# Date 2008-01-16 Time 01:58:46 PST -0800 (1200477526.33 s)
#phil __OFF__

Command line arguments: "../648.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32349
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 648

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.4607, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.40, per 1000 atoms: 1.20


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.98262
Completeness in resolution range: 0.9461
Completeness with d_max=infinity: 0.94323

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9826

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.98262
Completeness in resolution range: 0.9461
Completeness with d_max=infinity: 0.94323

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2428 [2177/2201]  1957   220  10.1%
  bin  2:  4.2428 -  3.3800 [2082/2102]  1874   208  10.0%
  bin  3:  3.3800 -  2.9564 [2070/2089]  1865   205   9.9%
  bin  4:  2.9564 -  2.6878 [2024/2054]  1818   206  10.2%
  bin  5:  2.6878 -  2.4961 [2050/2069]  1850   200   9.8%
  bin  6:  2.4961 -  2.3495 [2006/2031]  1801   205  10.2%
  bin  7:  2.3495 -  2.2322 [2015/2043]  1817   198   9.8%
  bin  8:  2.2322 -  2.1353 [2003/2039]  1801   202  10.1%
  bin  9:  2.1353 -  2.0533 [1995/2037]  1800   195   9.8%
  bin 10:  2.0533 -  1.9826 [1167/2040]  1047   120  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_648/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.48 -     2.17: 9
        2.17 -     2.85: 1090
        2.85 -     3.53: 4379
        3.53 -     4.22: 9194
        4.22 -     4.90: 13440
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.484 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.578 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.596 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.714 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.714 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28107 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_648/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_648/model_refine_001.geo

CPU time processing inputs: 9.03


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.4607 88.54975 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: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4831   r_free= 0.4689   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.284141                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7324 0.99   1414  154 0.4034 0.3773      6.6172      6.5413|
|  2:  4.7324 -  3.7756 0.99   1359  154 0.3936 0.4062      6.7766      6.8219|
|  3:  3.7756 -  3.3040 0.99   1330  146 0.4408 0.4054      6.6752      6.6439|
|  4:  3.3040 -  3.0045 0.99   1325  150 0.4868 0.4441      6.5462      6.4754|
|  5:  3.0045 -  2.7906 0.99   1308  147 0.5116 0.4651      6.3625      6.3742|
|  6:  2.7906 -  2.6270 0.99   1317  145 0.5120 0.5661      6.2802      6.2215|
|  7:  2.6270 -  2.4961 0.99   1311  143 0.5213 0.5058      6.2292       6.196|
|  8:  2.4961 -  2.3878 0.98   1288  143 0.5369 0.4826      6.1972      6.1795|
|  9:  2.3878 -  2.2963 0.98   1289  144 0.5154 0.5640       6.112      6.1845|
| 10:  2.2963 -  2.2173 1.00   1286  145 0.5380 0.4955      6.1107      6.0849|
| 11:  2.2173 -  2.1481 0.98   1295  145 0.5227 0.5144      6.0295      6.0411|
| 12:  2.1481 -  2.0869 0.98   1277  141 0.5292 0.5146      5.9695       5.955|
| 13:  2.0869 -  2.0321 0.96   1262  141 0.5290 0.5215      5.8716       5.824|
| 14:  2.0321 -  1.9826 0.43    569   61 0.5247 0.4846       5.891      5.8047|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7324  1414   154  0.70  33.93   0.79     0.75      70458.85|
|  2:  4.7324 -  3.7756  1359   154  0.72  33.84   0.87     0.79     102430.63|
|  3:  3.7756 -  3.3040  1330   146  0.62  42.33   0.83     0.74     107429.14|
|  4:  3.3040 -  3.0045  1325   150  0.53  49.44   0.77     0.62      96239.48|
|  5:  3.0045 -  2.7906  1308   147  0.43  57.49   0.75     0.50      79349.60|
|  6:  2.7906 -  2.6270  1317   145  0.37  62.12   0.71     0.43      73989.69|
|  7:  2.6270 -  2.4961  1311   143  0.33  64.87   0.72     0.39      68860.59|
|  8:  2.4961 -  2.3878  1288   143  0.33  64.91   0.72     0.39      61651.84|
