# Date 2008-01-16 Time 02:32:36 PST -0800 (1200479556.79 s)
#phil __OFF__

Command line arguments: "../875.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27635
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 875

-------------------------------------------------------------------------------
  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: (70.9525, 46.2261, 86.822, 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: 2.76, per 1000 atoms: 0.98


================================== 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: (70.9525, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 1.97321
Completeness in resolution range: 0.947885
Completeness with d_max=infinity: 0.945096

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1235
                             d_min =   1.9732

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: (70.9525, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 1.97321
Completeness in resolution range: 0.947885
Completeness with d_max=infinity: 0.945096

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1239 -  4.2232 [2172/2198]  1953   219  10.1%
  bin  2:  4.2232 -  3.3642 [2088/2108]  1881   207   9.9%
  bin  3:  3.3642 -  2.9425 [2064/2083]  1857   207  10.0%
  bin  4:  2.9425 -  2.6751 [2045/2075]  1839   206  10.1%
  bin  5:  2.6751 -  2.4842 [2011/2030]  1817   194   9.6%
  bin  6:  2.4842 -  2.3383 [2019/2044]  1809   210  10.4%
  bin  7:  2.3383 -  2.2216 [2011/2039]  1810   201  10.0%
  bin  8:  2.2216 -  2.1252 [2000/2036]  1802   198   9.9%
  bin  9:  2.1252 -  2.0436 [1991/2033]  1796   195   9.8%
  bin 10:  2.0436 -  1.9732 [1188/2020]  1066   122  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_875/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: 0.11 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: 24
        2.42 -     3.04: 2184
        3.04 -     3.66: 4714
        3.66 -     4.28: 9031
        4.28 -     4.90: 12316
  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 201 " - " O   HOH Z 349 "  2.072 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.217 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28264 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_875/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_875/model_refine_001.geo

