# Date 2008-01-16 Time 02:10:05 PST -0800 (1200478205.61 s)
#phil __OFF__

Command line arguments: "../722.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 = 23600
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 722

-------------------------------------------------------------------------------
  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: (70.25, 48.1033, 87.2539, 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: 3.28, per 1000 atoms: 1.16


================================== 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: (70.25, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0501 2.00065
Completeness in resolution range: 0.95449
Completeness with d_max=infinity: 0.951523

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0501
                             d_min =   2.0006

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: (70.25, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0501 2.00065
Completeness in resolution range: 0.95449
Completeness with d_max=infinity: 0.951523

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0505 -  4.2803 [2167/2195]  1950   217  10.0%
  bin  2:  4.2803 -  3.4104 [2053/2076]  1848   205  10.0%
  bin  3:  3.4104 -  2.9831 [2051/2073]  1846   205  10.0%
  bin  4:  2.9831 -  2.7121 [2025/2044]  1822   203  10.0%
  bin  5:  2.7121 -  2.5187 [2007/2036]  1798   209  10.4%
  bin  6:  2.5187 -  2.3708 [1996/2037]  1807   189   9.5%
  bin  7:  2.3708 -  2.2525 [1995/2030]  1796   199  10.0%
  bin  8:  2.2525 -  2.1547 [1979/2017]  1776   203  10.3%
  bin  9:  2.1547 -  2.0720 [1973/2005]  1781   192   9.7%
  bin 10:  2.0720 -  2.0006 [1343/2010]  1206   137  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_722/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 19
        2.42 -     3.04: 2157
        3.04 -     3.66: 4608
        3.66 -     4.28: 8840
        4.28 -     4.90: 12231
  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 277 " - " O   HOH Z 343 "  1.874 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.921 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.043 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.074 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27850 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_722/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_722/model_refine_001.geo

CPU time processing inputs: 9.20


============================ 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 = 70.25 48.10325 87.2539 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: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5002   r_free= 0.4851   ksol= 0.00   Bsol= 0.00   scale= 0.767    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.299571                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.7737 0.99   1399  157 0.4086 0.4178      6.6244      6.6367|
|  2:  4.7737 -  3.8093 0.99   1350  150 0.4381 0.4643      6.8587      6.9218|
|  3:  3.8093 -  3.3337 0.99   1326  150 0.4669 0.4199      6.7197      6.6552|
|  4:  3.3337 -  3.0316 0.99   1312  134 0.4948 0.4576      6.5589      6.4844|
|  5:  3.0316 -  2.8159 0.98   1291  148 0.5405 0.5205      6.3984      6.4373|
|  6:  2.8159 -  2.6508 0.98   1295  144 0.5334 0.4863      6.2965      6.1679|
|  7:  2.6508 -  2.5187 0.99   1291  156 0.5111 0.4763      6.2613      6.1748|
|  8:  2.5187 -  2.4095 0.99   1308  129 0.5228 0.4756      6.1763       6.166|
|  9:  2.4095 -  2.3171 0.98   1277  147 0.5380 0.5875      6.1197      6.1729|
| 10:  2.3171 -  2.2374 0.97   1260  142 0.5700 0.5239      6.1235      6.1301|
| 11:  2.2374 -  2.1677 0.98   1291  146 0.5415 0.5548      6.0334      6.0693|
| 12:  2.1677 -  2.1059 0.99   1275  136 0.5371 0.5268      5.9763      6.0056|
| 13:  2.1059 -  2.0506 0.97   1260  135 0.5351 0.5093      5.9006      5.8587|
| 14:  2.0506 -  2.0006 0.55    695   85 0.5559 0.5036      5.8542       5.752|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0505 -  4.7737  1399   157  0.65  39.00   0.78     0.67      87814.91|
|  2:  4.7737 -  3.8093  1350   150  0.66  39.09   0.85     0.70     122914.41|
|  3:  3.8093 -  3.3337  1326   150  0.56  47.09   0.79     0.66     127045.68|
|  4:  3.3337 -  3.0316  1312   134  0.48  53.32   0.77     0.57     106026.63|
|  5:  3.0316 -  2.8159  1291   148  0.42  58.54   0.71     0.49      82963.35|
|  6:  2.8159 -  2.6508  1295   144  0.42  58.61   0.69     0.47      68139.62|
|  7:  2.6508 -  2.5187  1291   156  0.39  60.64   0.74     0.43      63260.79|
|  8:  2.5187 -  2.4095  1308   129  0.34  64.37   0.72     0.39      60722.77|
|  9:  2.4095 -  2.3171  1277   147  0.27  69.98   0.69     0.32      60971.13|
| 10:  2.3171 -  2.2374  1260   142  0.25  71.32   0.70     0.30      55950.63|
| 11:  2.2374 -  2.1677  1291   146  0.26  70.93   0.72     0.31      51745.29|
| 12:  2.1677 -  2.1059  1275   136  0.27  69.53   0.75     0.35      46506.76|
| 13:  2.1059 -  2.0506  1260   135  0.29  68.80   0.71     0.34      38972.76|
| 14:  2.0506 -  2.0006   695    85  0.29  68.15   0.69     0.31      29020.39|
|alpha:            min =        0.30 max =            0.70 mean =         0.46|
|beta:             min =    29020.39 max =       127045.68 mean =     73541.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.40|
|phase err.(test): min =        0.00 max =           89.84 mean =        59.69|
|-----------------------------------------------------------------------------|