|  9:  2.3878 -  2.2963  1289   144  0.34  64.25   0.72     0.41      55939.34|
| 10:  2.2963 -  2.2173  1286   145  0.34  64.27   0.73     0.41      49502.91|
| 11:  2.2173 -  2.1481  1295   145  0.32  65.75   0.75     0.41      47793.06|
| 12:  2.1481 -  2.0869  1277   141  0.33  65.35   0.74     0.41      42353.17|
| 13:  2.0869 -  2.0321  1262   141  0.30  67.46   0.71     0.38      37952.23|
| 14:  2.0321 -  1.9826   569    61  0.31  67.12   0.77     0.34      32773.64|
|alpha:            min =        0.34 max =            0.79 mean =         0.51|
|beta:             min =    32773.64 max =       107429.14 mean =     67977.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.66|
|phase err.(test): min =        0.00 max =           89.87 mean =        56.93|
|-----------------------------------------------------------------------------|

============================== 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 = 14.035122             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.403   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.277575              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.718   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       27 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1493 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2615 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3885 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5046 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6535 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7672 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.020 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.882 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    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 = 11.999)------------------------------------------|
|    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: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4891   r_free= 0.4714   ksol= 0.00   Bsol= 0.00   scale= 0.756    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.286734                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4739   r_free= 0.4560   ksol= 0.35   Bsol= 20.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.44,7.97,12.07,0.00,0.00,0.00); trace/3= 8.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.276963                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.001369             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.340   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.144418              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.046   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4739      final r-factor (work) = 0.3921          |
| start r-factor (free) = 0.4560      final r-factor (free) = 0.4150          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.7009 = 12.00 * 0.50 * 6.2794 + 1.00 * 54.0201                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.3174 = 12.00 * 0.50 * 6.1953 + 1.00 * 0.1413                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3921      final r-factor (work) = 0.3468          |
| start r-factor (free) = 0.4150      final r-factor (free) = 0.3981          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1044 = 1.14 * 1.00 * 6.1953 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0058 = 1.14 * 1.00 * 6.1071 + 1.00 * 0.0167                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    60.11   13.16    None  None   None       |
|    all(noH): 2823   0      0.00    60.11   13.16    None  None   None       |
|    Sol.    : 438    0      0.00    60.11   24.46    None  None   None       |
|    Mac.    : 2385   0      0.00    53.85   11.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.011:  842   |   5:    30.055 -  36.066:  120        |
|      1:     6.011 -  12.022:  740   |   6:    36.066 -  42.077:   67        |
|      2:    12.022 -  18.033:  481   |   7:    42.077 -  48.088:   37        |
|      3:    18.033 -  24.044:  318   |   8:    48.088 -  54.099:   19        |