CPU time processing inputs: 7.70


============================ 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 = 70.9525 46.22605 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4636   r_free= 0.4541   ksol= 0.00   Bsol= 0.00   scale= 0.803    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.266459                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7108 0.99   1408  157 0.3935 0.3737      6.5795      6.5602|
|  2:  4.7108 -  3.7580 0.99   1351  151 0.3679 0.3618      6.7505      6.7079|
|  3:  3.7580 -  3.2885 0.99   1343  144 0.3990 0.3620      6.6122      6.5865|
|  4:  3.2885 -  2.9904 0.99   1324  152 0.4510 0.4162      6.5144      6.4671|
|  5:  2.9904 -  2.7775 0.99   1320  147 0.4965 0.4757      6.3517      6.3622|
|  6:  2.7775 -  2.6146 0.99   1303  142 0.4865 0.5175       6.261      6.1986|
|  7:  2.6146 -  2.4842 0.99   1298  140 0.5209 0.5000      6.2477      6.2046|
|  8:  2.4842 -  2.3765 0.98   1289  146 0.5100 0.4503      6.1621      6.1736|
|  9:  2.3765 -  2.2854 0.98   1279  150 0.5003 0.5197      6.1044      6.1617|
| 10:  2.2854 -  2.2068 1.00   1313  147 0.5190 0.4981      6.1005      6.0558|
| 11:  2.2068 -  2.1379 0.98   1289  134 0.5099 0.5081      6.0327      6.0225|
| 12:  2.1379 -  2.0770 0.98   1261  144 0.5227 0.5872      5.9573      6.0225|
| 13:  2.0770 -  2.0224 0.99   1294  136 0.5233 0.5107      5.8722      5.7936|
| 14:  2.0224 -  1.9732 0.43    558   69 0.5445 0.5058      5.8951      5.8092|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7108  1408   157  0.70  33.97   0.79     0.75      69629.61|
|  2:  4.7108 -  3.7580  1351   151  0.75  30.82   0.88     0.82      87860.21|
|  3:  3.7580 -  3.2885  1343   144  0.66  38.58   0.87     0.78      93061.96|
|  4:  3.2885 -  2.9904  1324   152  0.59  45.03   0.80     0.68      84027.99|
|  5:  2.9904 -  2.7775  1320   147  0.48  53.30   0.75     0.58      73166.40|
|  6:  2.7775 -  2.6146  1303   142  0.46  55.45   0.73     0.51      64443.35|
|  7:  2.6146 -  2.4842  1298   140  0.40  59.70   0.75     0.46      62001.24|
|  8:  2.4842 -  2.3765  1289   146  0.37  62.23   0.73     0.43      57632.15|
|  9:  2.3765 -  2.2854  1279   150  0.38  61.24   0.73     0.44      52490.36|
| 10:  2.2854 -  2.2068  1313   147  0.39  61.05   0.75     0.46      46680.79|
| 11:  2.2068 -  2.1379  1289   134  0.37  62.48   0.78     0.45      45824.60|
| 12:  2.1379 -  2.0770  1261   144  0.32  66.04   0.75     0.41      43345.40|
| 13:  2.0770 -  2.0224  1294   136  0.31  66.79   0.72     0.40      37786.71|
| 14:  2.0224 -  1.9732   558    69  0.40  60.14   0.72     0.43      28344.34|
|alpha:            min =        0.40 max =            0.82 mean =         0.55|
|beta:             min =    28344.34 max =        93061.96 mean =     62118.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.52|
|phase err.(test): min =        0.00 max =           89.96 mean =        53.76|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.730295             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.578   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.021935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.107   (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:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      688 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1506 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2625 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3957 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5060 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6559 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7683 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.796 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.800 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4707   r_free= 0.4570   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.269205                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4563   r_free= 0.4377   ksol= 0.35   Bsol= 10.85   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.82,9.75,8.33,0.00,0.00,0.00); trace/3= 8.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.259795                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.130217             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.157   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.980238              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.705   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4563      final r-factor (work) = 0.3640          |
| start r-factor (free) = 0.4377      final r-factor (free) = 0.3838          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.5310 = 10.13 * 0.50 * 6.2654 + 1.00 * 53.7963                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.3203 = 10.13 * 0.50 * 6.1575 + 1.00 * 0.1320                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3640      final r-factor (work) = 0.3129          |
| start r-factor (free) = 0.3838      final r-factor (free) = 0.3627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0502 = 0.98 * 1.00 * 6.1575 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9429 = 0.98 * 1.00 * 6.0476 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.07   12.54    None  None   None       |
|    all(noH): 2823   0      0.00    77.07   12.54    None  None   None       |
|    Sol.    : 438    0      0.00    77.07   26.61    None  None   None       |
|    Mac.    : 2385   0      0.00    66.47   9.96     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.707: 1215   |   5:    38.536 -  46.243:   72        |
|      1:     7.707 -  15.414:  770   |   6:    46.243 -  53.950:   32        |
|      2:    15.414 -  23.122:  410   |   7:    53.950 -  61.658:   14        |
|      3:    23.122 -  30.829:  197   |   8:    61.658 -  69.365:    5        |
|      4:    30.829 -  38.536:  106   |   9:    69.365 -  77.072:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3129 r_free = 0.3627             target_work(ml) = 6.021         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3126 r_free = 0.3627             target_work(ml) = 6.020         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3126   r_free= 0.3627   ksol= 0.35   Bsol= 10.85   scale= 1.110   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.82,9.75,8.33,0.00,0.00,0.00); trace/3= 8.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.019748                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3081   r_free= 0.3556   ksol= 0.35   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.36,5.36,4.94,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.019008                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.920642              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.579   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.472961              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.283  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3081      final r-factor (work) = 0.2356          |
| start r-factor (free) = 0.3556      final r-factor (free) = 0.2863          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9844 = 3.92 * 0.50 * 6.0461 + 1.00 * 0.1320                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6295 = 3.92 * 0.50 * 5.8968 + 1.00 * 0.0699                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2356      final r-factor (work) = 0.2152          |
| start r-factor (free) = 0.2863      final r-factor (free) = 0.2708          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8040 = 0.47 * 1.00 * 5.8968 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7281 = 0.47 * 1.00 * 5.7420 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.89   12.58    None  None   None       |
|    all(noH): 2823   0      0.00    83.89   12.58    None  None   None       |
|    Sol.    : 438    0      1.02    83.89   32.49    None  None   None       |
|    Mac.    : 2385   0      0.00    72.56   8.92     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 -   8.389: 1444   |   5:    41.945 -  50.333:   72        |
|      1:     8.389 -  16.778:  729   |   6:    50.333 -  58.722:   40        |
|      2:    16.778 -  25.167:  236   |   7:    58.722 -  67.111:   10        |
|      3:    25.167 -  33.556:  149   |   8:    67.111 -  75.500:    3        |
|      4:    33.556 -  41.945:  138   |   9:    75.500 -  83.889:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2152 r_free = 0.2708             target_work(ml) = 5.715         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2150 r_free = 0.2705             target_work(ml) = 5.715         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2150   r_free= 0.2705   ksol= 0.35   Bsol= 50.00   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.36,5.36,4.94,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.715027                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2139   r_free= 0.2686   ksol= 0.34   Bsol= 50.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.91,3.17,3.91,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.714162                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.014201              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.402  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.641198              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.037  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2139      final r-factor (work) = 0.1526          |
| start r-factor (free) = 0.2686      final r-factor (free) = 0.1997          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5999 = 4.01 * 0.50 * 5.7446 + 1.00 * 0.0699                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2514 = 4.01 * 0.50 * 5.5718 + 1.00 * 0.0682                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1526      final r-factor (work) = 0.1378          |
| start r-factor (free) = 0.1997      final r-factor (free) = 0.1866          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5848 = 0.64 * 1.00 * 5.5718 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4508 = 0.64 * 1.00 * 5.3621 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.07   13.06    None  None   None       |
|    all(noH): 2823   0      0.00    84.07   13.06    None  None   None       |
|    Sol.    : 438    0      1.75    84.07   37.06    None  None   None       |
|    Mac.    : 2385   0      0.00    80.24   8.66     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 -   8.407: 1560   |   5:    42.036 -  50.443:   89        |
|      1:     8.407 -  16.814:  642   |   6:    50.443 -  58.850:   69        |
|      2:    16.814 -  25.221:  180   |   7:    58.850 -  67.257:   35        |
|      3:    25.221 -  33.629:  121   |   8:    67.257 -  75.664:    8        |