============================== 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 = 16.558080             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.724   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.617039              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.860   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      166 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      677 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1474 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2574 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3854 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4993 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6471 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7614 |
|-----------------------------------------------------------------------------|
|-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 |       54.445 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.772 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    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 = 12.263)------------------------------------------|
|    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: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5054   r_free= 0.4871   ksol= 0.00   Bsol= 0.00   scale= 0.739    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.301086                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4938   r_free= 0.4775   ksol= 0.30   Bsol= 20.00   scale= 0.956   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.61,12.02,8.25,0.00,0.00,0.00); trace/3= 8.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.294033                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.525874             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.768   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.436846              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.228   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4938      final r-factor (work) = 0.4241          |
| start r-factor (free) = 0.4775      final r-factor (free) = 0.4319          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 103.3416 = 15.53 * 0.50 * 6.2988 + 1.00 * 54.4447                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.5440 = 15.53 * 0.50 * 6.2351 + 1.00 * 0.1413                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4241      final r-factor (work) = 0.3827          |
| start r-factor (free) = 0.4319      final r-factor (free) = 0.4268          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9736 = 1.44 * 1.00 * 6.2351 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8902 = 1.44 * 1.00 * 6.1717 + 1.00 * 0.0224                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    120.59  15.71    None  None   None       |
|    all(noH): 2823   0      0.00    120.59  15.71    None  None   None       |
|    Sol.    : 438    0      0.00    120.59  27.68    None  None   None       |
|    Mac.    : 2385   0      0.00    78.93   13.51    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 -  12.059: 1400   |   5:    60.295 -  72.354:   18        |
|      1:    12.059 -  24.118:  823   |   6:    72.354 -  84.412:   12        |
|      2:    24.118 -  36.177:  359   |   7:    84.412 -  96.471:    3        |
|      3:    36.177 -  48.236:  160   |   8:    96.471 - 108.530:    0        |
|      4:    48.236 -  60.295:   46   |   9:   108.530 - 120.589:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3827 r_free = 0.4268             target_work(ml) = 6.160         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3820 r_free = 0.4260             target_work(ml) = 6.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3820   r_free= 0.4260   ksol= 0.30   Bsol= 20.00   scale= 1.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.61,12.02,8.25,0.00,0.00,0.00); trace/3= 8.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.159278                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3792   r_free= 0.4199   ksol= 0.30   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,7.33,4.45,0.00,0.00,0.00); trace/3= 4.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.160441                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.322025             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.133  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.505367              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.370  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3792      final r-factor (work) = 0.3161          |
| start r-factor (free) = 0.4199      final r-factor (free) = 0.3861          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.0423 = 11.32 * 0.50 * 6.1652 + 1.00 * 0.1409                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.4971 = 11.32 * 0.50 * 6.0754 + 1.00 * 0.1044                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3161      final r-factor (work) = 0.3063          |
| start r-factor (free) = 0.3861      final r-factor (free) = 0.3713          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0923 = 0.51 * 1.00 * 6.0754 + 1.00 * 0.0220                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0577 = 0.51 * 1.00 * 6.0296 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.49  14.13    None  None   None       |
|    all(noH): 2823   0      0.00    110.49  14.13    None  None   None       |
|    Sol.    : 438    0      0.00    110.49  27.76    None  None   None       |
|    Mac.    : 2385   0      0.00    67.76   11.62    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 -  11.050: 1485   |   5:    55.247 -  66.297:   25        |
|      1:    11.050 -  22.099:  781   |   6:    66.297 -  77.346:    5        |
|      2:    22.099 -  33.148:  345   |   7:    77.346 -  88.396:    4        |
|      3:    33.148 -  44.198:  134   |   8:    88.396 -  99.445:    0        |
|      4:    44.198 -  55.247:   42   |   9:    99.445 - 110.494:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3063 r_free = 0.3713             target_work(ml) = 6.020         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3062 r_free = 0.3709             target_work(ml) = 6.019         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3062   r_free= 0.3709   ksol= 0.30   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,7.33,4.45,0.00,0.00,0.00); trace/3= 4.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.019390                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3062   r_free= 0.3704   ksol= 0.32   Bsol= 69.28   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,5.27,3.15,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.020498                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.938265              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.634  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.344935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.569  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3062      final r-factor (work) = 0.2516          |
| start r-factor (free) = 0.3704      final r-factor (free) = 0.2998          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0232 = 6.94 * 0.50 * 6.0300 + 1.00 * 0.1044                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.6972 = 6.94 * 0.50 * 5.9419 + 1.00 * 0.0839                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2516      final r-factor (work) = 0.2344          |
| start r-factor (free) = 0.2998      final r-factor (free) = 0.2826          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0602 = 0.34 * 1.00 * 5.9419 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0121 = 0.34 * 1.00 * 5.8002 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.59   14.14    None  None   None       |
|    all(noH): 2823   0      0.00    97.59   14.14    None  None   None       |
|    Sol.    : 438    0      1.76    97.59   32.39    None  None   None       |
|    Mac.    : 2385   0      0.00    66.32   10.79    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 -   9.759: 1427   |   5:    48.793 -  58.551:   52        |
|      1:     9.759 -  19.517:  760   |   6:    58.551 -  68.310:   18        |
|      2:    19.517 -  29.276:  275   |   7:    68.310 -  78.069:    2        |
|      3:    29.276 -  39.034:  178   |   8:    78.069 -  87.827:    3        |
|      4:    39.034 -  48.793:  107   |   9:    87.827 -  97.586:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2344 r_free = 0.2826             target_work(ml) = 5.782         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2341 r_free = 0.2827             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2341   r_free= 0.2827   ksol= 0.32   Bsol= 69.28   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,5.27,3.15,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.781500                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2336   r_free= 0.2820   ksol= 0.32   Bsol= 62.67   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.78,3.44,2.39,0.00,0.00,0.00); trace/3= 2.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.781666                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.413681              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.429  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.330597              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.623  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2336      final r-factor (work) = 0.1743          |
| start r-factor (free) = 0.2820      final r-factor (free) = 0.2176          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7851 = 5.41 * 0.50 * 5.8006 + 1.00 * 0.0839                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4004 = 5.41 * 0.50 * 5.6552 + 1.00 * 0.0928                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1743      final r-factor (work) = 0.1586          |
| start r-factor (free) = 0.2176      final r-factor (free) = 0.2022          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8798 = 0.33 * 1.00 * 5.6552 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8162 = 0.33 * 1.00 * 5.4604 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.56   14.30    None  None   None       |