|      4:    24.044 -  30.055:  193   |   9:    54.099 -  60.110:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3468 r_free = 0.3981             target_work(ml) = 6.090         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3460 r_free = 0.3987             target_work(ml) = 6.089         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3460   r_free= 0.3987   ksol= 0.35   Bsol= 20.00   scale= 1.104   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.44,7.97,12.07,0.00,0.00,0.00); trace/3= 8.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.089196                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3437   r_free= 0.3956   ksol= 0.34   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,4.29,8.50,0.00,0.00,0.00); trace/3= 5.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.090483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.271466             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.157   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.521999              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.664  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3437      final r-factor (work) = 0.2468          |
| start r-factor (free) = 0.3956      final r-factor (free) = 0.3065          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.4887 = 10.27 * 0.50 * 6.1038 + 1.00 * 0.1413                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.6828 = 10.27 * 0.50 * 5.9544 + 1.00 * 0.1028                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2468      final r-factor (work) = 0.2149          |
| start r-factor (free) = 0.3065      final r-factor (free) = 0.2754          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1249 = 0.52 * 1.00 * 5.9544 + 1.00 * 0.0168                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0152 = 0.52 * 1.00 * 5.7537 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 41     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.38   12.82    None  None   None       |
|    all(noH): 2823   0      0.00    71.38   12.82    None  None   None       |
|    Sol.    : 438    0      0.00    71.38   32.63    None  None   None       |
|    Mac.    : 2385   0      0.00    57.52   9.18     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 -   7.138: 1205   |   5:    35.691 -  42.829:  110        |
|      1:     7.138 -  14.276:  790   |   6:    42.829 -  49.967:   68        |
|      2:    14.276 -  21.414:  330   |   7:    49.967 -  57.105:   35        |
|      3:    21.414 -  28.553:  145   |   8:    57.105 -  64.243:   11        |
|      4:    28.553 -  35.691:  125   |   9:    64.243 -  71.381:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2149 r_free = 0.2754             target_work(ml) = 5.703         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2149 r_free = 0.2751             target_work(ml) = 5.703         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2149   r_free= 0.2751   ksol= 0.34   Bsol= 50.00   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,4.29,8.50,0.00,0.00,0.00); trace/3= 5.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.703158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2126   r_free= 0.2750   ksol= 0.32   Bsol= 59.52   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.12,2.48,5.32,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.703254                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.674236              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.710   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.678784              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.309  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2126      final r-factor (work) = 0.1700          |
| start r-factor (free) = 0.2750      final r-factor (free) = 0.2250          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8062 = 2.67 * 0.50 * 5.7612 + 1.00 * 0.1028                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5654 = 2.67 * 0.50 * 5.6119 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1700      final r-factor (work) = 0.1585          |
| start r-factor (free) = 0.2250      final r-factor (free) = 0.2143          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8211 = 0.68 * 1.00 * 5.6119 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7305 = 0.68 * 1.00 * 5.4747 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.37   13.58    None  None   None       |
