xyz:   7.093  0.087  0.286 83.091  0.030  2.198   5.3449e-02
   2_adp:   7.093  0.087  0.286 83.091  0.030  2.198   5.3449e-02
   2_occ:   7.093  0.087  0.286 83.091  0.030  2.198   5.3449e-02
   3_bss:   7.093  0.087  0.286 83.091  0.030  2.198   5.3449e-02
   3_xyz:   6.834  0.057  0.471 81.172  0.026  2.338   3.9211e-02
   3_adp:   6.834  0.057  0.471 81.172  0.026  2.338   3.9211e-02
   3_occ:   6.834  0.057  0.471 81.172  0.026  2.338   3.9211e-02
   4_bss:   6.834  0.057  0.471 81.172  0.026  2.338   3.9211e-02
   4_xyz:   7.561  0.048  0.688 82.714  0.032  2.309   5.4707e-02
   4_adp:   7.561  0.048  0.688 82.714  0.032  2.309   5.4707e-02
   4_occ:   7.561  0.048  0.688 82.714  0.032  2.309   5.4707e-02
   5_bss:   7.561  0.048  0.688 82.714  0.032  2.309   5.4707e-02
   5_xyz:   6.507  0.032  0.486 81.827  0.026  2.348   3.9100e-02
   5_adp:   6.507  0.032  0.486 81.827  0.026  2.348   3.9100e-02
   5_occ:   6.507  0.032  0.486 81.827  0.026  2.348   3.9100e-02
   5_bss:   6.507  0.032  0.486 81.827  0.026  2.348   3.9100e-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:  73.31   0.00  12.06  72.11   0.00   9.19  73.31   0.00  27.66
   1_occ:  73.31   0.00  12.06  72.11   0.00   9.19  73.31   0.00  27.66
   2_bss:  73.31   0.00  12.06  72.11   0.00   9.19  73.31   0.00  27.66
   2_xyz:  73.31   0.00  12.06  72.11   0.00   9.19  73.31   0.00  27.66
   2_adp:  74.95   0.00  12.20  74.95   0.00   8.45  68.01   1.31  32.60
   2_occ:  74.95   0.00  12.20  74.95   0.00   8.45  68.01   1.31  32.60
   3_bss:  74.95   0.00  12.20  74.95   0.00   8.45  68.01   1.31  32.60
   3_xyz:  74.95   0.00  12.20  74.95   0.00   8.45  68.01   1.31  32.60
   3_adp:  76.29   0.00  12.28  76.29   0.00   8.28  65.26   1.41  34.06
   3_occ:  76.29   0.00  12.28  76.29   0.00   8.28  65.26   1.41  34.06
   4_bss:  76.29   0.00  12.28  76.29   0.00   8.28  65.26   1.41  34.06
   4_xyz:  76.29   0.00  12.28  76.29   0.00   8.28  65.26   1.41  34.06
   4_adp:  81.45   0.00  12.37  81.45   0.00   8.23  69.81   1.24  34.92
   4_occ:  81.45   0.00  12.37  81.45   0.00   8.23  69.81   1.24  34.92
   5_bss:  81.45   0.00  12.37  81.45   0.00   8.23  69.81   1.24  34.92
   5_xyz:  81.45   0.00  12.37  81.45   0.00   8.23  69.81   1.24  34.92
   5_adp:  81.10   0.00  12.29  81.10   0.00   8.21  69.43   1.35  34.47
   5_occ:  81.10   0.00  12.29  81.10   0.00   8.21  69.43   1.35  34.47
   5_bss:  83.69   2.59  14.88  83.69   2.59  10.81  72.03   3.95  37.07
------------------------------------------------------------------------
 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:    1.200    0.024    0.414
   1_adp:    1.200    0.024    0.414
   1_occ:    1.200    0.024    0.414
   2_bss:    1.200    0.024    0.414
   2_xyz:    1.557    0.027    0.576
   2_adp:    1.557    0.027    0.576
   2_occ:    1.557    0.027    0.576
   3_bss:    1.557    0.027    0.576
   3_xyz:    1.596    0.060    0.620
   3_adp:    1.596    0.060    0.620
   3_occ:    1.596    0.060    0.620
   4_bss:    1.596    0.060    0.620
   4_xyz:    1.661    0.039    0.654
   4_adp:    1.661    0.039    0.654
   4_occ:    1.661    0.039    0.654
   5_bss:    1.661    0.039    0.654
   5_xyz:    1.763    0.071    0.659
   5_adp:    1.763    0.071    0.659
   5_occ:    1.763    0.071    0.659
   5_bss:    1.763    0.071    0.659
------------------------------------------------------------------------

CPU time actual refinement: 347.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_442/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_442/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_442/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_442/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_442/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.37 
  Macro-tasks:
    bulk solvent and scale       = 40.30  
    individual site refinement   = 145.48 
    weights calculation          = 31.96  
    collect and process          = 6.59   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 224.45 
  Micro-tasks:
    mask                            = 1.86   
    f_calc                          = 109.46 
    alpha_beta                      = 8.10   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 121.19 
    fmodel                         = 7.68   
    r_factors                      = 0.27   
    phase_errors                   = 10.70  
    foms                           = 0.33   
    TOTAL for micro-tasks          = 260.74 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.818 micro seconds
Total CPU time: 6.02 minutes
from_scatterers_fft:    672 calls, 109.16 s
gradients_fft:          616 calls, 107.45 s

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

# Date 2008-01-16 Time 01:34:30 PST -0800 (1200476070.67 s)
Start R-work = 0.4624, R-free = 0.4549 (no bulk solvent and anisotropic scale)
Final R-work = 0.1314, R-free = 0.1733 (no bulk solvent and anisotropic scale)

Start R-work = 0.4539, R-free = 0.4470
Final R-work = 0.1142, R-free = 0.1571