|    all(noH): 2823   0      0.00    87.56   14.30    None  None   None       |
|    Sol.    : 438    0      1.81    87.56   37.20    None  None   None       |
|    Mac.    : 2385   0      0.00    74.20   10.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.756: 1375   |   5:    43.781 -  52.538:  118        |
|      1:     8.756 -  17.513:  792   |   6:    52.538 -  61.294:   53        |
|      2:    17.513 -  26.269:  207   |   7:    61.294 -  70.050:   24        |
|      3:    26.269 -  35.025:  143   |   8:    70.050 -  78.807:    9        |
|      4:    35.025 -  43.781:  100   |   9:    78.807 -  87.563:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1586 r_free = 0.2022             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1585 r_free = 0.2025             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1585   r_free= 0.2025   ksol= 0.32   Bsol= 62.67   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.78,3.44,2.39,0.00,0.00,0.00); trace/3= 2.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.429075                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1584   r_free= 0.2024   ksol= 0.33   Bsol= 62.67   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.48,2.16,2.23,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.429097                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.976463              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.612   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347512              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.296  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1584      final r-factor (work) = 0.1337          |
| start r-factor (free) = 0.2024      final r-factor (free) = 0.1785          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9525 = 3.98 * 0.50 * 5.4620 + 1.00 * 0.0928                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7334 = 3.98 * 0.50 * 5.3544 + 1.00 * 0.0875                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1337      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.1785      final r-factor (free) = 0.1753          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8724 = 0.35 * 1.00 * 5.3544 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8542 = 0.35 * 1.00 * 5.2723 + 1.00 * 0.0220                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.93   14.26    None  None   None       |
|    all(noH): 2823   0      0.00    87.93   14.26    None  None   None       |
|    Sol.    : 438    0      2.10    87.93   38.49    None  None   None       |
|    Mac.    : 2385   0      0.00    78.17   9.81     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:     0.000 -   8.793: 1420   |   5:    43.964 -  52.757:  103        |
|      1:     8.793 -  17.586:  794   |   6:    52.757 -  61.550:   60        |
|      2:    17.586 -  26.379:  182   |   7:    61.550 -  70.343:   35        |
|      3:    26.379 -  35.172:  112   |   8:    70.343 -  79.136:   13        |
|      4:    35.172 -  43.964:  101   |   9:    79.136 -  87.929:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1285 r_free = 0.1753             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1283 r_free = 0.1753             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1753   ksol= 0.33   Bsol= 62.67   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.48,2.16,2.23,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.260098                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.7737 0.99   1399  157 0.1040 0.1370      5.4474      5.6193|
|  2:  4.7737 -  3.8093 0.99   1350  150 0.0921 0.1157       5.506      5.6924|
|  3:  3.8093 -  3.3337 0.99   1326  150 0.1209 0.1745      5.5909      5.9702|
|  4:  3.3337 -  3.0316 0.99   1312  134 0.1418 0.1781       5.571      5.7167|
|  5:  3.0316 -  2.8159 0.98   1291  148 0.1602 0.1801       5.477      5.5881|
|  6:  2.8159 -  2.6508 0.98   1295  144 0.1459 0.2296      5.3454      5.6215|
|  7:  2.6508 -  2.5187 0.99   1291  156 0.1419 0.1916      5.2912      5.5118|
|  8:  2.5187 -  2.4095 0.99   1308  129 0.1391 0.1876      5.2142      5.4237|
|  9:  2.4095 -  2.3171 0.98   1277  147 0.1387 0.1971      5.1483      5.4012|
| 10:  2.3171 -  2.2374 0.97   1260  142 0.1344 0.1925      5.0902       5.309|
| 11:  2.2374 -  2.1677 0.98   1291  146 0.1327 0.2012      5.0365      5.3383|
| 12:  2.1677 -  2.1059 0.99   1275  136 0.1266 0.1893      4.9566      5.2424|
| 13:  2.1059 -  2.0506 0.97   1260  135 0.1301 0.1815      4.8962      5.0885|
| 14:  2.0506 -  2.0006 0.55    695   85 0.1286 0.1863      4.7991       5.026|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0505 -  4.7737  1399   157  0.93  10.16   0.96     0.93       8385.42|
|  2:  4.7737 -  3.8093  1350   150  0.94   9.28   1.01     0.99      10642.76|
|  3:  3.8093 -  3.3337  1326   150  0.92  12.87   1.02     1.01      12816.35|
|  4:  3.3337 -  3.0316  1312   134  0.90  15.94   1.00     0.99      12802.50|
|  5:  3.0316 -  2.8159  1291   148  0.88  18.70   1.00     0.98      10867.14|
|  6:  2.8159 -  2.6508  1295   144  0.88  18.63   0.98     0.93       8943.24|
|  7:  2.6508 -  2.5187  1291   156  0.89  17.84   0.99     0.95       7936.06|
|  8:  2.5187 -  2.4095  1308   129  0.89  17.61   0.99     0.95       7026.71|
|  9:  2.4095 -  2.3171  1277   147  0.88  18.40   1.00     0.96       6358.47|
| 10:  2.3171 -  2.2374  1260   142  0.88  18.25   0.99     0.95       5583.56|
| 11:  2.2374 -  2.1677  1291   146  0.88  18.26   0.99     0.94       5240.11|
| 12:  2.1677 -  2.1059  1275   136  0.90  16.99   1.00     0.99       4551.24|
| 13:  2.1059 -  2.0506  1260   135  0.89  17.69   0.99     0.97       4005.20|
| 14:  2.0506 -  2.0006   695    85  0.89  17.33   0.95     0.91       3252.28|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3252.28 max =        12816.35 mean =      7939.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.88 mean =        16.17|
|phase err.(test): min =        0.00 max =           89.92 mean =        15.38|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1757   ksol= 0.33   Bsol= 64.17   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,0.31,0.71,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.260522                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1757   ksol= 0.33   Bsol= 64.17   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,0.31,0.71,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.260522                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.7737 0.99   1399  157 0.1044 0.1387      5.4497      5.6203|
|  2:  4.7737 -  3.8093 0.99   1350  150 0.0927 0.1152      5.5121      5.6979|
|  3:  3.8093 -  3.3337 0.99   1326  150 0.1213 0.1751      5.5943      5.9709|
|  4:  3.3337 -  3.0316 0.99   1312  134 0.1416 0.1785      5.5702      5.7156|
|  5:  3.0316 -  2.8159 0.98   1291  148 0.1602 0.1801      5.4771      5.5872|
|  6:  2.8159 -  2.6508 0.98   1295  144 0.1455 0.2283      5.3439      5.6191|
|  7:  2.6508 -  2.5187 0.99   1291  156 0.1418 0.1918      5.2904      5.5123|
|  8:  2.5187 -  2.4095 0.99   1308  129 0.1389 0.1877      5.2141      5.4256|
|  9:  2.4095 -  2.3171 0.98   1277  147 0.1384 0.1972      5.1478      5.4012|
| 10:  2.3171 -  2.2374 0.97   1260  142 0.1343 0.1933      5.0897      5.3107|
| 11:  2.2374 -  2.1677 0.98   1291  146 0.1324 0.2005      5.0354       5.337|
| 12:  2.1677 -  2.1059 0.99   1275  136 0.1265 0.1899      4.9562      5.2439|
| 13:  2.1059 -  2.0506 0.97   1260  135 0.1302 0.1808      4.8959      5.0875|
| 14:  2.0506 -  2.0006 0.55    695   85 0.1285 0.1856      4.7983      5.0237|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0505 -  4.7737  1399   157  0.93  10.29   0.96     0.93       8412.20|
|  2:  4.7737 -  3.8093  1350   150  0.94   9.32   1.00     0.99      10719.94|
|  3:  3.8093 -  3.3337  1326   150  0.92  12.95   1.01     1.01      12944.11|
|  4:  3.3337 -  3.0316  1312   134  0.90  15.94   1.00     0.98      12772.99|
|  5:  3.0316 -  2.8159  1291   148  0.88  18.66   0.99     0.98      10841.43|
|  6:  2.8159 -  2.6508  1295   144  0.88  18.59   0.97     0.93       8912.16|
|  7:  2.6508 -  2.5187  1291   156  0.89  17.83   0.98     0.95       7936.36|
|  8:  2.5187 -  2.4095  1308   129  0.89  17.62   0.98     0.95       7037.60|
|  9:  2.4095 -  2.3171  1277   147  0.88  18.41   0.99     0.95       6369.67|
| 10:  2.3171 -  2.2374  1260   142  0.88  18.24   0.99     0.95       5580.32|
| 11:  2.2374 -  2.1677  1291   146  0.88  18.25   0.98     0.94       5242.62|
| 12:  2.1677 -  2.1059  1275   136  0.90  16.98   0.99     0.98       4549.02|
| 13:  2.1059 -  2.0506  1260   135  0.89  17.67   0.98     0.96       3998.04|
| 14:  2.0506 -  2.0006   695    85  0.89  17.28   0.95     0.91       3234.14|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3234.14 max =        12944.11 mean =      7950.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.18|
|phase err.(test): min =        0.00 max =           89.66 mean =        15.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.263)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.50    89.42   15.76    None  None   None       |
|    all(noH): 2823   0      1.50    89.42   15.76    None  None   None       |
|    Sol.    : 438    0      3.60    89.42   39.98    None  None   None       |
|    Mac.    : 2385   0      1.50    79.67   11.31    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:     1.496 -  10.289: 1420   |   5:    45.460 -  54.253:  103        |
|      1:    10.289 -  19.082:  794   |   6:    54.253 -  63.046:   60        |
|      2:    19.082 -  27.875:  182   |   7:    63.046 -  71.839:   35        |
|      3:    27.875 -  36.667:  112   |   8:    71.839 -  80.632:   13        |
|      4:    36.667 -  45.460:  101   |   9:    80.632 -  89.425:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 331         
Filter by distance & map next to the model:
   mapped sites are within: 0.405 - 5.332
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 331
   mapped sites are within: 0.762 - 5.332