|    all(noH): 2823   0      0.00    82.37   13.58    None  None   None       |
|    Sol.    : 438    0      0.82    82.37   38.42    None  None   None       |
|    Mac.    : 2385   0      0.00    79.14   9.02     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 -   8.237: 1460   |   5:    41.185 -  49.422:  103        |
|      1:     8.237 -  16.474:  694   |   6:    49.422 -  57.659:   69        |
|      2:    16.474 -  24.711:  210   |   7:    57.659 -  65.896:   51        |
|      3:    24.711 -  32.948:  131   |   8:    65.896 -  74.133:   13        |
|      4:    32.948 -  41.185:   83   |   9:    74.133 -  82.370:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1585 r_free = 0.2143             target_work(ml) = 5.451         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1584 r_free = 0.2142             target_work(ml) = 5.450         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1584   r_free= 0.2142   ksol= 0.32   Bsol= 59.52   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.12,2.48,5.32,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.450426                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1582   r_free= 0.2141   ksol= 0.33   Bsol= 59.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,1.97,4.41,0.00,0.00,0.00); trace/3= 2.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.450206                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.734847              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.114   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.308489              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.156  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1582      final r-factor (work) = 0.1327          |
| start r-factor (free) = 0.2141      final r-factor (free) = 0.1849          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5499 = 2.73 * 0.50 * 5.4760 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4215 = 2.73 * 0.50 * 5.3798 + 1.00 * 0.0649                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1327      final r-factor (work) = 0.1295          |
| start r-factor (free) = 0.1849      final r-factor (free) = 0.1784          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6741 = 0.31 * 1.00 * 5.3798 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6443 = 0.31 * 1.00 * 5.2912 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.93   13.27    None  None   None       |
|    all(noH): 2823   0      0.00    81.93   13.27    None  None   None       |
|    Sol.    : 438    0      1.76    81.93   37.93    None  None   None       |
|    Mac.    : 2385   0      0.00    79.63   8.74     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 -   8.193: 1527   |   5:    40.966 -  49.160:   98        |
|      1:     8.193 -  16.387:  667   |   6:    49.160 -  57.353:   69        |
|      2:    16.387 -  24.580:  189   |   7:    57.353 -  65.546:   53        |
|      3:    24.580 -  32.773:  106   |   8:    65.546 -  73.740:   12        |
|      4:    32.773 -  40.966:   93   |   9:    73.740 -  81.933:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1295 r_free = 0.1784             target_work(ml) = 5.271         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1293 r_free = 0.1783             target_work(ml) = 5.270         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1293   r_free= 0.1783   ksol= 0.33   Bsol= 59.52   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,1.97,4.41,0.00,0.00,0.00); trace/3= 2.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.270498                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1295   r_free= 0.1783   ksol= 0.33   Bsol= 59.52   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.60,1.81,4.03,0.00,0.00,0.00); trace/3= 2.