|      4:    33.629 -  42.036:  115   |   9:    75.664 -  84.071:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1378 r_free = 0.1866             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1377 r_free = 0.1866             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1377   r_free= 0.1866   ksol= 0.34   Bsol= 50.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.91,3.17,3.91,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.324270                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1377   r_free= 0.1859   ksol= 0.33   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,2.18,3.47,0.00,0.00,0.00); trace/3= 2.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.322315                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.879542              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.152  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.178809              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.578  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1377      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1859      final r-factor (free) = 0.1739          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1099 = 1.88 * 0.50 * 5.3649 + 1.00 * 0.0682                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0230 = 1.88 * 0.50 * 5.2867 + 1.00 * 0.0547                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1260      final r-factor (work) = 0.1254          |
| start r-factor (free) = 0.1739      final r-factor (free) = 0.1692          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9579 = 0.18 * 1.00 * 5.2867 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9485 = 0.18 * 1.00 * 5.2498 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.07   12.57    None  None   None       |
|    all(noH): 2823   0      0.00    81.07   12.57    None  None   None       |
|    Sol.    : 438    0      2.31    81.07   35.32    None  None   None       |
|    Mac.    : 2385   0      0.00    79.78   8.40     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 -   8.107: 1578   |   5:    40.534 -  48.641:   94        |
|      1:     8.107 -  16.214:  652   |   6:    48.641 -  56.748:   62        |
|      2:    16.214 -  24.321:  167   |   7:    56.748 -  64.855:   32        |
|      3:    24.321 -  32.427:  114   |   8:    64.855 -  72.961:   12        |
|      4:    32.427 -  40.534:  108   |   9:    72.961 -  81.068:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1254 r_free = 0.1692             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1253 r_free = 0.1691             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1691   ksol= 0.33   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,2.18,3.47,0.00,0.00,0.00); trace/3= 2.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.235293                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1690   ksol= 0.33   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,1.95,3.43,0.00,0.00,0.00); trace/3= 2.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.235079                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.892346              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.888  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.431847              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.670  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1253      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0214 = 1.89 * 0.50 * 5.2492 + 1.00 * 0.0547                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9896 = 1.89 * 0.50 * 5.2091 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1182      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1608      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2592 = 0.43 * 1.00 * 5.2091 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2473 = 0.43 * 1.00 * 5.1785 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.27   12.55    None  None   None       |
|    all(noH): 2823   0      0.00    82.27   12.55    None  None   None       |
|    Sol.    : 438    0      1.96    78.84   35.40    None  None   None       |
|    Mac.    : 2385   0      0.00    82.27   8.35     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 -   8.227: 1589   |   5:    41.133 -  49.360:   92        |
|      1:     8.227 -  16.453:  648   |   6:    49.360 -  57.587:   64        |
|      2:    16.453 -  24.680:  163   |   7:    57.587 -  65.813:   31        |
|      3:    24.680 -  32.907:  112   |   8:    65.813 -  74.040:   12        |
|      4:    32.907 -  41.133:  108   |   9:    74.040 -  82.267:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1162 r_free = 0.1604             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1161 r_free = 0.1604             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1604   ksol= 0.33   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,1.95,3.43,0.00,0.00,0.00); trace/3= 2.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.178526                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7108 0.99   1408  157 0.0998 0.1282      5.3818      5.5503|
|  2:  4.7108 -  3.7580 0.99   1351  151 0.0889 0.1181      5.4571      5.6511|
|  3:  3.7580 -  3.2885 0.99   1343  144 0.1114 0.1501      5.5081      5.8386|
|  4:  3.2885 -  2.9904 0.99   1324  152 0.1253 0.1699      5.4746      5.6182|
|  5:  2.9904 -  2.7775 0.99   1320  147 0.1413 0.1737      5.3656      5.5869|
|  6:  2.7775 -  2.6146 0.99   1303  142 0.1245 0.2028      5.2178      5.5202|
|  7:  2.6146 -  2.4842 0.99   1298  140 0.1325 0.1603      5.2079      5.3367|
|  8:  2.4842 -  2.3765 0.98   1289  146 0.1219 0.1717      5.0993      5.3511|
|  9:  2.3765 -  2.2854 0.98   1279  150 0.1264 0.1851       5.084      5.3519|
| 10:  2.2854 -  2.2068 1.00   1313  147 0.1174 0.1711       4.983      5.1945|
| 11:  2.2068 -  2.1379 0.98   1289  134 0.1160 0.1955      4.9811      5.3749|
| 12:  2.1379 -  2.0770 0.98   1261  144 0.1156 0.1679      4.8894      5.1644|
| 13:  2.0770 -  2.0224 0.99   1294  136 0.1196 0.1666      4.8141      5.0267|
| 14:  2.0224 -  1.9732 0.43    558   69 0.1039 0.1494      4.7077      4.8706|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7108  1408   157  0.94   9.11   0.98     0.96       7067.61|
|  2:  4.7108 -  3.7580  1351   151  0.95   8.01   1.01     1.00       9179.18|
|  3:  3.7580 -  3.2885  1343   144  0.93  11.69   1.02     1.02      10868.08|
|  4:  3.2885 -  2.9904  1324   152  0.92  14.20   1.01     0.98      10692.06|
|  5:  2.9904 -  2.7775  1320   147  0.90  16.51   0.99     0.97       8787.95|
|  6:  2.7775 -  2.6146  1303   142  0.90  16.29   0.98     0.96       7173.27|
|  7:  2.6146 -  2.4842  1298   140  0.90  16.05   0.99     0.95       6464.41|
|  8:  2.4842 -  2.3765  1289   146  0.90  15.95   0.99     0.97       5632.27|
|  9:  2.3765 -  2.2854  1279   150  0.90  16.39   1.00     0.96       5509.83|
| 10:  2.2854 -  2.2068  1313   147  0.90  16.43   1.00     0.96       4637.94|
| 11:  2.2068 -  2.1379  1289   134  0.90  16.40   0.99     0.94       4626.97|
| 12:  2.1379 -  2.0770  1261   144  0.90  16.15   1.01     1.01       4122.27|
| 13:  2.0770 -  2.0224  1294   136  0.89  17.20   1.00     0.98       3536.33|
| 14:  2.0224 -  1.9732   558    69  0.92  14.64   0.98     0.96       2828.79|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2828.79 max =        10868.08 mean =      6701.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.58|
|phase err.(test): min =        0.00 max =           89.52 mean =        13.93|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1597   ksol= 0.33   Bsol= 52.52   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,-0.58,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.177994                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1597   ksol= 0.33   Bsol= 52.52   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,-0.58,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.177994                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7108 0.99   1408  157 0.0997 0.1258      5.3779      5.5312|
|  2:  4.7108 -  3.7580 0.99   1351  151 0.0895 0.1165      5.4581      5.6462|
|  3:  3.7580 -  3.2885 0.99   1343  144 0.1118 0.1479      5.5076      5.8291|
|  4:  3.2885 -  2.9904 0.99   1324  152 0.1253 0.1709       5.474      5.6221|
|  5:  2.9904 -  2.7775 0.99   1320  147 0.1415 0.1733      5.3649      5.5822|
|  6:  2.7775 -  2.6146 0.99   1303  142 0.1245 0.2025      5.2172      5.5181|
|  7:  2.6146 -  2.4842 0.99   1298  140 0.1324 0.1603       5.207      5.3361|
|  8:  2.4842 -  2.3765 0.98   1289  146 0.1217 0.1715      5.0978      5.3509|
|  9:  2.3765 -  2.2854 0.98   1279  150 0.1263 0.1846      5.0836      5.3515|
| 10:  2.2854 -  2.2068 1.00   1313  147 0.1173 0.1712      4.9829      5.1965|
| 11:  2.2068 -  2.1379 0.98   1289  134 0.1161 0.1953      4.9817      5.3744|
| 12:  2.1379 -  2.0770 0.98   1261  144 0.1156 0.1682      4.8895      5.1657|
| 13:  2.0770 -  2.0224 0.99   1294  136 0.1197 0.1665      4.8143      5.0266|
| 14:  2.0224 -  1.9732 0.43    558   69 0.1039 0.1497      4.7077      4.8711|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7108  1408   157  0.94   9.01   0.98     0.95       6897.65|
|  2:  4.7108 -  3.7580  1351   151  0.95   7.92   1.01     1.00       9005.60|
|  3:  3.7580 -  3.2885  1343   144  0.93  11.64   1.02     1.02      10735.39|
|  4:  3.2885 -  2.9904  1324   152  0.92  14.17   1.01     0.98      10647.92|
|  5:  2.9904 -  2.7775  1320   147  0.90  16.45   0.99     0.97       8748.17|
|  6:  2.7775 -  2.6146  1303   142  0.90  16.26   0.98     0.96       7152.44|
|  7:  2.6146 -  2.4842  1298   140  0.90  16.03   0.99     0.95       6453.40|
|  8:  2.4842 -  2.3765  1289   146  0.90  15.94   0.99     0.97       5624.62|
|  9:  2.3765 -  2.2854  1279   150  0.90  16.39   1.00     0.96       5504.62|
| 10:  2.2854 -  2.2068  1313   147  0.90  16.43   1.00     0.96       4640.99|
| 11:  2.2068 -  2.1379  1289   134  0.90  16.42   0.99     0.94       4637.02|
| 12:  2.1379 -  2.0770  1261   144  0.90  16.17   1.01     1.01       4128.31|
| 13:  2.0770 -  2.0224  1294   136  0.89  17.21   1.00     0.98       3539.09|
| 14:  2.0224 -  1.9732   558    69  0.92  14.64   0.98     0.96       2829.01|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2829.01 max =        10735.39 mean =      6657.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.55|
|phase err.(test): min =        0.00 max =           88.93 mean =        13.92|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.52    84.79   15.07    None  None   None       |
|    all(noH): 2823   0      2.52    84.79   15.07    None  None   None       |
|    Sol.    : 438    0      4.48    81.36   37.92    None  None   None       |
|    Mac.    : 2385   0      2.52    84.79   10.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.521 -  10.747: 1589   |   5:    43.654 -  51.881:   92        |
|      1:    10.747 -  18.974:  648   |   6:    51.881 -  60.107:   64        |
|      2:    18.974 -  27.201:  163   |   7:    60.107 -  68.334:   31        |
|      3:    27.201 -  35.427:  112   |   8:    68.334 -  76.561:   12        |
|      4:    35.427 -  43.654:  108   |   9:    76.561 -  84.787:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.352 - 4.771
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 315 from: 319
   mapped sites are within: 0.729 - 4.771