peak=    7.251 closest distance to " O   HOH Z 120 " =    1.481
peak=    7.223 closest distance to " O   HOH Z 400 " =    1.088
peak=    7.196 closest distance to " CG2 VAL A 230 " =    1.238
peak=    6.549 closest distance to " CG1 ILE A 234 " =    1.461
peak=    6.219 closest distance to " O   HOH Z 210 " =    1.617
peak=    5.639 closest distance to " CG  LEU A   5 " =    1.281
peak=    5.369 closest distance to " NH2 ARG A  56 " =    2.306
peak=    5.254 closest distance to " O   HOH Z 128 " =    1.789
peak=    5.084 closest distance to " CB  VAL A 230 " =    1.241
peak=    4.954 closest distance to " O   GLN A  11 " =    1.020
peak=    4.906 closest distance to " O   HOH Z 431 " =    1.650
peak=    4.890 closest distance to " CB  SER A  63 " =    1.212
peak=    4.857 closest distance to " O   HOH Z 425 " =    1.776
peak=    4.806 closest distance to " O   HOH Z 403 " =    2.088
peak=    4.773 closest distance to " O   HOH Z 422 " =    1.124
peak=    4.727 closest distance to " CB  VAL A 296 " =    1.452
peak=    4.669 closest distance to " O   HOH Z 124 " =    1.373
peak=    4.663 closest distance to " CG1 VAL A 296 " =    1.204
peak=    4.605 closest distance to " O   HOH Z 404 " =    1.380
peak=    4.585 closest distance to " O   HOH Z 117 " =    1.219
peak=    4.577 closest distance to " O   HOH Z 412 " =    3.257
peak=    4.575 closest distance to " O   HOH Z 144 " =    2.011
peak=    4.519 closest distance to " O   HOH Z 433 " =    2.103
peak=    4.467 closest distance to " CB  GLN A 183 " =    1.214
peak=    4.465 closest distance to " NE2 GLN A  11 " =    1.132
peak=    4.462 closest distance to " CD2 LEU A 228 " =    1.128
peak=    4.436 closest distance to " O   ASP A 124 " =    1.457
peak=    4.419 closest distance to " OD1 ASN A 301 " =    1.125
peak=    4.403 closest distance to " CD  LYS A 166 " =    1.596
peak=    4.390 closest distance to " CB  GLN A 223 " =    1.431
peak=    4.380 closest distance to " O   HOH Z 102 " =    1.467
peak=    4.375 closest distance to " O   HOH Z 139 " =    1.417
peak=    4.341 closest distance to " O   HOH Z  49 " =    1.379
peak=    4.326 closest distance to " O   HOH Z 234 " =    3.513
peak=    4.324 closest distance to " O   HOH Z 248 " =    1.736
peak=    4.321 closest distance to " CA  TYR A  30 " =    0.946
peak=    4.296 closest distance to " O   HOH Z 130 " =    2.669
peak=    4.263 closest distance to " NH2 ARG A 156 " =    1.215
peak=    4.258 closest distance to " O   HOH Z 193 " =    1.837
peak=    4.258 closest distance to " O   HOH Z  44 " =    2.185
peak=    4.248 closest distance to " O   HOH Z 426 " =    1.319
peak=    4.222 closest distance to " O   HOH Z 146 " =    1.872
peak=    4.187 closest distance to " O   HOH Z 176 " =    2.397
peak=    4.187 closest distance to " O   HOH Z  40 " =    2.113
peak=    4.182 closest distance to " CA  ARG A 195 " =    1.163
peak=    4.175 closest distance to " OE1 GLN A  55 " =    1.494
peak=    4.164 closest distance to " CG  PRO A  54 " =    1.248
peak=    4.157 closest distance to " O   HOH Z  80 " =    2.146
peak=    4.154 closest distance to " N   SER A 164 " =    0.917
peak=    4.115 closest distance to " CZ  PHE A 218 " =    1.238
peak=    4.112 closest distance to " O   HOH Z 265 " =    2.085
peak=    4.089 closest distance to " CG  PRO A 280 " =    0.873
peak=    4.088 closest distance to " CD2 TRP A 179 " =    1.290
peak=    4.076 closest distance to " CE  LYS A 119 " =    1.454
peak=    4.075 closest distance to " CB  TRP A 179 " =    1.313
peak=    4.062 closest distance to " O   HOH Z 388 " =    1.203
peak=    4.058 closest distance to " O   HOH Z 130 " =    1.130
peak=    4.053 closest distance to " O   HOH Z 417 " =    3.122
peak=    4.050 closest distance to " NE2 HIS A 115 " =    1.163
peak=    4.049 closest distance to " CG  LEU A 228 " =    1.213
peak=    4.040 closest distance to " CG AARG A 275 " =    1.185
peak=    4.030 closest distance to " O   HOH Z 126 " =    2.353
peak=    4.026 closest distance to " O   PRO A 198 " =    1.549
peak=    4.020 closest distance to " O  BHOH Z 338 " =    0.997
peak=    4.020 closest distance to " CB  PRO A  54 " =    0.900
peak=    4.018 closest distance to " CG  GLN A  77 " =    0.917
peak=    3.999 closest distance to " CB  ALA A 100 " =    1.333
peak=    3.997 closest distance to " O   HOH Z 357 " =    2.256
peak=    3.995 closest distance to " CG2 THR A 221 " =    1.129
peak=    3.988 closest distance to " CA  ALA A  51 " =    1.136
peak=    3.986 closest distance to " CB  ARG A 275 " =    0.837
peak=    3.978 closest distance to " O   HOH Z  57 " =    2.228
peak=    3.972 closest distance to " O   HOH Z 415 " =    1.727
peak=    3.968 closest distance to " O   HOH Z 261 " =    2.354
peak=    3.957 closest distance to " CG1 ILE A  33 " =    1.232
peak=    3.955 closest distance to " O   HOH Z 394 " =    1.785
peak=    3.941 closest distance to " O   HOH Z 146 " =    1.708
peak=    3.939 closest distance to " CE1 HIS A 108 " =    1.073
peak=    3.921 closest distance to " O   HOH Z 183 " =    1.714
peak=    3.916 closest distance to " O   HOH Z 423 " =    1.747
peak=    3.896 closest distance to " CB  GLU A 152 " =    1.128
peak=    3.859 closest distance to " O   HOH Z 134 " =    2.385
peak=    3.854 closest distance to " O   HOH Z 131 " =    2.328
peak=    3.842 closest distance to " CB  ASN A 148 " =    1.371
peak=    3.828 closest distance to " O   HOH Z 154 " =    1.652
peak=    3.824 closest distance to " O   HOH Z  53 " =    1.306
peak=    3.823 closest distance to " OE1 GLU A   2 " =    1.498
peak=    3.806 closest distance to " O   HOH Z 214 " =    1.479
peak=    3.793 closest distance to " O   SER A  87 " =    2.299
peak=    3.772 closest distance to " O   HOH Z 346 " =    1.646
peak=    3.772 closest distance to " O   HOH Z 227 " =    1.713
peak=    3.767 closest distance to " O   HOH Z 232 " =    2.198
peak=    3.762 closest distance to " CG  PRO A 243 " =    1.269
peak=    3.758 closest distance to " O   HOH Z 395 " =    1.486
peak=    3.758 closest distance to " O   HOH Z 196 " =    1.535
peak=    3.755 closest distance to " CG  PRO A 198 " =    1.189
peak=    3.749 closest distance to " O   HOH Z  15 " =    2.293
peak=    3.746 closest distance to " O   HOH Z 418 " =    1.719
peak=    3.741 closest distance to " CB  TRP A 266 " =    1.017
peak=    3.735 closest distance to " O   HOH Z 247 " =    1.523
peak=    3.722 closest distance to " O   ALA A 165 " =    1.318
peak=    3.720 closest distance to " O   HOH Z 142 " =    1.632
peak=    3.719 closest distance to " CB  SER A 141 " =    1.134
peak=    3.714 closest distance to " OE1 GLN A  11 " =    2.128
peak=    3.700 closest distance to " O   HOH Z 409 " =    3.720
peak=    3.684 closest distance to " CB  SER A  62 " =    0.949
peak=    3.677 closest distance to " O   HOH Z 126 " =    1.614
peak=    3.672 closest distance to " CG1 VAL A 153 " =    1.027
peak=    3.661 closest distance to " O   ASP A 200 " =    1.675
peak=    3.650 closest distance to " O   HOH Z 414 " =    1.858
peak=    3.643 closest distance to " O   HOH Z 389 " =    2.136
peak=    3.636 closest distance to " O   HOH Z  48 " =    1.868
peak=    3.625 closest distance to " CA  VAL A  41 " =    0.874
peak=    3.620 closest distance to " O   HOH Z  90 " =    3.681
peak=    3.617 closest distance to " CB  VAL A 202 " =    1.396
peak=    3.617 closest distance to " CD  PRO A  54 " =    1.051
peak=    3.616 closest distance to " O   HOH Z 343 " =    2.785
peak=    3.611 closest distance to " CG  PRO A 213 " =    1.224
peak=    3.611 closest distance to " CA  SER A  12 " =    1.406
peak=    3.604 closest distance to " O  BHOH Z  74 " =    1.323
peak=    3.595 closest distance to " O   HOH Z 280 " =    2.947
peak=    3.595 closest distance to " O   HOH Z  61 " =    1.475
peak=    3.590 closest distance to " CB  ASN A 187 " =    1.200
peak=    3.590 closest distance to " O   HOH Z  63 " =    2.434
peak=    3.587 closest distance to " CB BVAL A  41 " =    1.286
peak=    3.582 closest distance to " CB  GLU A 175 " =    1.415
peak=    3.581 closest distance to " CB  GLU A 128 " =    1.213
peak=    3.578 closest distance to " CG2 ILE A 234 " =    1.071
peak=    3.572 closest distance to " CD1 LEU A 228 " =    1.597
peak=    3.558 closest distance to " OD1 ASN A 217 " =    1.760
peak=    3.558 closest distance to " O   HOH Z  44 " =    1.752
peak=    3.554 closest distance to " O   HOH Z   4 " =    1.550
peak=    3.552 closest distance to " CD  ARG A  36 " =    1.093
peak=    3.548 closest distance to " N   ASN A  39 " =    1.216
peak=    3.544 closest distance to " O   HOH Z 427 " =    2.785
peak=    3.544 closest distance to " O   HOH Z 359 " =    1.547
peak=    3.540 closest distance to " N   ALA A 256 " =    1.050
peak=    3.539 closest distance to " CB  ASN A 285 " =    0.852
peak=    3.539 closest distance to " O   HOH Z 435 " =    1.802
peak=    3.529 closest distance to " O   HOH Z 396 " =    1.343
peak=    3.523 closest distance to " CG2 THR A 220 " =    0.799
peak=    3.522 closest distance to " CD  ARG A 159 " =    0.825
peak=    3.510 closest distance to " O   HOH Z 393 " =    3.472
peak=    3.508 closest distance to " O   HOH Z  59 " =    2.029
peak=    3.506 closest distance to " CG2 VAL A 197 " =    1.217
peak=    3.506 closest distance to " CB  LEU A 261 " =    0.964
peak=    3.506 closest distance to " CZ3 TRP A  85 " =    0.926
peak=    3.505 closest distance to " CB  ARG A 219 " =    1.591
peak=    3.504 closest distance to " NE2 GLN A 194 " =    1.553
peak=    3.501 closest distance to " CB  ARG A 275 " =    1.227
peak=    3.497 closest distance to " CD1 LEU A 101 " =    1.283
peak=    3.492 closest distance to " O   HOH Z  95 " =    1.647
peak=    3.492 closest distance to " O   HOH Z 234 " =    1.888
peak=    3.490 closest distance to " O   HOH Z 369 " =    1.634
peak=    3.488 closest distance to " O   GLY A  91 " =    1.202
peak=    3.488 closest distance to " O   HOH Z 174 " =    2.003
peak=    3.485 closest distance to " CB  ARG A  79 " =    1.060
peak=    3.485 closest distance to " O   HOH Z 299 " =    4.137
peak=    3.477 closest distance to " CA  ARG A  66 " =    0.949
peak=    3.472 closest distance to " NH1AARG A 145 " =    1.356
peak=    3.472 closest distance to " O   VAL A  72 " =    1.398
peak=    3.465 closest distance to " CG  GLN A  11 " =    1.185
peak=    3.464 closest distance to " CB  GLN A  88 " =    1.245
peak=    3.458 closest distance to " C   VAL A 265 " =    1.127