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.270624                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.505391              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.063  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.486205              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.159  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1295      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1783      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3387 = 3.51 * 0.50 * 5.2911 + 1.00 * 0.0649                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2544 = 3.51 * 0.50 * 5.2357 + 1.00 * 0.0779                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1661      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 28.7357 = 5.49 * 1.00 * 5.2357 + 1.00 * 0.0118                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 28.4736 = 5.49 * 1.00 * 5.1873 + 1.00 * 0.0149                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.70   13.47    None  None   None       |
|    all(noH): 2823   0      0.00    92.70   13.47    None  None   None       |
|    Sol.    : 438    0      1.85    92.70   39.08    None  None   None       |
|    Mac.    : 2385   0      0.00    85.34   8.77     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.270: 1676   |   5:    46.352 -  55.622:   91        |
|      1:     9.270 -  18.541:  582   |   6:    55.622 -  64.892:   55        |
|      2:    18.541 -  27.811:  157   |   7:    64.892 -  74.163:   32        |
|      3:    27.811 -  37.081:  117   |   8:    74.163 -  83.433:   13        |
|      4:    37.081 -  46.352:   94   |   9:    83.433 -  92.703:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1659             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1157 r_free = 0.1658             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1658   ksol= 0.33   Bsol= 59.52   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.60,1.81,4.03,0.00,0.00,0.00); trace/3= 2.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.187309                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7324 0.99   1414  154 0.0990 0.1318      5.4056      5.5664|
|  2:  4.7324 -  3.7756 0.99   1359  154 0.0861 0.1173      5.4584      5.6827|
|  3:  3.7756 -  3.3040 0.99   1330  146 0.1112 0.1538      5.5136      5.8509|
|  4:  3.3040 -  3.0045 0.99   1325  150 0.1269 0.1806      5.4815      5.6709|
|  5:  3.0045 -  2.7906 0.99   1308  147 0.1382 0.1649      5.3687      5.5736|
|  6:  2.7906 -  2.6270 0.99   1317  145 0.1283 0.2237      5.2512      5.5648|
|  7:  2.6270 -  2.4961 0.99   1311  143 0.1366 0.1679      5.2339      5.3793|
|  8:  2.4961 -  2.3878 0.98   1288  143 0.1211 0.1698      5.1335      5.3871|
|  9:  2.3878 -  2.2963 0.98   1289  144 0.1250 0.1967      5.0857      5.3761|
| 10:  2.2963 -  2.2173 1.00   1286  145 0.1167 0.1759      4.9938      5.2335|
| 11:  2.2173 -  2.1481 0.98   1295  145 0.1183 0.1928      4.9786      5.3272|
| 12:  2.1481 -  2.0869 0.98   1277  141 0.1206 0.1786      4.9316      5.2167|
| 13:  2.0869 -  2.0321 0.96   1262  141 0.1075 0.1782      4.7825      5.0142|
| 14:  2.0321 -  1.9826 0.43    569   61 0.0863 0.1582      4.6132      4.9338|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7324  1414   154  0.93   9.85   0.97     0.95       8016.08|
|  2:  4.7324 -  3.7756  1359   154  0.95   8.47   1.01     1.00       9874.33|
|  3:  3.7756 -  3.3040  1330   146  0.93  12.19   1.03     1.02      11264.04|
|  4:  3.3040 -  3.0045  1325   150  0.91  14.28   1.01     0.99      10888.26|
|  5:  3.0045 -  2.7906  1308   147  0.90  16.47   1.00     0.98       9141.38|
|  6:  2.7906 -  2.6270  1317   145  0.89  17.30   0.98     0.95       7807.95|
|  7:  2.6270 -  2.4961  1311   143  0.89  17.23   0.98     0.95       7173.34|
|  8:  2.4961 -  2.3878  1288   143  0.90  16.78   0.99     0.97       6276.68|
|  9:  2.3878 -  2.2963  1289   144  0.90  16.60   0.99     0.95       5596.43|
| 10:  2.2963 -  2.2173  1286   145  0.89  16.68   1.00     0.96       4842.04|
| 11:  2.2173 -  2.1481  1295   145  0.89  17.68   0.99     0.94       4894.24|
| 12:  2.1481 -  2.0869  1277   141  0.89  17.14   1.00     0.99       4505.30|
| 13:  2.0869 -  2.0321  1262   141  0.89  17.02   0.99     0.96       3510.24|
| 14:  2.0321 -  1.9826   569    61  0.93  12.59   0.97     0.95       2419.28|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2419.28 max =        11264.04 mean =      7103.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.05|