peak=   10.864 closest distance to " CB  VAL A 230 " =    1.475
peak=    8.861 closest distance to " CG2 VAL A 296 " =    1.366
peak=    6.486 closest distance to " CD2 LEU A   5 " =    1.272
peak=    6.461 closest distance to " CG  ARG A 138 " =    1.055
peak=    6.041 closest distance to " NE2 GLN A  11 " =    1.189
peak=    5.833 closest distance to " CG  LEU A   5 " =    1.215
peak=    5.799 closest distance to " CD1AILE A 234 " =    1.081
peak=    5.604 closest distance to " O   HOH Z 130 " =    1.131
peak=    5.599 closest distance to " O   HOH Z 142 " =    2.093
peak=    5.586 closest distance to " CG  PRO A  54 " =    1.374
peak=    5.492 closest distance to " NH2 ARG A  56 " =    2.096
peak=    5.407 closest distance to " CG  LEU A 228 " =    1.083
peak=    5.325 closest distance to " O   HOH Z   9 " =    1.598
peak=    5.211 closest distance to " O   HOH Z 232 " =    2.332
peak=    5.177 closest distance to " NH1 ARG A 138 " =    1.025
peak=    4.961 closest distance to " CB  PRO A  54 " =    1.023
peak=    4.959 closest distance to " CB  GLN A 223 " =    1.410
peak=    4.939 closest distance to " CB  GLN A 183 " =    1.235
peak=    4.847 closest distance to " CG  PRO A 198 " =    1.261
peak=    4.844 closest distance to " O   HOH Z   7 " =    1.357
peak=    4.767 closest distance to " O   HOH Z 427 " =    2.576
peak=    4.751 closest distance to " CB  ASN A 148 " =    1.358
peak=    4.642 closest distance to " O   HOH Z 369 " =    2.013
peak=    4.627 closest distance to " O   HOH Z 126 " =    2.047
peak=    4.480 closest distance to " O   HOH Z 425 " =    1.527
peak=    4.477 closest distance to " O   PRO A 198 " =    1.578
peak=    4.461 closest distance to " CB  SER A  63 " =    1.267
peak=    4.447 closest distance to " CB  ARG A 275 " =    0.908
peak=    4.442 closest distance to " O   HOH Z 298 " =    1.876
peak=    4.393 closest distance to " O   HOH Z 287 " =    1.958
peak=    4.363 closest distance to " CB  VAL A 230 " =    1.137
peak=    4.348 closest distance to " ND2 ASN A 187 " =    1.566
peak=    4.342 closest distance to " O   HOH Z  78 " =    1.632
peak=    4.315 closest distance to " CD2 LEU A 228 " =    1.199
peak=    4.283 closest distance to " CG  PRO A 213 " =    1.259
peak=    4.259 closest distance to " CB  SER A   3 " =    1.405
peak=    4.247 closest distance to " CB  TRP A 266 " =    0.993
peak=    4.236 closest distance to " O   HOH Z 193 " =    1.728
peak=    4.210 closest distance to " O   HOH Z   2 " =    1.767
peak=    4.201 closest distance to " CG  LEU A 167 " =    1.213
peak=    4.201 closest distance to " O   HOH Z 303 " =    2.300
peak=    4.182 closest distance to " O   HOH Z 423 " =    1.626
peak=    4.174 closest distance to " O   HOH Z  55 " =    2.185
peak=    4.168 closest distance to " O   HOH Z  68 " =    2.106
peak=    4.166 closest distance to " CB  ASN A  39 " =    0.975
peak=    4.147 closest distance to " O   HOH Z  44 " =    2.401
peak=    4.144 closest distance to " O   HOH Z 316 " =    3.049
peak=    4.128 closest distance to " O   HOH Z 272 " =    1.806
peak=    4.128 closest distance to " CB BVAL A  41 " =    1.214
peak=    4.046 closest distance to " O   HOH Z 368 " =    1.993
peak=    4.042 closest distance to " O   HOH Z 234 " =    3.742
peak=    4.027 closest distance to " CB  VAL A 265 " =    1.323
peak=    4.024 closest distance to " CD  ARG A 159 " =    0.753
peak=    4.019 closest distance to " CB  SER A 216 " =    0.862
peak=    4.011 closest distance to " CG  PRO A 243 " =    1.142
peak=    4.007 closest distance to " NH2AARG A 190 " =    1.800
peak=    3.991 closest distance to " CA  SER A  87 " =    0.939
peak=    3.979 closest distance to " CB  GLU A 152 " =    1.265
peak=    3.979 closest distance to " O   HOH Z  63 " =    1.330
peak=    3.975 closest distance to " N   PHE A 130 " =    1.263
peak=    3.945 closest distance to " O   HOH Z 346 " =    1.613
peak=    3.936 closest distance to " O   SER A  87 " =    2.350
peak=    3.929 closest distance to " O   HOH Z 410 " =    1.492
peak=    3.923 closest distance to " CD  ARG A  66 " =    2.403
peak=    3.918 closest distance to " O   HOH Z 392 " =    1.315
peak=    3.907 closest distance to " CB  ASN A 187 " =    1.105
peak=    3.881 closest distance to " O   HOH Z 214 " =    2.120
peak=    3.880 closest distance to " CB  ASN A 142 " =    1.018
peak=    3.876 closest distance to " O   HOH Z 144 " =    2.438
peak=    3.860 closest distance to " O   HOH Z 353 " =    2.546
peak=    3.848 closest distance to " CB  VAL A 202 " =    1.653
peak=    3.847 closest distance to " CB  GLU A 128 " =    1.066
peak=    3.843 closest distance to " O   HOH Z  78 " =    1.835
peak=    3.838 closest distance to " O   HOH Z 411 " =    3.534
peak=    3.838 closest distance to " NH1AARG A 145 " =    1.117
peak=    3.835 closest distance to " O   HOH Z  88 " =    3.174
peak=    3.810 closest distance to " O   HOH Z 380 " =    1.706
peak=    3.805 closest distance to " OG  SER A  62 " =    2.860
peak=    3.803 closest distance to " O   HOH Z  30 " =    1.708
peak=    3.795 closest distance to " O   HOH Z 419 " =    1.927
peak=    3.790 closest distance to " CB  ARG A  79 " =    1.482
peak=    3.780 closest distance to " CB  GLU A 277 " =    3.565
peak=    3.758 closest distance to " CA  TYR A  30 " =    0.957
peak=    3.756 closest distance to " CB  LEU A 143 " =    1.154
peak=    3.755 closest distance to " CG2 THR A 221 " =    1.036
peak=    3.750 closest distance to " O   HOH Z 158 " =    3.055
peak=    3.748 closest distance to " CB  VAL A 250 " =    1.081
peak=    3.730 closest distance to " ND1 HIS A  86 " =    1.753
peak=    3.727 closest distance to " OD1 ASN A  69 " =    2.617
peak=    3.724 closest distance to " CB  THR A 157 " =    1.130
peak=    3.721 closest distance to " O   HOH Z 222 " =    2.330
peak=    3.719 closest distance to " CG  GLN A  88 " =    1.096
peak=    3.713 closest distance to " OG  SER A  97 " =    2.895
peak=    3.708 closest distance to " CD  ARG A 138 " =    1.196
peak=    3.689 closest distance to " O   HOH Z 184 " =    1.353
peak=    3.689 closest distance to " O   HOH Z 437 " =    2.079
peak=    3.683 closest distance to " O   HOH Z 352 " =    1.761
peak=    3.677 closest distance to " O   HOH Z 389 " =    1.934
peak=    3.666 closest distance to " CG BARG A 102 " =    1.877
peak=    3.665 closest distance to " O   HOH Z 193 " =    1.857
peak=    3.648 closest distance to " CA  TYR A 116 " =    1.428
peak=    3.647 closest distance to " CA  VAL A 296 " =    1.087
peak=    3.642 closest distance to " CZ  PHE A 218 " =    1.091
peak=    3.639 closest distance to " CE  LYS A  76 " =    0.879
peak=    3.638 closest distance to " CG2 VAL A 257 " =    0.886
peak=    3.637 closest distance to " CD  LYS A 166 " =    1.376
peak=    3.633 closest distance to " O   HOH Z 193 " =    1.909
peak=    3.630 closest distance to " CD1 ILE A  33 " =    1.759
peak=    3.629 closest distance to " O   HOH Z 148 " =    3.471
peak=    3.629 closest distance to " CB  GLN A  88 " =    1.293
peak=    3.628 closest distance to " O   HOH Z   1 " =    1.954
peak=    3.623 closest distance to " CB  LEU A 228 " =    1.187
peak=    3.618 closest distance to " O   HOH Z 183 " =    1.326
peak=    3.608 closest distance to " O   HOH Z  59 " =    1.835
peak=    3.606 closest distance to " CB  SER A 212 " =    1.281
peak=    3.604 closest distance to " CG1 ILE A 151 " =    1.218
peak=    3.602 closest distance to " O   HOH Z 133 " =    2.374
peak=    3.600 closest distance to " O   HOH Z  61 " =    1.544
peak=    3.586 closest distance to " O   HOH Z 366 " =    2.963
peak=    3.584 closest distance to " OD2 ASP A 286 " =    2.776
peak=    3.584 closest distance to " CA  ASN A 215 " =    1.133
peak=    3.579 closest distance to " O   HOH Z 175 " =    2.116
peak=    3.565 closest distance to " CA  ALA A  51 " =    1.027
peak=    3.560 closest distance to " CA  ALA A  21 " =    1.214
peak=    3.559 closest distance to " O   HOH Z  21 " =    1.682
peak=    3.555 closest distance to " O   HOH Z 403 " =    1.570
peak=    3.548 closest distance to " CE1 TYR A 186 " =    1.363
peak=    3.545 closest distance to " CB  TRP A 179 " =    1.444
peak=    3.536 closest distance to " CB  ARG A 190 " =    1.679
peak=    3.529 closest distance to " O   HOH Z 128 " =    1.824
peak=    3.528 closest distance to " O   HOH Z 180 " =    2.077
peak=    3.527 closest distance to " CA  THR A 264 " =    0.729
peak=    3.518 closest distance to " O   HOH Z 148 " =    2.168
peak=    3.516 closest distance to " CB  LYS A 117 " =    1.263
peak=    3.512 closest distance to " CB  MET A  40 " =    0.817
peak=    3.502 closest distance to " O   HOH Z   3 " =    1.982
peak=    3.487 closest distance to " OE2 GLU A   2 " =    1.814
peak=    3.480 closest distance to " O   HOH Z 116 " =    3.038
peak=    3.479 closest distance to " O   HOH Z 209 " =    2.461
peak=    3.479 closest distance to " CA  LYS A 117 " =    1.137
peak=    3.479 closest distance to " O   HOH Z  10 " =    1.776
peak=    3.475 closest distance to " O   HOH Z 195 " =    1.419
peak=    3.461 closest distance to " O   HOH Z 133 " =    1.697
peak=    3.453 closest distance to " O   HOH Z 109 " =    2.448
peak=    3.452 closest distance to " O   HOH Z 435 " =    1.988
peak=    3.451 closest distance to " CA  ARG A 195 " =    1.230
peak=    3.449 closest distance to " CB  SER A 210 " =    0.807
peak=    3.448 closest distance to " O   HOH Z 273 " =    2.745
peak=    3.443 closest distance to " CA  GLY A 267 " =    1.004
peak=    3.442 closest distance to " CG1 VAL A 153 " =    1.022
peak=    3.442 closest distance to " CB  TRP A 150 " =    1.375
peak=    3.439 closest distance to " O   HOH Z 248 " =    1.695
peak=    3.439 closest distance to " CB  ILE A 234 " =    0.925
peak=    3.438 closest distance to " O   HOH Z 263 " =    1.674
peak=    3.437 closest distance to " O   HOH Z 305 " =    3.455
peak=    3.437 closest distance to " O   HOH Z 128 " =    2.099
peak=    3.434 closest distance to " C   ALA A 299 " =    0.989
peak=    3.433 closest distance to " O   HOH Z 343 " =    3.362