peak=    3.450 closest distance to " CA  ALA A 295 " =    1.111
peak=    3.448 closest distance to " CB  MET A 105 " =    1.289
peak=    3.445 closest distance to " O   HOH Z 150 " =    1.867
peak=    3.442 closest distance to " O   HOH Z 327 " =    1.633
peak=    3.442 closest distance to " OE1 GLN A  88 " =    0.924
peak=    3.438 closest distance to " CA  TYR A 116 " =    1.456
peak=    3.438 closest distance to " NH2 ARG A  79 " =    1.299
peak=    3.433 closest distance to " O   HOH Z 345 " =    1.815
peak=    3.431 closest distance to " NE1 TRP A  92 " =    1.569
peak=    3.423 closest distance to " O   HOH Z 189 " =    2.928
peak=    3.418 closest distance to " CB  TYR A 169 " =    0.789
peak=    3.414 closest distance to " CA  THR A 246 " =    0.954
peak=    3.414 closest distance to " O   HOH Z 273 " =    3.047
peak=    3.412 closest distance to " O   HOH Z  67 " =    2.068
peak=    3.408 closest distance to " O   HOH Z 301 " =    2.120
peak=    3.406 closest distance to " CB  SER A 210 " =    1.153
peak=    3.404 closest distance to " CE1 TYR A 186 " =    1.252
peak=    3.403 closest distance to " CB  GLU A  46 " =    1.011
peak=    3.400 closest distance to " O   PRO A 213 " =    1.400
peak=    3.397 closest distance to " CG2AVAL A 121 " =    1.811
peak=    3.397 closest distance to " CD2 TRP A 179 " =    2.305
peak=    3.396 closest distance to " CA  ASP A 191 " =    0.927
peak=    3.395 closest distance to " O   HOH Z 316 " =    3.104
peak=    3.393 closest distance to " CB  MET A  40 " =    0.768
peak=    3.391 closest distance to " O   HOH Z 189 " =    2.708
peak=    3.388 closest distance to " O   HOH Z 415 " =    1.200
peak=    3.388 closest distance to " CB  LEU A  83 " =    0.772
peak=    3.386 closest distance to " CA  ILE A 106 " =    0.762
peak=    3.382 closest distance to " O   HOH Z 162 " =    2.003
peak=    3.380 closest distance to " CG1 ILE A 120 " =    1.086
peak=    3.373 closest distance to " O   HOH Z  48 " =    2.897
peak=    3.373 closest distance to " CB  PHE A 283 " =    0.846
peak=    3.373 closest distance to " N   ASP A 162 " =    1.355
peak=    3.372 closest distance to " CG2 ILE A  20 " =    1.424
peak=    3.368 closest distance to " CB  TRP A 150 " =    1.488
peak=    3.359 closest distance to " O   HOH Z 313 " =    1.777
peak=    3.353 closest distance to " CB  THR A 235 " =    1.148
peak=    3.347 closest distance to " CD1 LEU A 300 " =    1.176
peak=    3.347 closest distance to " O   HOH Z 245 " =    1.342
peak=    3.346 closest distance to " CB  SER A  62 " =    1.043
peak=    3.343 closest distance to " CG  MET A 188 " =    0.923
peak=    3.339 closest distance to " CA  CYS A 254 " =    1.451
peak=    3.338 closest distance to " CA  ASP A 149 " =    1.099
peak=    3.338 closest distance to " CB  ALA A 248 " =    1.322
peak=    3.335 closest distance to " CG  ARG A  66 " =    0.996
peak=    3.333 closest distance to " O   HOH Z 132 " =    2.590
peak=    3.329 closest distance to " O   HOH Z 368 " =    3.220
peak=    3.325 closest distance to " CD  ARG A 195 " =    0.936
peak=    3.325 closest distance to " O   HOH Z 408 " =    2.065
peak=    3.322 closest distance to " OG  SER A 245 " =    1.515
peak=    3.321 closest distance to " OD2 ASP A 298 " =    3.433
peak=    3.317 closest distance to " CE3 TRP A  85 " =    1.148
peak=    3.314 closest distance to " O   PHE A  61 " =    1.377
peak=    3.313 closest distance to " NH2AARG A 275 " =    3.024
peak=    3.312 closest distance to " OH  TYR A 116 " =    1.404
peak=    3.311 closest distance to " CG1 ILE A  49 " =    1.668
peak=    3.311 closest distance to " CD2 LEU A 297 " =    0.944
peak=    3.310 closest distance to " CD1 LEU A 222 " =    0.768
peak=    3.310 closest distance to " O   PRO A  90 " =    1.439
peak=    3.305 closest distance to " CG2 VAL A 296 " =    0.987
peak=    3.301 closest distance to " O   HOH Z 336 " =    1.894
peak=    3.300 closest distance to " CA  ASN A 217 " =    1.257
peak=    3.300 closest distance to " O   HOH Z  39 " =    1.406
peak=    3.295 closest distance to " CB  THR A  31 " =    1.400
peak=    3.294 closest distance to " CA  GLY A 196 " =    0.893
peak=    3.294 closest distance to " O   HOH Z 420 " =    4.980
peak=    3.293 closest distance to " O   HOH Z 322 " =    2.311
peak=    3.284 closest distance to " CB  PRO A 198 " =    1.101
peak=    3.280 closest distance to " O   HOH Z 285 " =    2.658
peak=    3.278 closest distance to " CB  SER A  26 " =    1.648
peak=    3.272 closest distance to " OG1 THR A 294 " =    2.458
peak=    3.269 closest distance to " O   HOH Z 214 " =    2.346
peak=    3.267 closest distance to " OD2 ASP A 298 " =    0.835
peak=    3.267 closest distance to " CD  LYS A 119 " =    1.974
peak=    3.264 closest distance to " O   HOH Z 291 " =    1.510
peak=    3.260 closest distance to " OG ASER A 134 " =    2.924
peak=    3.259 closest distance to " O   HOH Z  26 " =    1.206
peak=    3.255 closest distance to " O   HOH Z 383 " =    2.126
peak=    3.249 closest distance to " N   ALA A   1 " =    1.165
peak=    3.249 closest distance to " O   HOH Z  43 " =    1.684
peak=    3.249 closest distance to " O   HOH Z 193 " =    2.104
peak=    3.247 closest distance to " CB  ARG A 190 " =    1.831
peak=    3.243 closest distance to " O   GLU A   2 " =    1.639
peak=    3.235 closest distance to " O   HOH Z 365 " =    2.426
peak=    3.230 closest distance to " N   ILE A  33 " =    1.084
peak=    3.227 closest distance to " CA  SER A  87 " =    0.980
peak=    3.226 closest distance to " O   ALA A 158 " =    1.345
peak=    3.226 closest distance to " O   HOH Z 251 " =    1.435
peak=    3.225 closest distance to " O   HOH Z 367 " =    1.681
peak=    3.224 closest distance to " O   HOH Z 271 " =    2.271
peak=    3.221 closest distance to " CA  CYS A 260 " =    1.566
peak=    3.220 closest distance to " CG2 THR A 279 " =    4.195
peak=    3.220 closest distance to " O   ASN A 284 " =    1.885
peak=    3.219 closest distance to " CB  TYR A  30 " =    1.042
peak=    3.219 closest distance to " CD ALYS A 290 " =    1.173
peak=    3.218 closest distance to " O   HOH Z 394 " =    4.019
peak=    3.217 closest distance to " CA  GLY A  80 " =    0.990
peak=    3.213 closest distance to " CA  LEU A  83 " =    1.387
peak=    3.213 closest distance to " O   HOH Z 406 " =    1.500
peak=    3.211 closest distance to " CB  ASN A 142 " =    1.137
peak=    3.211 closest distance to " O   HOH Z 155 " =    2.984
peak=    3.206 closest distance to " CG ALYS A 290 " =    1.013
peak=    3.204 closest distance to " CB  ALA A 242 " =    1.026
peak=    3.203 closest distance to " NH1 ARG A  14 " =    1.063
peak=    3.201 closest distance to " NH2BARG A 190 " =    1.909
peak=    3.199 closest distance to " O   ASN A  74 " =    1.590
peak=    3.195 closest distance to " CB  SER A  97 " =    0.975
peak=    3.193 closest distance to " CA  ASP A 140 " =    1.262
peak=    3.191 closest distance to " O   ARG A  14 " =    1.666
peak=    3.189 closest distance to " ND1 HIS A  81 " =    1.544
peak=    3.188 closest distance to " OG  SER A  62 " =    2.909
peak=    3.184 closest distance to " CB  SER A  97 " =    1.489
peak=    3.184 closest distance to " OG BSER A 164 " =    1.969
peak=    3.182 closest distance to " CD1 LEU A   5 " =    1.457
peak=    3.177 closest distance to " O   HOH Z 272 " =    1.981
peak=    3.176 closest distance to " CB  PHE A 204 " =    0.881
peak=    3.174 closest distance to " CG  MET A 185 " =    1.240
peak=    3.169 closest distance to " CA  ALA A 160 " =    1.002
peak=    3.168 closest distance to " N   VAL A 126 " =    1.811
peak=    3.164 closest distance to " CB  SER A  28 " =    1.079
peak=    3.162 closest distance to " CE1 TYR A  30 " =    1.050
peak=    3.161 closest distance to " CD  ARG A 269 " =    1.125
peak=    3.157 closest distance to " OE1 GLN A  58 " =    3.112
peak=    3.151 closest distance to " CD2 LEU A 228 " =    1.282
peak=    3.146 closest distance to " O   HOH Z 437 " =    2.295
peak=    3.144 closest distance to " CB  PRO A  90 " =    1.190
peak=    3.141 closest distance to " CB  SER A 288 " =    1.811
peak=    3.140 closest distance to " O   HOH Z 371 " =    3.288
peak=    3.138 closest distance to " C   ILE A 106 " =    1.842
peak=    3.134 closest distance to " O   HOH Z 214 " =    2.589
peak=    3.131 closest distance to " O   HOH Z 185 " =    1.737
peak=    3.128 closest distance to " O   HOH Z  46 " =    1.349
peak=    3.127 closest distance to " O   HOH Z 421 " =    1.769
peak=    3.126 closest distance to " O   HOH Z 419 " =    2.287
peak=    3.116 closest distance to " O   HOH Z 163 " =    2.010
peak=    3.110 closest distance to " CB  ASP A 140 " =    0.927
peak=    3.108 closest distance to " CG2 THR A  29 " =    1.535
peak=    3.104 closest distance to " CG  LYS A  76 " =    1.114
peak=    3.101 closest distance to " CB  ASN A 187 " =    2.244
peak=    3.100 closest distance to " CZ3 TRP A  92 " =    1.303
peak=    3.097 closest distance to " CG2 VAL A 126 " =    1.086
peak=    3.095 closest distance to " CG  GLU A  37 " =    0.989
peak=    3.094 closest distance to " O   HOH Z 281 " =    2.632
peak=    3.094 closest distance to " O   HOH Z 216 " =    5.332
peak=    3.090 closest distance to " CB  GLU A 277 " =    0.799
peak=    3.083 closest distance to " CB  VAL A 265 " =    1.306
peak=    3.083 closest distance to " O   HOH Z 377 " =    1.292
peak=    3.076 closest distance to " O   HOH Z  85 " =    1.983
peak=    3.075 closest distance to " O   HOH Z  54 " =    1.561
peak=    3.074 closest distance to " CG  GLN A  11 " =    0.767
peak=    3.072 closest distance to " CB  LYS A 289 " =    1.098
peak=    3.071 closest distance to " CA  ALA A  21 " =    1.240
peak=    3.069 closest distance to " CA  ASN A 249 " =    1.436
peak=    3.068 closest distance to " CB  SER A   3 " =    1.452
peak=    3.068 closest distance to " CB  ALA A  34 " =    0.847
peak=    3.067 closest distance to " CA  GLU A 128 " =    1.406
peak=    3.066 closest distance to " CB  MET A  47 " =    1.040
peak=    3.066 closest distance to " O   HOH Z 435 " =    2.662
peak=    3.061 closest distance to " CA  ALA A 100 " =    1.112
peak=    3.055 closest distance to " CB  ALA A  51 " =    0.852
peak=    3.054 closest distance to " O   HOH Z 327 " =    2.368
peak=    3.037 closest distance to " O   HOH Z   9 " =    2.408
peak=    3.032 closest distance to " CB  ALA A  71 " =    1.381
peak=    3.028 closest distance to " CZ2 TRP A 150 " =    1.150