|phase err.(test): min =        0.00 max =           89.77 mean =        14.45|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1659   ksol= 0.33   Bsol= 62.12   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,-0.68,1.47,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.187375                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1659   ksol= 0.33   Bsol= 62.12   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,-0.68,1.47,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.187375                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7324 0.99   1414  154 0.0990 0.1319      5.4061      5.5674|
|  2:  4.7324 -  3.7756 0.99   1359  154 0.0861 0.1174       5.459      5.6832|
|  3:  3.7756 -  3.3040 0.99   1330  146 0.1112 0.1539      5.5141      5.8519|
|  4:  3.3040 -  3.0045 0.99   1325  150 0.1269 0.1805      5.4816       5.671|
|  5:  3.0045 -  2.7906 0.99   1308  147 0.1382 0.1648      5.3684      5.5732|
|  6:  2.7906 -  2.6270 0.99   1317  145 0.1283 0.2238      5.2512       5.565|
|  7:  2.6270 -  2.4961 0.99   1311  143 0.1366 0.1682       5.234      5.3805|
|  8:  2.4961 -  2.3878 0.98   1288  143 0.1212 0.1696      5.1341      5.3868|
|  9:  2.3878 -  2.2963 0.98   1289  144 0.1249 0.1969      5.0859       5.377|
| 10:  2.2963 -  2.2173 1.00   1286  145 0.1167 0.1758      4.9938      5.2328|
| 11:  2.2173 -  2.1481 0.98   1295  145 0.1183 0.1924      4.9781      5.3261|
| 12:  2.1481 -  2.0869 0.98   1277  141 0.1206 0.1784      4.9313      5.2162|
| 13:  2.0869 -  2.0321 0.96   1262  141 0.1075 0.1784       4.782      5.0141|
| 14:  2.0321 -  1.9826 0.43    569   61 0.0864 0.1578      4.6129      4.9327|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7324  1414   154  0.93   9.86   0.97     0.95       8027.31|
|  2:  4.7324 -  3.7756  1359   154  0.95   8.49   1.01     1.00       9889.48|
|  3:  3.7756 -  3.3040  1330   146  0.93  12.20   1.03     1.03      11280.75|
|  4:  3.3040 -  3.0045  1325   150  0.91  14.29   1.01     1.00      10892.57|
|  5:  3.0045 -  2.7906  1308   147  0.90  16.46   1.00     0.99       9142.91|
|  6:  2.7906 -  2.6270  1317   145  0.89  17.30   0.98     0.95       7806.61|
|  7:  2.6270 -  2.4961  1311   143  0.89  17.24   0.99     0.95       7177.67|
|  8:  2.4961 -  2.3878  1288   143  0.90  16.80   1.00     0.97       6286.02|
|  9:  2.3878 -  2.2963  1289   144  0.90  16.61   1.00     0.96       5602.78|
| 10:  2.2963 -  2.2173  1286   145  0.89  16.67   1.01     0.97       4840.62|
| 11:  2.2173 -  2.1481  1295   145  0.89  17.66   0.99     0.95       4886.90|
| 12:  2.1481 -  2.0869  1277   141  0.89  17.13   1.00     1.00       4500.89|
| 13:  2.0869 -  2.0321  1262   141  0.89  17.01   0.99     0.97       3504.48|
| 14:  2.0321 -  1.9826   569    61  0.93  12.57   0.98     0.95       2413.66|
|alpha:            min =        0.95 max =            1.03 mean =         0.97|
|beta:             min =     2413.66 max =        11280.75 mean =      7106.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.05|
|phase err.(test): min =        0.00 max =           89.77 mean =        14.46|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.61    95.31   16.08    None  None   None       |
|    all(noH): 2823   0      2.61    95.31   16.08    None  None   None       |
|    Sol.    : 438    0      4.46    95.31   41.69    None  None   None       |
|    Mac.    : 2385   0      2.61    87.95   11.38    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:     2.606 -  11.877: 1676   |   5:    48.958 -  58.228:   91        |
|      1:    11.877 -  21.147:  582   |   6:    58.228 -  67.498:   55        |
|      2:    21.147 -  30.417:  157   |   7:    67.498 -  76.769:   32        |
|      3:    30.417 -  39.688:  117   |   8:    76.769 -  86.039:   13        |
|      4:    39.688 -  48.958:   94   |   9:    86.039 -  95.309:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 325         
Filter by distance & map next to the model:
   mapped sites are within: 0.221 - 4.950
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 325