peak=    3.433 closest distance to " O   HOH Z   1 " =    1.840
peak=    3.431 closest distance to " CA  ALA A 291 " =    0.905
peak=    3.430 closest distance to " CB  SER A  62 " =    1.146
peak=    3.428 closest distance to " CG2 ILE A 106 " =    1.107
peak=    3.424 closest distance to " CA  ILE A 234 " =    0.973
peak=    3.424 closest distance to " O   HOH Z 119 " =    1.564
peak=    3.423 closest distance to " O   HOH Z  61 " =    1.573
peak=    3.420 closest distance to " NH1 ARG A  14 " =    0.920
peak=    3.420 closest distance to " NZ  LYS A 117 " =    3.100
peak=    3.420 closest distance to " O   HOH Z 371 " =    2.759
peak=    3.418 closest distance to " O   HOH Z 359 " =    1.313
peak=    3.417 closest distance to " CD2 TYR A 186 " =    1.111
peak=    3.410 closest distance to " N   SER A 271 " =    0.969
peak=    3.405 closest distance to " O   HOH Z 303 " =    1.869
peak=    3.402 closest distance to " CE3 TRP A 150 " =    0.994
peak=    3.401 closest distance to " O   HOH Z 368 " =    3.565
peak=    3.398 closest distance to " CG1 ILE A 263 " =    1.244
peak=    3.397 closest distance to " CB  ASN A 110 " =    1.098
peak=    3.395 closest distance to " CZ  PHE A 192 " =    0.927
peak=    3.390 closest distance to " O   HOH Z 258 " =    2.235
peak=    3.386 closest distance to " CA  ILE A 106 " =    0.798
peak=    3.383 closest distance to " CG1 ILE A  33 " =    1.309
peak=    3.381 closest distance to " O   HOH Z 126 " =    1.469
peak=    3.375 closest distance to " O   HOH Z  97 " =    2.098
peak=    3.374 closest distance to " CA  LYS A 290 " =    1.305
peak=    3.372 closest distance to " CG  ARG A 159 " =    0.982
peak=    3.372 closest distance to " CB  ALA A 104 " =    0.746
peak=    3.365 closest distance to " CB  ALA A 291 " =    1.358
peak=    3.364 closest distance to " CG  MET A 185 " =    1.206
peak=    3.362 closest distance to " OG BSER A 212 " =    2.871
peak=    3.360 closest distance to " O   HOH Z 344 " =    2.946
peak=    3.357 closest distance to " O   HOH Z 422 " =    2.663
peak=    3.352 closest distance to " O   HOH Z 405 " =    1.367
peak=    3.348 closest distance to " NE2 HIS A 207 " =    1.222
peak=    3.347 closest distance to " O   HOH Z 290 " =    1.081
peak=    3.347 closest distance to " OG  SER A  62 " =    3.024
peak=    3.346 closest distance to " O   HOH Z 424 " =    2.545
peak=    3.346 closest distance to " OG BSER A 134 " =    2.964
peak=    3.346 closest distance to " CG  GLN A 278 " =    1.249
peak=    3.338 closest distance to " O   HOH Z 250 " =    1.379
peak=    3.338 closest distance to " CG1 ILE A  49 " =    1.485
peak=    3.333 closest distance to " O   HOH Z  58 " =    1.793
peak=    3.332 closest distance to " CB  MET A  47 " =    0.980
peak=    3.331 closest distance to " CE3 TRP A  85 " =    1.177
peak=    3.331 closest distance to " CA  ALA A 158 " =    1.215
peak=    3.331 closest distance to " NH2BARG A 190 " =    1.549
peak=    3.325 closest distance to " CD1 LEU A 300 " =    1.179
peak=    3.324 closest distance to " C   GLN A  88 " =    1.490
peak=    3.323 closest distance to " N   SER A 135 " =    1.206
peak=    3.322 closest distance to " CG1BVAL A  72 " =    1.480
peak=    3.320 closest distance to " CB  HIS A 108 " =    0.848
peak=    3.319 closest distance to " CB  ASP A 140 " =    0.869
peak=    3.319 closest distance to " CA  ASN A 127 " =    1.093
peak=    3.319 closest distance to " O   HOH Z 391 " =    2.906
peak=    3.317 closest distance to " CA  ASN A 217 " =    1.297
peak=    3.316 closest distance to " O   HOH Z 291 " =    1.725
peak=    3.315 closest distance to " O   HOH Z 173 " =    1.672
peak=    3.307 closest distance to " OE1 GLN A 240 " =    1.560
peak=    3.304 closest distance to " CA  ASP A 162 " =    1.002
peak=    3.301 closest distance to " N   GLN A 278 " =    1.297
peak=    3.297 closest distance to " CB  ILE A 120 " =    1.412
peak=    3.291 closest distance to " CB  SER A  26 " =    1.603
peak=    3.291 closest distance to " O   ALA A 291 " =    1.466
peak=    3.288 closest distance to " CD  ARG A  24 " =    1.121
peak=    3.285 closest distance to " N   ALA A   1 " =    2.105
peak=    3.284 closest distance to " O   HOH Z 284 " =    3.069
peak=    3.283 closest distance to " CG  GLN A  89 " =    1.487
peak=    3.278 closest distance to " O   HOH Z 147 " =    1.696
peak=    3.276 closest distance to " CB  ARG A 139 " =    1.022
peak=    3.275 closest distance to " O   HOH Z 110 " =    1.537
peak=    3.266 closest distance to " NE1 TRP A 274 " =    0.956
peak=    3.266 closest distance to " CA  ALA A 154 " =    1.017
peak=    3.265 closest distance to " O   HOH Z 334 " =    1.553
peak=    3.262 closest distance to " O   HOH Z  85 " =    2.011
peak=    3.261 closest distance to " O   HOH Z 213 " =    2.379
peak=    3.260 closest distance to " O   HOH Z 154 " =    1.810
peak=    3.258 closest distance to " O   HOH Z  20 " =    1.641
peak=    3.258 closest distance to " N   SER A  12 " =    1.616
peak=    3.255 closest distance to " CB  TYR A  30 " =    1.584
peak=    3.254 closest distance to " CD  ARG A 269 " =    0.979
peak=    3.253 closest distance to " O   HOH Z 145 " =    3.732
peak=    3.252 closest distance to " CB  ALA A  34 " =    1.089
peak=    3.249 closest distance to " CD BLYS A 290 " =    1.053
peak=    3.247 closest distance to " O   HOH Z 145 " =    1.519
peak=    3.243 closest distance to " N   ALA A 256 " =    1.045
peak=    3.241 closest distance to " CZ3 TRP A  92 " =    1.320
peak=    3.240 closest distance to " CB  ALA A   1 " =    4.771
peak=    3.239 closest distance to " CH2 TRP A 266 " =    1.118
peak=    3.238 closest distance to " CZ3 TRP A 123 " =    1.472
peak=    3.237 closest distance to " O   HOH Z 417 " =    1.183
peak=    3.236 closest distance to " CD2 TRP A 179 " =    1.287
peak=    3.235 closest distance to " N   ASN A 127 " =    1.334
peak=    3.234 closest distance to " O   HOH Z 146 " =    1.563
peak=    3.234 closest distance to " CA  ALA A 160 " =    0.926
peak=    3.232 closest distance to " CA  MET A 105 " =    0.963
peak=    3.230 closest distance to " O   HOH Z 409 " =    2.730
peak=    3.225 closest distance to " O   MET A 105 " =    1.731
peak=    3.222 closest distance to " CB  LEU A 237 " =    0.813
peak=    3.221 closest distance to " ND2 ASN A 249 " =    0.837
peak=    3.220 closest distance to " CA  ARG A  36 " =    1.086
peak=    3.219 closest distance to " OD1BASN A 224 " =    2.351
peak=    3.211 closest distance to " O   PRO A 198 " =    1.303
peak=    3.210 closest distance to " N   TYR A  15 " =    0.902
peak=    3.204 closest distance to " O   ALA A 158 " =    1.392
peak=    3.203 closest distance to " NH2BARG A 145 " =    2.006
peak=    3.201 closest distance to " O   HOH Z 135 " =    1.969
peak=    3.198 closest distance to " CE  LYS A  48 " =    1.158
peak=    3.198 closest distance to " CA  LEU A 282 " =    1.139
peak=    3.191 closest distance to " O   HOH Z  44 " =    2.726
peak=    3.189 closest distance to " O   HOH Z 373 " =    1.559
peak=    3.188 closest distance to " NZ  LYS A  48 " =    1.284
peak=    3.187 closest distance to " CB  GLU A  46 " =    0.979
peak=    3.185 closest distance to " O   HOH Z 329 " =    3.959
peak=    3.185 closest distance to " CB  ARG A 138 " =    1.410
peak=    3.178 closest distance to " O   HOH Z 383 " =    2.263
peak=    3.176 closest distance to " CG2 ILE A  20 " =    1.553
peak=    3.176 closest distance to " O   HOH Z 132 " =    2.525
peak=    3.171 closest distance to " O   HOH Z  40 " =    1.998
peak=    3.167 closest distance to " CA  TYR A 186 " =    1.559
peak=    3.166 closest distance to " O   HOH Z 340 " =    2.170
peak=    3.166 closest distance to " NH1BARG A 145 " =    1.283
peak=    3.158 closest distance to " CD  ARG A 195 " =    3.455
peak=    3.154 closest distance to " N   SER A  97 " =    0.845
peak=    3.154 closest distance to " CB  ALA A   9 " =    1.521
peak=    3.150 closest distance to " O   TYR A 116 " =    1.263
peak=    3.150 closest distance to " O   HOH Z 197 " =    3.395
peak=    3.146 closest distance to " CD1 LEU A 281 " =    1.054
peak=    3.146 closest distance to " CB  ALA A 114 " =    1.508
peak=    3.145 closest distance to " CB  GLN A 103 " =    0.985
peak=    3.143 closest distance to " O   HOH Z  43 " =    2.177
peak=    3.141 closest distance to " O   HOH Z 392 " =    1.931
peak=    3.141 closest distance to " O   HOH Z 172 " =    2.914
peak=    3.140 closest distance to " O   HOH Z 350 " =    1.555
peak=    3.133 closest distance to " O   HOH Z 435 " =    1.929
peak=    3.128 closest distance to " ND1 HIS A  81 " =    1.731
peak=    3.126 closest distance to " CB  ALA A 248 " =    1.320
peak=    3.125 closest distance to " CB  GLU A 277 " =    3.785
peak=    3.123 closest distance to " OE2 GLU A  53 " =    2.010
peak=    3.123 closest distance to " O   HOH Z 425 " =    1.969
peak=    3.121 closest distance to " O   HOH Z 260 " =    1.429
peak=    3.120 closest distance to " CA  LEU A 101 " =    1.628
peak=    3.117 closest distance to " O   HOH Z 294 " =    1.473
peak=    3.115 closest distance to " OG BSER A 164 " =    2.313
peak=    3.108 closest distance to " O   HOH Z 252 " =    1.751
peak=    3.105 closest distance to " O   HOH Z 326 " =    2.212
peak=    3.088 closest distance to " CA  ARG A 102 " =    1.142
peak=    3.077 closest distance to " O   HOH Z 238 " =    3.638
peak=    3.071 closest distance to " CB  LEU A 300 " =    0.854
peak=    3.070 closest distance to " O   HOH Z 105 " =    1.617
peak=    3.067 closest distance to " CB  PHE A 204 " =    0.775
peak=    3.064 closest distance to " OG1 THR A 264 " =    0.860
peak=    3.060 closest distance to " O   HOH Z 130 " =    3.418
peak=    3.056 closest distance to " O   HOH Z   9 " =    1.711
peak=    3.055 closest distance to " CD2 LEU A 255 " =    1.578
peak=    3.055 closest distance to " CB  TRP A 150 " =    1.172
peak=    3.048 closest distance to " O   PRO A  90 " =    1.683
peak=    3.009 closest distance to " CB  ALA A 227 " =    0.946