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 226         
Filter by distance & map next to the model:
   mapped sites are within: 0.641 - 5.535
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 224 from: 226
   mapped sites are within: 0.736 - 5.535

peak=   -5.242 closest distance to " CG2 VAL A 230 " =    0.956
peak=   -5.148 closest distance to " O   HOH Z 400 " =    0.883
peak=   -4.448 closest distance to " CD1 PHE A  59 " =    1.991
peak=   -4.422 closest distance to " O   HOH Z 166 " =    1.437
peak=   -4.227 closest distance to " O   HOH Z 411 " =    5.426
peak=   -4.219 closest distance to " CD  GLN A 223 " =    1.392
peak=   -4.217 closest distance to " CG1 VAL A 112 " =    2.570
peak=   -4.148 closest distance to " CG2 ILE A  49 " =    2.686
peak=   -4.095 closest distance to " O   HOH Z 351 " =    1.716
peak=   -4.086 closest distance to " OXT GLY A 302 " =    2.897
peak=   -4.053 closest distance to " CA  ASP A 298 " =    1.054
peak=   -4.046 closest distance to " CD  ARG A  14 " =    3.301
peak=   -4.024 closest distance to " CA  SER A 276 " =    1.453
peak=   -4.016 closest distance to " CG2BVAL A  41 " =    2.944
peak=   -3.950 closest distance to " CD  GLN A 223 " =    0.819
peak=   -3.935 closest distance to " CG  ARG A 269 " =    2.387
peak=   -3.922 closest distance to " CG1 VAL A 296 " =    1.016
peak=   -3.912 closest distance to " O   HOH Z  13 " =    1.756
peak=   -3.897 closest distance to " CB  ALA A 291 " =    2.576
peak=   -3.842 closest distance to " O   HOH Z 151 " =    1.031
peak=   -3.840 closest distance to " CG1 VAL A 250 " =    2.616
peak=   -3.828 closest distance to " OG  SER A  97 " =    2.418
peak=   -3.821 closest distance to " CD  GLN A  11 " =    1.271
peak=   -3.818 closest distance to " CG  PRO A 243 " =    1.776
peak=   -3.808 closest distance to " O   HOH Z  92 " =    1.234
peak=   -3.790 closest distance to " CA  SER A 164 " =    2.127
peak=   -3.768 closest distance to " CD1 TYR A 247 " =    2.353
peak=   -3.734 closest distance to " O  BHOH Z 338 " =    1.187
peak=   -3.734 closest distance to " O   HOH Z 174 " =    1.756
peak=   -3.729 closest distance to " CD  GLN A  73 " =    0.736
peak=   -3.725 closest distance to " O   HOH Z 136 " =    2.580
peak=   -3.704 closest distance to " O   SER A  95 " =    1.996
peak=   -3.690 closest distance to " CB  ALA A 161 " =    2.539
peak=   -3.685 closest distance to " CB  ALA A  10 " =    2.046
peak=   -3.679 closest distance to " O   HOH Z 103 " =    2.001
peak=   -3.673 closest distance to " O   HOH Z   5 " =    1.726
peak=   -3.672 closest distance to " O   HOH Z 124 " =    1.557
peak=   -3.669 closest distance to " N   ALA A 226 " =    2.133
peak=   -3.651 closest distance to " O   GLN A  11 " =    1.000
peak=   -3.646 closest distance to " CG  ASP A 231 " =    0.781
peak=   -3.641 closest distance to " O   HOH Z 184 " =    1.194
peak=   -3.641 closest distance to " O   HOH Z 136 " =    1.126
peak=   -3.637 closest distance to " OD1 ASN A 148 " =    1.401
peak=   -3.636 closest distance to " CB  SER A 146 " =    2.097
peak=   -3.636 closest distance to " O   HOH Z 252 " =    3.935
peak=   -3.635 closest distance to " O   HOH Z 290 " =    0.985
peak=   -3.625 closest distance to " O   HOH Z 407 " =    1.785
peak=   -3.624 closest distance to " CB  ALA A 248 " =    2.122
peak=   -3.623 closest distance to " C   VAL A 265 " =    1.024
peak=   -3.620 closest distance to " CD2 PHE A  61 " =    2.075
peak=   -3.610 closest distance to " NZ  LYS A 119 " =    1.990
peak=   -3.604 closest distance to " O   HOH Z 137 " =    1.377
peak=   -3.600 closest distance to " O   HOH Z 407 " =    3.372
peak=   -3.597 closest distance to " CG  MET A  93 " =    2.478
peak=   -3.594 closest distance to " CG  GLN A 103 " =    2.369
peak=   -3.589 closest distance to " CG2 THR A 182 " =    2.280
peak=   -3.587 closest distance to " O   HOH Z  52 " =    2.122
peak=   -3.581 closest distance to " O   PRO A 198 " =    1.306
peak=   -3.568 closest distance to " CA  GLY A 203 " =    2.410
peak=   -3.566 closest distance to " C   GLY A 133 " =    1.245
peak=   -3.562 closest distance to " O   HOH Z 210 " =    0.890
peak=   -3.551 closest distance to " OG BSER A 210 " =    1.192
peak=   -3.548 closest distance to " O   HOH Z 109 " =    3.229
peak=   -3.548 closest distance to " OE2 GLU A 277 " =    2.868
peak=   -3.546 closest distance to " O   HOH Z  37 " =    1.411
peak=   -3.545 closest distance to " CA  VAL A 197 " =    0.948
peak=   -3.542 closest distance to " O   HOH Z  60 " =    1.924
peak=   -3.538 closest distance to " OD1 ASP A 298 " =    2.154
peak=   -3.537 closest distance to " O   HOH Z  19 " =    2.085
peak=   -3.530 closest distance to " CD1 LEU A 167 " =    2.087
peak=   -3.529 closest distance to " O   HOH Z 252 " =    1.394
peak=   -3.525 closest distance to " NH2 ARG A  66 " =    1.477
peak=   -3.524 closest distance to " O   SER A 271 " =    2.172
peak=   -3.523 closest distance to " O   HOH Z 196 " =    1.710
peak=   -3.520 closest distance to " OD1 ASN A 301 " =    0.860
peak=   -3.517 closest distance to " O   HOH Z 234 " =    4.056
peak=   -3.515 closest distance to " O   HOH Z 285 " =    1.545
peak=   -3.512 closest distance to " CE3 TRP A 150 " =    2.440
peak=   -3.510 closest distance to " O   SER A 276 " =    1.619
peak=   -3.507 closest distance to " O   HOH Z 250 " =    1.639
peak=   -3.494 closest distance to " CB  PRO A 243 " =    2.888
peak=   -3.494 closest distance to " O   HOH Z 378 " =    1.380
peak=   -3.488 closest distance to " O   HOH Z  57 " =    0.919
peak=   -3.488 closest distance to " OD2 ASP A 298 " =    0.948
peak=   -3.481 closest distance to " O   HOH Z 388 " =    1.781
peak=   -3.479 closest distance to " CG1 VAL A 197 " =    2.387
peak=   -3.474 closest distance to " O   ALA A  34 " =    2.386
peak=   -3.473 closest distance to " OG  SER A  26 " =    1.109
peak=   -3.471 closest distance to " CH2 TRP A 179 " =    1.148
peak=   -3.465 closest distance to " O   HOH Z 377 " =    2.055
peak=   -3.464 closest distance to " NH2 ARG A  36 " =    1.205
peak=   -3.463 closest distance to " CB  ALA A  43 " =    2.595
peak=   -3.453 closest distance to " OE1 GLN A  88 " =    1.231
peak=   -3.442 closest distance to " O   HOH Z 384 " =    1.894
peak=   -3.441 closest distance to " O   HOH Z 275 " =    1.570
peak=   -3.427 closest distance to " CD2 LEU A 167 " =    1.851
peak=   -3.423 closest distance to " O   HOH Z  58 " =    1.126
peak=   -3.415 closest distance to " C   THR A 279 " =    1.152
peak=   -3.408 closest distance to " NH1 ARG A 195 " =    1.146
peak=   -3.403 closest distance to " CB  SER A 210 " =    1.206
peak=   -3.402 closest distance to " NH2 ARG A  79 " =    1.957
peak=   -3.395 closest distance to " OD1 ASP A 171 " =    1.561
peak=   -3.393 closest distance to " CD1 LEU A  25 " =    2.574
peak=   -3.392 closest distance to " C   ALA A 158 " =    1.428
peak=   -3.392 closest distance to " CD  ARG A 156 " =    2.144
peak=   -3.382 closest distance to " O   HOH Z 422 " =    1.073
peak=   -3.380 closest distance to " O   HOH Z  39 " =    2.377
peak=   -3.375 closest distance to " O   HOH Z 340 " =    1.346
peak=   -3.370 closest distance to " O   HOH Z 165 " =    1.781
peak=   -3.366 closest distance to " O   HOH Z 150 " =    1.179