   mapped sites are within: 0.724 - 4.950

peak=   10.691 closest distance to " CB  VAL A 230 " =    1.439
peak=    8.892 closest distance to " CG2 VAL A 296 " =    1.503
peak=    6.081 closest distance to " CD2 LEU A   5 " =    1.192
peak=    6.063 closest distance to " NE2 GLN A  11 " =    1.149
peak=    5.778 closest distance to " O   HOH Z 142 " =    2.208
peak=    5.458 closest distance to " CG  PRO A  54 " =    1.311
peak=    5.197 closest distance to " CG  LEU A   5 " =    1.157
peak=    5.186 closest distance to " CG  LEU A 228 " =    1.186
peak=    4.996 closest distance to " CB  GLN A 223 " =    1.549
peak=    4.942 closest distance to " O   HOH Z   9 " =    2.258
peak=    4.890 closest distance to " CB  GLN A 183 " =    1.287
peak=    4.878 closest distance to " NH2 ARG A  56 " =    1.994
peak=    4.807 closest distance to " O   HOH Z 232 " =    2.274
peak=    4.689 closest distance to " O   HOH Z 369 " =    2.261
peak=    4.688 closest distance to " O   HOH Z 427 " =    2.654
peak=    4.604 closest distance to " O   HOH Z 248 " =    1.473
peak=    4.526 closest distance to " NH2AARG A 190 " =    1.977
peak=    4.514 closest distance to " O   HOH Z   7 " =    1.277
peak=    4.439 closest distance to " CB  ASN A 148 " =    1.411
peak=    4.391 closest distance to " CB  PRO A  54 " =    1.030
peak=    4.380 closest distance to " O   HOH Z 359 " =    1.669
peak=    4.367 closest distance to " O   PRO A 198 " =    1.600
peak=    4.355 closest distance to " O   SER A  87 " =    2.366
peak=    4.347 closest distance to " CB  ASN A 142 " =    1.066
peak=    4.340 closest distance to " O   HOH Z 303 " =    2.052
peak=    4.330 closest distance to " O   HOH Z 287 " =    2.123
peak=    4.277 closest distance to " CZ  PHE A 218 " =    1.096
peak=    4.226 closest distance to " O   HOH Z 346 " =    1.558
peak=    4.216 closest distance to " O   HOH Z 406 " =    1.577
peak=    4.213 closest distance to " O   HOH Z 425 " =    1.468
peak=    4.198 closest distance to " CH2 TRP A 266 " =    1.146
peak=    4.169 closest distance to " ND2 ASN A 187 " =    1.645
peak=    4.119 closest distance to " O  BHOH Z 338 " =    2.454
peak=    4.114 closest distance to " CB  SER A  63 " =    1.258
peak=    4.095 closest distance to " O   HOH Z  78 " =    1.584
peak=    4.084 closest distance to " O   HOH Z  69 " =    0.836
peak=    4.083 closest distance to " CB  VAL A 265 " =    1.329
peak=    4.071 closest distance to " CB  ARG A 190 " =    1.420
peak=    4.052 closest distance to " O   HOH Z  61 " =    1.765
peak=    4.045 closest distance to " O   HOH Z 126 " =    2.150
peak=    4.044 closest distance to " CG  LEU A 167 " =    1.264
peak=    4.034 closest distance to " CE  LYS A  76 " =    0.869
peak=    4.020 closest distance to " CG  PRO A 243 " =    1.143
peak=    4.017 closest distance to " O   HOH Z 126 " =    1.577
peak=    4.005 closest distance to " CB  GLU A 277 " =    3.622
peak=    4.002 closest distance to " O   HOH Z 265 " =    1.873
peak=    3.993 closest distance to " O   HOH Z 214 " =    2.435
peak=    3.992 closest distance to " O   HOH Z 353 " =    2.582
peak=    3.982 closest distance to " CD2 LEU A 228 " =    1.211
peak=    3.979 closest distance to " CA  ARG A 195 " =    1.157
peak=    3.974 closest distance to " O   HOH Z  10 " =    1.719
peak=    3.945 closest distance to " O   HOH Z 251 " =    1.587
peak=    3.920 closest distance to " CA  TYR A  30 " =    1.023
peak=    3.911 closest distance to " O   HOH Z 188 " =    2.987
peak=    3.905 closest distance to " O   HOH Z 422 " =    2.629
peak=    3.900 closest distance to " CB  TYR A 169 " =    0.770
peak=    3.894 closest distance to " CA  VAL A 125 " =    1.206
peak=    3.893 closest distance to " CB  ARG A  79 " =    1.469
peak=    3.882 closest distance to " CG  GLN A  58 " =    0.900
peak=    3.880 closest distance to " O   HOH Z 298 " =    1.758
peak=    3.873 closest distance to " CB  ARG A 275 " =    0.986
peak=    3.867 closest distance to " O   HOH Z 380 " =    1.849
peak=    3.866 closest distance to " CD  ARG A 159 " =    0.724
peak=    3.866 closest distance to " O   HOH Z 258 " =    1.876
peak=    3.861 closest distance to " O   HOH Z 127 " =    1.110