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.737 - 5.340
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 199
   mapped sites are within: 0.737 - 5.340

peak=   -5.098 closest distance to " CG2 VAL A 230 " =    0.822
peak=   -4.440 closest distance to " CG  ARG A 138 " =    0.963
peak=   -4.408 closest distance to " CD  ARG A 156 " =    2.053
peak=   -4.289 closest distance to " CD  ARG A  14 " =    3.174
peak=   -4.286 closest distance to " CB  PRO A 243 " =    2.631
peak=   -4.171 closest distance to " O   HOH Z 266 " =    5.150
peak=   -4.098 closest distance to " OG BSER A 134 " =    1.407
peak=   -4.014 closest distance to " O   HOH Z 290 " =    1.203
peak=   -4.004 closest distance to " O   HOH Z 231 " =    0.873
peak=   -3.999 closest distance to " CD1 LEU A 255 " =    2.917
peak=   -3.991 closest distance to " O   HOH Z 351 " =    1.490
peak=   -3.939 closest distance to " O   PRO A 198 " =    1.196
peak=   -3.918 closest distance to " CB  ALA A  43 " =    2.560
peak=   -3.907 closest distance to " CA  GLY A 241 " =    2.302
peak=   -3.878 closest distance to " O   HOH Z 231 " =    1.813
peak=   -3.876 closest distance to " OG  SER A  87 " =    1.370
peak=   -3.847 closest distance to " CG2 VAL A 296 " =    1.422
peak=   -3.832 closest distance to " N   THR A 157 " =    1.424
peak=   -3.816 closest distance to " O   HOH Z 185 " =    2.191
peak=   -3.811 closest distance to " CB  ALA A 248 " =    2.078
peak=   -3.781 closest distance to " NH2 ARG A  79 " =    1.971
peak=   -3.780 closest distance to " CD  GLN A  58 " =    0.941
peak=   -3.779 closest distance to " CZ3 TRP A 179 " =    1.206
peak=   -3.771 closest distance to " O   HOH Z  43 " =    1.838
peak=   -3.754 closest distance to " CD2 LEU A   5 " =    0.969
peak=   -3.749 closest distance to " O   HOH Z 211 " =    1.370
peak=   -3.737 closest distance to " O   GLY A 203 " =    2.447
peak=   -3.731 closest distance to " CE2 TYR A  30 " =    2.644
peak=   -3.731 closest distance to " O   VAL A  67 " =    2.446
peak=   -3.728 closest distance to " O   HOH Z 389 " =    2.028
peak=   -3.697 closest distance to " O   HOH Z 166 " =    2.012
peak=   -3.677 closest distance to " CA  ASP A  27 " =    2.391
peak=   -3.674 closest distance to " CB  PRO A 163 " =    2.429
peak=   -3.671 closest distance to " O   HOH Z 191 " =    5.327
peak=   -3.670 closest distance to " O   ILE A  49 " =    1.709
peak=   -3.667 closest distance to " O   ARG A 145 " =    1.378
peak=   -3.651 closest distance to " CB  ALA A 161 " =    2.586
peak=   -3.641 closest distance to " O   SER A  22 " =    2.313
peak=   -3.638 closest distance to " CB  TYR A  15 " =    2.136
peak=   -3.632 closest distance to " O   HOH Z 359 " =    3.359
peak=   -3.628 closest distance to " O   VAL A 189 " =    2.606
peak=   -3.625 closest distance to " O   HOH Z  51 " =    0.980
peak=   -3.607 closest distance to " O   HOH Z 377 " =    1.983
peak=   -3.605 closest distance to " C   HIS A 108 " =    1.210
peak=   -3.591 closest distance to " CA  GLY A 203 " =    2.374
peak=   -3.584 closest distance to " CD  ARG A 138 " =    1.339
peak=   -3.581 closest distance to " CD2 LEU A 237 " =    2.828
peak=   -3.574 closest distance to " CG  MET A 105 " =    1.020
peak=   -3.567 closest distance to " CZ2 TRP A 274 " =    0.886
peak=   -3.567 closest distance to " CD  LYS A 289 " =    2.468
peak=   -3.566 closest distance to " O   HOH Z 359 " =    1.600
peak=   -3.565 closest distance to " C   LEU A 222 " =    0.823
peak=   -3.558 closest distance to " O   HOH Z 140 " =    1.353
peak=   -3.558 closest distance to " O   GLY A  80 " =    2.523
peak=   -3.554 closest distance to " CG1 VAL A 112 " =    2.619
peak=   -3.551 closest distance to " CA  GLY A  98 " =    1.889
peak=   -3.547 closest distance to " CD1 LEU A 228 " =    2.325
peak=   -3.544 closest distance to " O   HOH Z 394 " =    1.459
peak=   -3.542 closest distance to " OG  SER A  97 " =    2.199
peak=   -3.541 closest distance to " O   GLY A 211 " =    1.188
peak=   -3.541 closest distance to " CG  GLN A 223 " =    2.143
peak=   -3.539 closest distance to " O   GLY A  17 " =    1.260
peak=   -3.537 closest distance to " CB  CYS A 201 " =    2.257
peak=   -3.533 closest distance to " N   ALA A 226 " =    2.101
peak=   -3.527 closest distance to " O   PRO A 163 " =    1.932
peak=   -3.526 closest distance to " O   HOH Z 292 " =    1.623
peak=   -3.513 closest distance to " O   HOH Z  65 " =    1.054
peak=   -3.512 closest distance to " ND2 ASN A 249 " =    2.434
peak=   -3.511 closest distance to " O   SER A 135 " =    1.460
peak=   -3.504 closest distance to " CB  PHE A 192 " =    1.799
peak=   -3.499 closest distance to " O   HOH Z 131 " =    4.078
peak=   -3.497 closest distance to " CB  CYS A 201 " =    2.510
peak=   -3.488 closest distance to " O   HOH Z  60 " =    2.330
peak=   -3.482 closest distance to " OE1 GLN A  88 " =    1.196
peak=   -3.478 closest distance to " O   HOH Z 111 " =    2.100
peak=   -3.476 closest distance to " O   HOH Z  11 " =    1.930
peak=   -3.464 closest distance to " O   HOH Z 377 " =    0.949
peak=   -3.461 closest distance to " O   HOH Z 282 " =    5.106
peak=   -3.447 closest distance to " C   MET A 188 " =    1.464
peak=   -3.445 closest distance to " CA  ASP A 298 " =    1.059
peak=   -3.439 closest distance to " CG  TRP A 266 " =    1.765
peak=   -3.438 closest distance to " O   PRO A 198 " =    1.347
peak=   -3.436 closest distance to " O   HOH Z  52 " =    1.371
peak=   -3.434 closest distance to " O   HOH Z 389 " =    1.481
peak=   -3.428 closest distance to " CG  ASP A 231 " =    0.748
peak=   -3.422 closest distance to " C   GLU A 236 " =    0.841
peak=   -3.419 closest distance to " CE  LYS A  76 " =    2.763
peak=   -3.419 closest distance to " O   HOH Z 281 " =    2.693
peak=   -3.411 closest distance to " C   ALA A 158 " =    1.409
peak=   -3.410 closest distance to " NH2AARG A 275 " =    5.340
peak=   -3.409 closest distance to " CG2 THR A  18 " =    2.858
peak=   -3.403 closest distance to " O   HOH Z 176 " =    0.775
peak=   -3.401 closest distance to " O   HOH Z  73 " =    2.207
peak=   -3.401 closest distance to " O   HOH Z 201 " =    1.875
peak=   -3.397 closest distance to " ND2 ASN A 187 " =    1.526
peak=   -3.389 closest distance to " CE2 TYR A 116 " =    3.102
peak=   -3.387 closest distance to " ND2 ASN A  60 " =    1.572
peak=   -3.386 closest distance to " O   HOH Z 298 " =    1.114