peak=   -3.366 closest distance to " O   HOH Z  56 " =    1.846
peak=   -3.365 closest distance to " O   HOH Z 120 " =    1.731
peak=   -3.360 closest distance to " CE2 TYR A  30 " =    2.552
peak=   -3.347 closest distance to " N   THR A 235 " =    1.243
peak=   -3.345 closest distance to " O   HOH Z 394 " =    1.710
peak=   -3.335 closest distance to " O   HOH Z 368 " =    2.001
peak=   -3.333 closest distance to " O   HOH Z 216 " =    1.494
peak=   -3.332 closest distance to " CD  PRO A 213 " =    2.192
peak=   -3.332 closest distance to " O   HOH Z 134 " =    1.915
peak=   -3.326 closest distance to " O   HOH Z 150 " =    1.632
peak=   -3.324 closest distance to " O   HOH Z 414 " =    2.005
peak=   -3.324 closest distance to " O   ASP A 107 " =    1.766
peak=   -3.323 closest distance to " O   SER A 206 " =    1.324
peak=   -3.322 closest distance to " O   HOH Z 401 " =    1.407
peak=   -3.319 closest distance to " CD2 HIS A 115 " =    1.066
peak=   -3.314 closest distance to " O   HOH Z 265 " =    1.303
peak=   -3.313 closest distance to " CZ  TYR A 169 " =    1.689
peak=   -3.311 closest distance to " OH  TYR A 247 " =    2.101
peak=   -3.309 closest distance to " O   HOH Z 422 " =    1.663
peak=   -3.305 closest distance to " CB  PHE A 192 " =    2.182
peak=   -3.305 closest distance to " OG  SER A  87 " =    1.740
peak=   -3.304 closest distance to " C   ASN A 285 " =    2.377
peak=   -3.304 closest distance to " O   HOH Z 198 " =    1.240
peak=   -3.300 closest distance to " O   HOH Z 156 " =    3.538
peak=   -3.298 closest distance to " CE2 PHE A  61 " =    2.500
peak=   -3.293 closest distance to " O   PHE A  59 " =    2.304
peak=   -3.292 closest distance to " O   HOH Z   6 " =    2.067
peak=   -3.292 closest distance to " O   HOH Z 396 " =    2.197
peak=   -3.291 closest distance to " CG  LEU A   5 " =    1.357
peak=   -3.289 closest distance to " O   TYR A  15 " =    1.686
peak=   -3.287 closest distance to " ND2 ASN A 249 " =    2.056
peak=   -3.281 closest distance to " O   HOH Z 423 " =    2.528
peak=   -3.279 closest distance to " CG1 VAL A 112 " =    2.640
peak=   -3.277 closest distance to " CG  ASP A  50 " =    2.363
peak=   -3.277 closest distance to " O   HOH Z 166 " =    1.293
peak=   -3.272 closest distance to " CD2 PHE A 225 " =    1.144
peak=   -3.269 closest distance to " CE  MET A 105 " =    2.082
peak=   -3.268 closest distance to " CA  TRP A 274 " =    1.088
peak=   -3.266 closest distance to " O   HOH Z 231 " =    1.888
peak=   -3.266 closest distance to " OG1 THR A  82 " =    1.547
peak=   -3.265 closest distance to " O   HOH Z  33 " =    2.030
peak=   -3.264 closest distance to " O   GLN A  94 " =    2.496
peak=   -3.262 closest distance to " CB  ALA A 291 " =    2.381
peak=   -3.258 closest distance to " O   HOH Z   7 " =    1.400
peak=   -3.255 closest distance to " N   VAL A 230 " =    1.045
peak=   -3.255 closest distance to " O   HOH Z 331 " =    1.270
peak=   -3.254 closest distance to " O   HOH Z 418 " =    1.473
peak=   -3.251 closest distance to " O   HOH Z 244 " =    1.947
peak=   -3.250 closest distance to " O   HOH Z 120 " =    0.816
peak=   -3.250 closest distance to " NZ  LYS A  76 " =    2.175
peak=   -3.249 closest distance to " O   ASN A 187 " =    1.717
peak=   -3.248 closest distance to " O   HOH Z 435 " =    1.446
peak=   -3.247 closest distance to " O   HOH Z 222 " =    1.390
peak=   -3.245 closest distance to " CB  ASP A 162 " =    2.552
peak=   -3.239 closest distance to " N   SER A   3 " =    2.424
peak=   -3.236 closest distance to " O   HOH Z  35 " =    1.134
peak=   -3.236 closest distance to " O   VAL A  67 " =    2.922
peak=   -3.234 closest distance to " O   HOH Z 200 " =    1.311
peak=   -3.231 closest distance to " O   HOH Z  11 " =    1.910
peak=   -3.230 closest distance to " O   HOH Z  30 " =    0.766
peak=   -3.227 closest distance to " CZ  ARG A 259 " =    0.847
peak=   -3.227 closest distance to " CG  PRO A 280 " =    2.034
peak=   -3.226 closest distance to " NE  ARG A  66 " =    4.667
peak=   -3.226 closest distance to " O   HOH Z 394 " =    5.535
peak=   -3.223 closest distance to " CG2 VAL A 112 " =    2.503
peak=   -3.220 closest distance to " CE2 PHE A 218 " =    2.531
peak=   -3.217 closest distance to " ND2 ASN A  45 " =    2.318
peak=   -3.212 closest distance to " O   HOH Z 424 " =    2.830
peak=   -3.210 closest distance to " O   HOH Z 301 " =    2.403
peak=   -3.209 closest distance to " ND2 ASN A  39 " =    1.192
peak=   -3.208 closest distance to " NE2 GLN A  58 " =    4.527
peak=   -3.203 closest distance to " CE  MET A 105 " =    2.299
peak=   -3.200 closest distance to " O   HOH Z 264 " =    1.891
peak=   -3.195 closest distance to " CG  LEU A  83 " =    2.155
peak=   -3.191 closest distance to " O   HOH Z 288 " =    1.256
peak=   -3.191 closest distance to " O   VAL A 125 " =    2.147
peak=   -3.191 closest distance to " CD  GLN A  88 " =    0.952
peak=   -3.181 closest distance to " N   ASP A 272 " =    1.211
peak=   -3.180 closest distance to " CG  ARG A 259 " =    2.516
peak=   -3.172 closest distance to " CB  PRO A 163 " =    2.673
peak=   -3.166 closest distance to " O   HOH Z 259 " =    1.320
peak=   -3.165 closest distance to " O   HOH Z 171 " =    2.285
peak=   -3.164 closest distance to " ND2 ASN A  60 " =    1.471
peak=   -3.163 closest distance to " O   HOH Z 411 " =    1.841
peak=   -3.157 closest distance to " O   ASP A 298 " =    1.875
peak=   -3.155 closest distance to " O   HOH Z  73 " =    2.329
peak=   -3.152 closest distance to " O   HOH Z 310 " =    4.143
peak=   -3.147 closest distance to " O   HOH Z 378 " =    1.292
peak=   -3.146 closest distance to " OH  TYR A 169 " =    0.891
peak=   -3.144 closest distance to " OD1 ASN A 187 " =    1.620
peak=   -3.142 closest distance to " O   ASP A  27 " =    2.138
peak=   -3.138 closest distance to " O   HOH Z  64 " =    1.537
peak=   -3.134 closest distance to " CB  TRP A  85 " =    2.602
peak=   -3.131 closest distance to " O   HOH Z 377 " =    0.830
peak=   -3.131 closest distance to " O   GLY A 241 " =    2.358
peak=   -3.128 closest distance to " CD  PRO A 243 " =    1.869
peak=   -3.128 closest distance to " O   HOH Z 397 " =    1.150
peak=   -3.125 closest distance to " NE2 GLN A  88 " =    1.062
peak=   -3.124 closest distance to " C   THR A 264 " =    1.396
peak=   -3.116 closest distance to " CB  HIS A  86 " =    2.482
peak=   -3.110 closest distance to " O   HOH Z 425 " =    1.059
peak=   -3.097 closest distance to " CD1 ILE A 106 " =    2.109
peak=   -3.092 closest distance to " O   HOH Z  90 " =    1.840
peak=   -3.091 closest distance to " NH2 ARG A 159 " =    2.422
peak=   -3.088 closest distance to " CD2 TYR A 293 " =    1.936
peak=   -3.080 closest distance to " O   HOH Z 423 " =    1.249
peak=   -3.079 closest distance to " CD2 LEU A 237 " =    2.849
peak=   -3.064 closest distance to " CB  PRO A 163 " =    2.438
peak=   -3.064 closest distance to " O   VAL A 174 " =    2.183
peak=   -3.063 closest distance to " O   ASN A 301 " =    1.018
peak=   -3.062 closest distance to " O   HOH Z 109 " =    1.184
peak=   -3.042 closest distance to " CA  GLY A 241 " =    3.260
peak=   -3.034 closest distance to " C   LEU A 222 " =    0.880
peak=   -3.016 closest distance to " CG  PRO A 163 " =    1.648

================= 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    :  0.5002 0.4851   6.299571e+00   6.282596e+00
   1_bss:  0.4938 0.4775   6.294033e+00   6.278344e+00
   1_xyz:  0.4241 0.4319   6.224380e+00   6.230300e+00
   1_adp:  0.3827 0.4268   6.159949e+00   6.220241e+00
   1_occ:  0.3820 0.4260   6.159278e+00   6.220460e+00
   2_bss:  0.3792 0.4199   6.160441e+00   6.219873e+00
   2_xyz:  0.3161 0.3861   6.037830e+00   6.158352e+00
   2_adp:  0.3063 0.3713   6.020049e+00   6.137887e+00
   2_occ:  0.3062 0.3709   6.019390e+00   6.137287e+00
   3_bss:  0.3062 0.3704   6.020498e+00   6.138421e+00
   3_xyz:  0.2516 0.2998   5.834288e+00   5.974736e+00
   3_adp:  0.2344 0.2826   5.781781e+00   5.929912e+00
   3_occ:  0.2341 0.2827   5.781500e+00   5.930902e+00
   4_bss:  0.2336 0.2820   5.781666e+00   5.930395e+00
   4_xyz:  0.1743 0.2176   5.508726e+00   5.696099e+00
   4_adp:  0.1586 0.2022   5.429212e+00   5.625236e+00
   4_occ:  0.1585 0.2025   5.429075e+00   5.625919e+00
   5_bss:  0.1584 0.2024   5.429097e+00   5.624205e+00
   5_xyz:  0.1337 0.1785   5.290753e+00   5.509275e+00
   5_adp:  0.1285 0.1753   5.260869e+00   5.486778e+00
   5_occ:  0.1283 0.1753   5.260098e+00   5.486497e+00
   5_bss:  0.1284 0.1757   5.260522e+00   5.486853e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   5.608  12.017   8.249   0.000   0.000   0.000
   1_xyz:  0.300  20.000   5.608  12.017   8.249   0.000   0.000   0.000
   1_adp:  0.300  20.000   5.608  12.017   8.249   0.000   0.000   0.000
   1_occ:  0.300  20.000   5.608  12.017   8.249   0.000   0.000   0.000
   2_bss:  0.300  50.000   2.136   7.332   4.449   0.000   0.000   0.000
   2_xyz:  0.300  50.000   2.136   7.332   4.449   0.000   0.000   0.000
   2_adp:  0.300  50.000   2.136   7.332   4.449   0.000   0.000   0.000
   2_occ:  0.300  50.000   2.136   7.332   4.449   0.000   0.000   0.000
   3_bss:  0.322  69.280   1.688   5.269   3.150   0.000   0.000   0.000
   3_xyz:  0.322  69.280   1.688   5.269   3.150   0.000   0.000   0.000
   3_adp:  0.322  69.280   1.688   5.269   3.150   0.000   0.000   0.000
   3_occ:  0.322  69.280   1.688   5.269   3.150   0.000   0.000   0.000
   4_bss:  0.323  62.673   0.784   3.442   2.387   0.000   0.000   0.000
   4_xyz:  0.323  62.673   0.784   3.442   2.387   0.000   0.000   0.000
   4_adp:  0.323  62.673   0.784   3.442   2.387   0.000   0.000   0.000
   4_occ:  0.323  62.673   0.784   3.442   2.387   0.000   0.000   0.000
   5_bss:  0.326  62.673   0.475   2.164   2.229   0.000   0.000   0.000
   5_xyz:  0.326  62.673   0.475   2.164   2.229   0.000   0.000   0.000
   5_adp:  0.326  62.673   0.475   2.164   2.229   0.000   0.000   0.000
   5_occ:  0.326  62.673   0.475   2.164   2.229   0.000   0.000   0.000
   5_bss:  0.327  64.169  -1.016   0.306   0.710   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.427 0.4018  0.4603    73527.352
   1_bss:  59.194 0.4037  0.5925    72246.449
   1_xyz:  50.545 0.5133  0.7357    56099.619
   1_adp:  48.697 0.5364  0.8395    53449.317
   1_occ:  48.715 0.5361  0.8375    53431.149
   2_bss:  48.396 0.5401  0.7394    52963.332
   2_xyz:  43.358 0.6016  0.8237    43322.279
   2_adp:  41.747 0.6216  0.8343    40852.354
   2_occ:  41.674 0.6225  0.8350    40723.043
   3_bss:  41.534 0.6242  0.8025    40604.789
   3_xyz:  31.349 0.7430  0.9264    24795.503
   3_adp:  29.171 0.7676  0.9441    22010.091
   3_occ:  29.210 0.7672  0.9435    22052.695
   4_bss:  29.151 0.7678  0.9072    21978.233
   4_xyz:  21.221 0.8497  0.9677    12143.942
   4_adp:  19.391 0.8677  0.9714    10559.490
   4_occ:  19.401 0.8676  0.9714    10587.585
   5_bss:  19.334 0.8683  0.9525    10522.872
   5_xyz:  16.678 0.8924  0.9662     8254.944
   5_adp:  16.104 0.8977  0.9633     7935.640
   5_occ:  16.094 0.8978  0.9631     7937.499
   5_bss:  16.101 0.8977  0.9589     7949.009
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4445e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4445e+01
   1_xyz:   1.676  0.013  0.107 18.171  0.007  4.124   1.4133e-01
   1_adp:   1.676  0.013  0.107 18.171  0.007  4.124   1.4133e-01
   1_occ:   1.676  0.013  0.107 18.171  0.007  4.124   1.4133e-01
   2_bss:   1.676  0.013  0.107 18.171  0.007  4.124   1.4133e-01
   2_xyz:   1.344  0.010  0.089 16.895  0.005  4.107   1.0435e-01
   2_adp:   1.344  0.010  0.089 16.895  0.005  4.107   1.0435e-01
   2_occ:   1.344  0.010  0.089 16.895  0.005  4.107   1.0435e-01
   3_bss:   1.344  0.010  0.089 16.895  0.005  4.107   1.0435e-01
   3_xyz:   1.191  0.009  0.085 15.672  0.004  4.112   8.3853e-02
   3_adp:   1.191  0.009  0.085 15.672  0.004  4.112   8.3853e-02
   3_occ:   1.191  0.009  0.085 15.672  0.004  4.112   8.3853e-02
   4_bss:   1.191  0.009  0.085 15.672  0.004  4.112   8.3853e-02
   4_xyz:   1.187  0.010  0.083 15.630  0.005  4.113   9.2806e-02
   4_adp:   1.187  0.010  0.083 15.630  0.005  4.113   9.2806e-02
   4_occ:   1.187  0.010  0.083 15.630  0.005  4.113   9.2806e-02
   5_bss:   1.187  0.010  0.083 15.630  0.005  4.113   9.2806e-02
   5_xyz:   1.232  0.011  0.093 15.649  0.004  4.126   8.7542e-02
   5_adp:   1.232  0.011  0.093 15.649  0.004  4.126   8.7542e-02
   5_occ:   1.232  0.011  0.093 15.649  0.004  4.126   8.7542e-02
   5_bss:   1.232  0.011  0.093 15.649  0.004  4.126   8.7542e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0585e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0585e+00
   1_xyz:  14.730  0.116  0.464 88.643  0.041  2.276   1.0156e-01
   1_adp:  14.730  0.116  0.464 88.643  0.041  2.276   1.0156e-01
   1_occ:  14.730  0.116  0.464 88.643  0.041  2.276   1.0156e-01
   2_bss:  14.730  0.116  0.464 88.643  0.041  2.276   1.0156e-01
   2_xyz:   8.055  0.072  0.305 88.243  0.025  2.110   6.3030e-02
   2_adp:   8.055  0.072  0.305 88.243  0.025  2.110   6.3030e-02
   2_occ:   8.055  0.072  0.305 88.243  0.025  2.110   6.3030e-02
   3_bss:   8.055  0.072  0.305 88.243  0.025  2.110   6.3030e-02
   3_xyz:   6.765  0.048  0.280 87.003  0.038  2.268   1.0185e-01
   3_adp:   6.765  0.048  0.280 87.003  0.038  2.268   1.0185e-01
   3_occ:   6.765  0.048  0.280 87.003  0.038  2.268   1.0185e-01
   4_bss:   6.765  0.048  0.280 87.003  0.038  2.268   1.0185e-01
   4_xyz:   7.581  0.068  0.273 89.646  0.046  2.115   1.7459e-01
   4_adp:   7.581  0.068  0.273 89.646  0.046  2.115   1.7459e-01
   4_occ:   7.581  0.068  0.273 89.646  0.046  2.115   1.7459e-01
   5_bss:   7.581  0.068  0.273 89.646  0.046  2.115   1.7459e-01
   5_xyz:   8.236  0.056  0.531 85.304  0.038  2.141   5.6680e-02
   5_adp:   8.236  0.056  0.531 85.304  0.038  2.141   5.6680e-02
   5_occ:   8.236  0.056  0.531 85.304  0.038  2.141   5.6680e-02
   5_bss:   8.236  0.056  0.531 85.304  0.038  2.141   5.6680e-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: 120.59   0.00  15.71  78.93   0.00  13.51 120.59   0.00  27.68
   1_occ: 120.59   0.00  15.71  78.93   0.00  13.51 120.59   0.00  27.68
   2_bss: 120.59   0.00  15.71  78.93   0.00  13.51 120.59   0.00  27.68
   2_xyz: 120.59   0.00  15.71  78.93   0.00  13.51 120.59   0.00  27.68
   2_adp: 110.49   0.00  14.13  67.76   0.00  11.62 110.49   0.00  27.76
   2_occ: 110.49   0.00  14.13  67.76   0.00  11.62 110.49   0.00  27.76
   3_bss: 110.49   0.00  14.13  67.76   0.00  11.62 110.49   0.00  27.76
   3_xyz: 110.49   0.00  14.13  67.76   0.00  11.62 110.49   0.00  27.76
   3_adp:  97.59   0.00  14.14  66.32   0.00  10.79  97.59   1.76  32.39
   3_occ:  97.59   0.00  14.14  66.32   0.00  10.79  97.59   1.76  32.39
   4_bss:  97.59   0.00  14.14  66.32   0.00  10.79  97.59   1.76  32.39
   4_xyz:  97.59   0.00  14.14  66.32   0.00  10.79  97.59   1.76  32.39
   4_adp:  87.56   0.00  14.30  74.20   0.00  10.10  87.56   1.81  37.20
   4_occ:  87.56   0.00  14.30  74.20   0.00  10.10  87.56   1.81  37.20
   5_bss:  87.56   0.00  14.30  74.20   0.00  10.10  87.56   1.81  37.20
   5_xyz:  87.56   0.00  14.30  74.20   0.00  10.10  87.56   1.81  37.20
   5_adp:  87.93   0.00  14.26  78.17   0.00   9.81  87.93   2.10  38.49
   5_occ:  87.93   0.00  14.26  78.17   0.00   9.81  87.93   2.10  38.49
   5_bss:  89.42   1.50  15.76  79.67   1.50  11.31  89.42   3.60  39.98
------------------------------------------------------------------------
 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:    1.125    0.014    0.407
   1_adp:    1.125    0.014    0.407
   1_occ:    1.125    0.014    0.407
   2_bss:    1.125    0.014    0.407
   2_xyz:    1.543    0.054    0.579
   2_adp:    1.543    0.054    0.579
   2_occ:    1.543    0.054    0.579
   3_bss:    1.543    0.054    0.579
   3_xyz:    1.710    0.066    0.704
   3_adp:    1.710    0.066    0.704
   3_occ:    1.710    0.066    0.704
   4_bss:    1.710    0.066    0.704
   4_xyz:    1.849    0.045    0.837
   4_adp:    1.849    0.045    0.837
   4_occ:    1.849    0.045    0.837
   5_bss:    1.849    0.045    0.837
   5_xyz:    2.008    0.051    0.880
   5_adp:    2.008    0.051    0.880
   5_occ:    2.008    0.051    0.880
   5_bss:    2.008    0.051    0.880
------------------------------------------------------------------------

CPU time actual refinement: 335.45


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_722/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_722/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_722/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_722/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_722/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.30 
  Macro-tasks:
    bulk solvent and scale       = 41.42  
    individual site refinement   = 134.86 
    weights calculation          = 32.19  
    collect and process          = 6.38   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 214.98 
  Micro-tasks:
    mask                            = 3.03   
    f_calc                          = 103.77 
    alpha_beta                      = 8.13   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 113.10 
    fmodel                         = 7.44   
    r_factors                      = 0.17   
    phase_errors                   = 10.23  
    foms                           = 0.18   
    TOTAL for micro-tasks          = 247.20 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.811 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    627 calls, 103.54 s
gradients_fft:          572 calls, 100.86 s

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

# Date 2008-01-16 Time 02:15:53 PST -0800 (1200478553.89 s)
Start R-work = 0.5002, R-free = 0.4851 (no bulk solvent and anisotropic scale)
Final R-work = 0.1448, R-free = 0.1914 (no bulk solvent and anisotropic scale)

Start R-work = 0.4938, R-free = 0.4775
Final R-work = 0.1284, R-free = 0.1757