peak=   -3.386 closest distance to " O   VAL A  67 " =    2.789
peak=   -3.381 closest distance to " N   ALA A  43 " =    2.490
peak=   -3.374 closest distance to " N   ASP A 270 " =    1.466
peak=   -3.373 closest distance to " O   HOH Z 407 " =    3.200
peak=   -3.371 closest distance to " O   HOH Z  39 " =    1.080
peak=   -3.368 closest distance to " CG2 THR A 178 " =    2.273
peak=   -3.368 closest distance to " CB  ALA A 244 " =    2.150
peak=   -3.359 closest distance to " O   HOH Z 177 " =    1.755
peak=   -3.357 closest distance to " O   HOH Z 350 " =    1.932
peak=   -3.352 closest distance to " OH  TYR A 214 " =    1.104
peak=   -3.351 closest distance to " CB  TRP A  85 " =    2.534
peak=   -3.350 closest distance to " CG  GLN A  88 " =    0.737
peak=   -3.348 closest distance to " OG1 THR A 178 " =    1.261
peak=   -3.348 closest distance to " N   GLN A  58 " =    1.909
peak=   -3.348 closest distance to " CB  PHE A 130 " =    1.321
peak=   -3.347 closest distance to " O   HOH Z 100 " =    1.237
peak=   -3.346 closest distance to " C   LYS A  76 " =    1.301
peak=   -3.346 closest distance to " O   HOH Z 134 " =    3.020
peak=   -3.331 closest distance to " O   HOH Z 198 " =    2.128
peak=   -3.327 closest distance to " O   HOH Z 102 " =    1.569
peak=   -3.322 closest distance to " OXT GLY A 302 " =    3.168
peak=   -3.316 closest distance to " O   HOH Z 426 " =    2.320
peak=   -3.316 closest distance to " OD1 ASN A 187 " =    1.578
peak=   -3.316 closest distance to " CE BMET A  47 " =    1.641
peak=   -3.315 closest distance to " N   ALA A 248 " =    1.544
peak=   -3.313 closest distance to " CG1 VAL A 197 " =    2.394
peak=   -3.313 closest distance to " CG  PHE A 283 " =    2.676
peak=   -3.312 closest distance to " CB  ASP A 132 " =    2.348
peak=   -3.310 closest distance to " CD2 LEU A 167 " =    1.851
peak=   -3.306 closest distance to " O   HOH Z 134 " =    3.697
peak=   -3.298 closest distance to " O   HOH Z 427 " =    1.770
peak=   -3.297 closest distance to " CB  ALA A 227 " =    2.424
peak=   -3.294 closest distance to " OG  SER A 206 " =    1.755
peak=   -3.287 closest distance to " CD  PRO A 213 " =    2.043
peak=   -3.282 closest distance to " O   HOH Z 166 " =    1.346
peak=   -3.276 closest distance to " CA  GLY A 133 " =    1.932
peak=   -3.275 closest distance to " CG2 VAL A 202 " =    2.687
peak=   -3.274 closest distance to " CD  PRO A 243 " =    2.073
peak=   -3.273 closest distance to " O   HOH Z  90 " =    2.849
peak=   -3.273 closest distance to " O   LEU A 101 " =    2.797
peak=   -3.259 closest distance to " O   SER A 271 " =    2.177
peak=   -3.253 closest distance to " OH  TYR A 172 " =    1.783
peak=   -3.247 closest distance to " O   HOH Z   2 " =    1.792
peak=   -3.238 closest distance to " CD2 HIS A 207 " =    2.457
peak=   -3.231 closest distance to " CE3 TRP A 150 " =    2.219
peak=   -3.228 closest distance to " CG1 VAL A 296 " =    1.476
peak=   -3.226 closest distance to " O   ALA A 180 " =    1.228
peak=   -3.224 closest distance to " CB  ALA A 114 " =    2.353
peak=   -3.224 closest distance to " CB  ALA A 248 " =    2.425
peak=   -3.218 closest distance to " O   HOH Z 313 " =    1.474
peak=   -3.217 closest distance to " CE2 PHE A 218 " =    2.477
peak=   -3.215 closest distance to " O   HOH Z 385 " =    2.061
peak=   -3.214 closest distance to " CD1 PHE A  61 " =    2.918
peak=   -3.213 closest distance to " O   HOH Z  24 " =    1.254
peak=   -3.212 closest distance to " O   HOH Z 111 " =    4.467
peak=   -3.211 closest distance to " ND2BASN A 224 " =    1.549
peak=   -3.210 closest distance to " CB  ALA A 291 " =    2.175
peak=   -3.206 closest distance to " CD  GLU A 277 " =    1.267
peak=   -3.204 closest distance to " CD1 ILE A 199 " =    2.551
peak=   -3.200 closest distance to " O   HOH Z 348 " =    1.772
peak=   -3.192 closest distance to " OD1 ASN A 301 " =    1.908
peak=   -3.191 closest distance to " O   HOH Z 108 " =    1.578
peak=   -3.190 closest distance to " O   HOH Z  63 " =    1.963
peak=   -3.189 closest distance to " CD1 LEU A 101 " =    2.291
peak=   -3.188 closest distance to " N   SER A 212 " =    1.978
peak=   -3.186 closest distance to " O   HOH Z  40 " =    3.858
peak=   -3.182 closest distance to " CD  ARG A 139 " =    1.604
peak=   -3.180 closest distance to " CG1 VAL A 230 " =    1.967
peak=   -3.177 closest distance to " OG BSER A 134 " =    1.838
peak=   -3.170 closest distance to " CD2 TYR A 293 " =    1.925
peak=   -3.169 closest distance to " O   GLY A  80 " =    2.602
peak=   -3.166 closest distance to " CG2 ILE A 151 " =    2.597
peak=   -3.163 closest distance to " O   HOH Z  38 " =    1.721
peak=   -3.155 closest distance to " CB  PRO A  54 " =    2.509
peak=   -3.152 closest distance to " O   HOH Z 241 " =    1.320
peak=   -3.152 closest distance to " OG ASER A 134 " =    1.416
peak=   -3.150 closest distance to " O   HOH Z 114 " =    1.947
peak=   -3.145 closest distance to " O   HOH Z 275 " =    1.493
peak=   -3.141 closest distance to " O   HOH Z 412 " =    4.258
peak=   -3.139 closest distance to " CE3 TRP A  70 " =    1.688
peak=   -3.139 closest distance to " CD1 PHE A  59 " =    2.025
peak=   -3.134 closest distance to " CZ2 TRP A 179 " =    2.387
peak=   -3.133 closest distance to " O   HOH Z 353 " =    1.939
peak=   -3.129 closest distance to " N   VAL A  72 " =    1.457
peak=   -3.123 closest distance to " O   HOH Z 357 " =    1.927
peak=   -3.121 closest distance to " OG  SER A  63 " =    1.102
peak=   -3.112 closest distance to " O   HOH Z 371 " =    1.431
peak=   -3.110 closest distance to " CG1 VAL A 250 " =    2.781
peak=   -3.108 closest distance to " CE  MET A 105 " =    2.431
peak=   -3.108 closest distance to " NH2BARG A 275 " =    1.624
peak=   -3.101 closest distance to " N   MET A 188 " =    1.741
peak=   -3.090 closest distance to " O   HOH Z 139 " =    1.039
peak=   -3.088 closest distance to " CG  GLU A 152 " =    1.549
peak=   -3.084 closest distance to " CD1 TYR A 247 " =    2.530
peak=   -3.084 closest distance to " O   HOH Z 149 " =    2.233
peak=   -3.075 closest distance to " CE BMET A  47 " =    1.142
peak=   -3.062 closest distance to " ND2 ASN A  45 " =    1.408
peak=   -3.057 closest distance to " NH2 ARG A 219 " =    1.687
peak=   -3.052 closest distance to " CD1 ILE A 239 " =    2.253
peak=   -3.040 closest distance to " OD1 ASP A 171 " =    1.637

================= 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    :  0.4636 0.4541   6.266459e+00   6.246662e+00
   1_bss:  0.4563 0.4377   6.259795e+00   6.236765e+00
   1_xyz:  0.3640 0.3838   6.121571e+00   6.152382e+00
   1_adp:  0.3129 0.3627   6.020528e+00   6.115363e+00
   1_occ:  0.3126 0.3627   6.019748e+00   6.115842e+00
   2_bss:  0.3081 0.3556   6.019008e+00   6.112834e+00
   2_xyz:  0.2356 0.2863   5.785121e+00   5.927896e+00
   2_adp:  0.2152 0.2708   5.715361e+00   5.877695e+00
   2_occ:  0.2150 0.2705   5.715027e+00   5.877658e+00
   3_bss:  0.2139 0.2686   5.714162e+00   5.875447e+00
   3_xyz:  0.1526 0.1997   5.409877e+00   5.616377e+00
   3_adp:  0.1378 0.1866   5.324589e+00   5.545279e+00
   3_occ:  0.1377 0.1866   5.324270e+00   5.544958e+00
   4_bss:  0.1377 0.1859   5.322315e+00   5.541994e+00
   4_xyz:  0.1260 0.1739   5.248069e+00   5.477412e+00
   4_adp:  0.1254 0.1692   5.235769e+00   5.452761e+00
   4_occ:  0.1253 0.1691   5.235293e+00   5.452028e+00
   5_bss:  0.1253 0.1690   5.235079e+00   5.451820e+00
   5_xyz:  0.1182 0.1608   5.187159e+00   5.413502e+00
   5_adp:  0.1162 0.1604   5.178810e+00   5.412804e+00
   5_occ:  0.1161 0.1604   5.178526e+00   5.412440e+00
   5_bss:  0.1163 0.1597   5.177994e+00   5.409764e+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:  0.349  10.847   7.821   9.751   8.335   0.000   0.000   0.000
   1_xyz:  0.349  10.847   7.821   9.751   8.335   0.000   0.000   0.000
   1_adp:  0.349  10.847   7.821   9.751   8.335   0.000   0.000   0.000
   1_occ:  0.349  10.847   7.821   9.751   8.335   0.000   0.000   0.000
   2_bss:  0.354  50.000   4.358   5.358   4.939   0.000   0.000   0.000
   2_xyz:  0.354  50.000   4.358   5.358   4.939   0.000   0.000   0.000
   2_adp:  0.354  50.000   4.358   5.358   4.939   0.000   0.000   0.000
   2_occ:  0.354  50.000   4.358   5.358   4.939   0.000   0.000   0.000
   3_bss:  0.344  50.000   2.912   3.173   3.908   0.000   0.000   0.000
   3_xyz:  0.344  50.000   2.912   3.173   3.908   0.000   0.000   0.000
   3_adp:  0.344  50.000   2.912   3.173   3.908   0.000   0.000   0.000
   3_occ:  0.344  50.000   2.912   3.173   3.908   0.000   0.000   0.000
   4_bss:  0.328  50.000   2.344   2.181   3.472   0.000   0.000   0.000
   4_xyz:  0.328  50.000   2.344   2.181   3.472   0.000   0.000   0.000
   4_adp:  0.328  50.000   2.344   2.181   3.472   0.000   0.000   0.000
   4_occ:  0.328  50.000   2.344   2.181   3.472   0.000   0.000   0.000
   5_bss:  0.328  50.000   2.182   1.945   3.435   0.000   0.000   0.000
   5_xyz:  0.328  50.000   2.182   1.945   3.435   0.000   0.000   0.000
   5_adp:  0.328  50.000   2.182   1.945   3.435   0.000   0.000   0.000
   5_occ:  0.328  50.000   2.182   1.945   3.435   0.000   0.000   0.000
   5_bss:  0.328  52.521  -0.339  -0.575   0.914   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.541 0.4762  0.5513    62113.368
   1_bss:  53.675 0.4730  0.7026    60190.151
   1_xyz:  44.165 0.5909  0.8563    43381.182
   1_adp:  39.403 0.6496  0.9709    37545.128
   1_occ:  39.440 0.6491  0.9693    37575.014
   2_bss:  39.034 0.6539  0.8568    37011.061
   2_xyz:  29.446 0.7632  0.9649    21779.473
   2_adp:  26.985 0.7908  0.9861    19047.594
   2_occ:  26.994 0.7906  0.9857    19030.668
   3_bss:  26.870 0.7920  0.9335    18888.917
   3_xyz:  19.358 0.8674  0.9926    10347.272
   3_adp:  17.633 0.8838  0.9975     8997.287
   3_occ:  17.629 0.8838  0.9973     8985.301
   4_bss:  17.567 0.8842  0.9736     8912.787
   4_xyz:  16.029 0.8979  0.9781     7689.602
   4_adp:  15.401 0.9037  0.9783     7353.045
   4_occ:  15.388 0.9038  0.9781     7333.144
   5_bss:  15.383 0.9038  0.9731     7328.937
   5_xyz:  14.552 0.9106  0.9770     6726.800
   5_adp:  14.520 0.9110  0.9737     6711.408
   5_occ:  14.515 0.9110  0.9736     6701.576
   5_bss:  14.488 0.9111  0.9734     6656.626
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3796e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3796e+01
   1_xyz:   1.622  0.013  0.104 18.204  0.006  4.109   1.3202e-01
   1_adp:   1.622  0.013  0.104 18.204  0.006  4.109   1.3202e-01
   1_occ:   1.622  0.013  0.104 18.204  0.006  4.109   1.3202e-01
   2_bss:   1.622  0.013  0.104 18.204  0.006  4.109   1.3202e-01
   2_xyz:   1.071  0.007  0.075 16.024  0.004  4.123   6.9903e-02
   2_adp:   1.071  0.007  0.075 16.024  0.004  4.123   6.9903e-02
   2_occ:   1.071  0.007  0.075 16.024  0.004  4.123   6.9903e-02
   3_bss:   1.071  0.007  0.075 16.024  0.004  4.123   6.9903e-02
   3_xyz:   1.076  0.007  0.083 15.863  0.004  4.123   6.8188e-02
   3_adp:   1.076  0.007  0.083 15.863  0.004  4.123   6.8188e-02
   3_occ:   1.076  0.007  0.083 15.863  0.004  4.123   6.8188e-02
   4_bss:   1.076  0.007  0.083 15.863  0.004  4.123   6.8188e-02
   4_xyz:   0.916  0.006  0.072 15.567  0.003  4.125   5.4745e-02
   4_adp:   0.916  0.006  0.072 15.567  0.003  4.125   5.4745e-02
   4_occ:   0.916  0.006  0.072 15.567  0.003  4.125   5.4745e-02
   5_bss:   0.916  0.006  0.072 15.567  0.003  4.125   5.4745e-02
   5_xyz:   0.995  0.007  0.079 15.561  0.003  4.111   6.0900e-02
   5_adp:   0.995  0.007  0.079 15.561  0.003  4.111   6.0900e-02
   5_occ:   0.995  0.007  0.079 15.561  0.003  4.111   6.0900e-02
   5_bss:   0.995  0.007  0.079 15.561  0.003  4.111   6.0900e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9743e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9743e+00
   1_xyz:  12.900  0.177  0.418 87.437  0.033  2.218   9.5252e-02
   1_adp:  12.900  0.177  0.418 87.437  0.033  2.218   9.5252e-02
   1_occ:  12.900  0.177  0.418 87.437  0.033  2.218   9.5252e-02
   2_bss:  12.900  0.177  0.418 87.437  0.033  2.218   9.5252e-02
   2_xyz:   8.071  0.081  0.292 89.115  0.042  2.306   4.8203e-02
   2_adp:   8.071  0.081  0.292 89.115  0.042  2.306   4.8203e-02
   2_occ:   8.071  0.081  0.292 89.115  0.042  2.306   4.8203e-02
   3_bss:   8.071  0.081  0.292 89.115  0.042  2.306   4.8203e-02
   3_xyz:   7.590  0.068  0.434 81.727  0.027  2.250   4.4815e-02
   3_adp:   7.590  0.068  0.434 81.727  0.027  2.250   4.4815e-02
   3_occ:   7.590  0.068  0.434 81.727  0.027  2.250   4.4815e-02
   4_bss:   7.590  0.068  0.434 81.727  0.027  2.250   4.4815e-02
   4_xyz:   7.564  0.048  0.330 82.822  0.035  2.372   3.1455e-02
   4_adp:   7.564  0.048  0.330 82.822  0.035  2.372   3.1455e-02
   4_occ:   7.564  0.048  0.330 82.822  0.035  2.372   3.1455e-02
   5_bss:   7.564  0.048  0.330 82.822  0.035  2.372   3.1455e-02
   5_xyz:   8.982  0.061  0.393 84.236  0.037  2.314   4.0725e-02
   5_adp:   8.982  0.061  0.393 84.236  0.037  2.314   4.0725e-02
   5_occ:   8.982  0.061  0.393 84.236  0.037  2.314   4.0725e-02
   5_bss:   8.982  0.061  0.393 84.236  0.037  2.314   4.0725e-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:  77.07   0.00  12.54  66.47   0.00   9.96  77.07   0.00  26.61
   1_occ:  77.07   0.00  12.54  66.47   0.00   9.96  77.07   0.00  26.61
   2_bss:  77.07   0.00  12.54  66.47   0.00   9.96  77.07   0.00  26.61
   2_xyz:  77.07   0.00  12.54  66.47   0.00   9.96  77.07   0.00  26.61
   2_adp:  83.89   0.00  12.58  72.56   0.00   8.92  83.89   1.02  32.49
   2_occ:  83.89   0.00  12.58  72.56   0.00   8.92  83.89   1.02  32.49
   3_bss:  83.89   0.00  12.58  72.56   0.00   8.92  83.89   1.02  32.49
   3_xyz:  83.89   0.00  12.58  72.56   0.00   8.92  83.89   1.02  32.49
   3_adp:  84.07   0.00  13.06  80.24   0.00   8.66  84.07   1.75  37.06
   3_occ:  84.07   0.00  13.06  80.24   0.00   8.66  84.07   1.75  37.06
   4_bss:  84.07   0.00  13.06  80.24   0.00   8.66  84.07   1.75  37.06
   4_xyz:  84.07   0.00  13.06  80.24   0.00   8.66  84.07   1.75  37.06
   4_adp:  81.07   0.00  12.57  79.78   0.00   8.40  81.07   2.31  35.32
   4_occ:  81.07   0.00  12.57  79.78   0.00   8.40  81.07   2.31  35.32
   5_bss:  81.07   0.00  12.57  79.78   0.00   8.40  81.07   2.31  35.32
   5_xyz:  81.07   0.00  12.57  79.78   0.00   8.40  81.07   2.31  35.32
   5_adp:  82.27   0.00  12.55  82.27   0.00   8.35  78.84   1.96  35.40
   5_occ:  82.27   0.00  12.55  82.27   0.00   8.35  78.84   1.96  35.40
   5_bss:  84.79   2.52  15.07  84.79   2.52  10.87  81.36   4.48  37.92
------------------------------------------------------------------------
 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:    1.228    0.012    0.406
   1_adp:    1.228    0.012    0.406
   1_occ:    1.228    0.012    0.406
   2_bss:    1.228    0.012    0.406
   2_xyz:    1.479    0.041    0.533
   2_adp:    1.479    0.041    0.533
   2_occ:    1.479    0.041    0.533
   3_bss:    1.479    0.041    0.533
   3_xyz:    1.581    0.019    0.629
   3_adp:    1.581    0.019    0.629
   3_occ:    1.581    0.019    0.629
   4_bss:    1.581    0.019    0.629
   4_xyz:    1.774    0.030    0.648
   4_adp:    1.774    0.030    0.648
   4_occ:    1.774    0.030    0.648
   5_bss:    1.774    0.030    0.648
   5_xyz:    1.829    0.046    0.669
   5_adp:    1.829    0.046    0.669
   5_occ:    1.829    0.046    0.669
   5_bss:    1.829    0.046    0.669
------------------------------------------------------------------------

CPU time actual refinement: 279.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_875/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_875/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_875/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_875/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_875/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 279.24 
  Macro-tasks:
    bulk solvent and scale       = 35.24  
    individual site refinement   = 120.38 
    weights calculation          = 26.21  
    collect and process          = 5.44   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 187.36 
  Micro-tasks:
    mask                            = 2.01   
    f_calc                          = 84.68  
    alpha_beta                      = 7.18   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 95.64  
    fmodel                         = 5.97   
    r_factors                      = 0.19   
    phase_errors                   = 8.77   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 205.68 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.847 micro seconds
Total CPU time: 4.84 minutes
from_scatterers_fft:    656 calls, 84.40 s
gradients_fft:          600 calls, 83.27 s

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

# Date 2008-01-16 Time 02:37:26 PST -0800 (1200479846.84 s)
Start R-work = 0.4636, R-free = 0.4541 (no bulk solvent and anisotropic scale)
Final R-work = 0.1333, R-free = 0.1769 (no bulk solvent and anisotropic scale)

Start R-work = 0.4563, R-free = 0.4377
Final R-work = 0.1163, R-free = 0.1597