peak=    3.853 closest distance to " CA  LYS A 117 " =    1.272
peak=    3.846 closest distance to " CD2 TRP A 179 " =    1.286
peak=    3.809 closest distance to " O   HOH Z  43 " =    1.920
peak=    3.800 closest distance to " CB  GLU A 128 " =    1.002
peak=    3.798 closest distance to " CG2 ILE A 234 " =    0.995
peak=    3.793 closest distance to " O   HOH Z 423 " =    1.455
peak=    3.791 closest distance to " CG  PRO A 198 " =    1.240
peak=    3.783 closest distance to " CA  ALA A  51 " =    0.995
peak=    3.778 closest distance to " CB  TRP A 266 " =    1.084
peak=    3.771 closest distance to " O   HOH Z   3 " =    2.058
peak=    3.769 closest distance to " CB  VAL A 230 " =    1.189
peak=    3.753 closest distance to " CG  LYS A  76 " =    1.628
peak=    3.749 closest distance to " CG2 VAL A 257 " =    0.841
peak=    3.746 closest distance to " NH1AARG A 145 " =    1.219
peak=    3.743 closest distance to " O   HOH Z 222 " =    2.377
peak=    3.739 closest distance to " OD1 ASN A  69 " =    2.483
peak=    3.735 closest distance to " O   HOH Z 193 " =    1.737
peak=    3.729 closest distance to " O   HOH Z 290 " =    1.020
peak=    3.722 closest distance to " O   HOH Z 261 " =    1.812
peak=    3.720 closest distance to " O   HOH Z 218 " =    1.575
peak=    3.720 closest distance to " CB BVAL A  41 " =    1.206
peak=    3.718 closest distance to " N   PHE A 130 " =    1.337
peak=    3.707 closest distance to " CB  THR A  52 " =    0.830
peak=    3.702 closest distance to " CB  ASP A 124 " =    0.798
peak=    3.699 closest distance to " CB  GLU A  46 " =    0.981
peak=    3.691 closest distance to " CG AARG A 275 " =    1.286
peak=    3.690 closest distance to " O   HOH Z 272 " =    1.713
peak=    3.683 closest distance to " O   HOH Z  65 " =    0.962
peak=    3.672 closest distance to " CB  LYS A 117 " =    1.221
peak=    3.671 closest distance to " CB  GLU A 152 " =    1.175
peak=    3.671 closest distance to " CA  SER A  87 " =    1.031
peak=    3.665 closest distance to " CB  VAL A 202 " =    1.577
peak=    3.657 closest distance to " O   HOH Z 211 " =    1.118
peak=    3.656 closest distance to " O   HOH Z 411 " =    3.699
peak=    3.656 closest distance to " CB  SER A 216 " =    0.903
peak=    3.652 closest distance to " O   HOH Z  59 " =    1.779
peak=    3.651 closest distance to " O   HOH Z  92 " =    2.360
peak=    3.650 closest distance to " CE3 TRP A 150 " =    1.093
peak=    3.647 closest distance to " O   HOH Z 234 " =    3.650
peak=    3.638 closest distance to " CB  ASP A 140 " =    0.983
peak=    3.638 closest distance to " O   HOH Z  88 " =    2.990
peak=    3.637 closest distance to " O   HOH Z 280 " =    2.980
peak=    3.634 closest distance to " N   ALA A 256 " =    1.134
peak=    3.623 closest distance to " CA  ALA A 160 " =    1.007
peak=    3.622 closest distance to " OE2 GLU A   2 " =    2.004
peak=    3.621 closest distance to " O   HOH Z 180 " =    2.240
peak=    3.620 closest distance to " O   HOH Z 419 " =    2.000
peak=    3.616 closest distance to " O   HOH Z 158 " =    3.074
peak=    3.607 closest distance to " CB  ASN A  39 " =    0.973
peak=    3.605 closest distance to " CB  SER A  97 " =    0.923
peak=    3.601 closest distance to " O   HOH Z  30 " =    1.526
peak=    3.597 closest distance to " CG2 THR A 221 " =    1.161
peak=    3.587 closest distance to " CA  ALA A 291 " =    0.832
peak=    3.586 closest distance to " O   HOH Z 365 " =    2.929
peak=    3.581 closest distance to " O   HOH Z 368 " =    2.139
peak=    3.577 closest distance to " CA  PHE A 283 " =    1.214
peak=    3.575 closest distance to " N   ASN A  39 " =    1.239
peak=    3.555 closest distance to " O   HOH Z   1 " =    1.859
peak=    3.547 closest distance to " OE2 GLU A  53 " =    1.916
peak=    3.547 closest distance to " O   HOH Z 203 " =    1.674
peak=    3.539 closest distance to " O   HOH Z 112 " =    0.892
peak=    3.536 closest distance to " CB  ARG A 138 " =    0.902
peak=    3.536 closest distance to " O   HOH Z 371 " =    2.782
peak=    3.531 closest distance to " CB  ASN A 215 " =    1.224
peak=    3.530 closest distance to " O   HOH Z 303 " =    2.872
peak=    3.528 closest distance to " CD  ARG A 269 " =    0.978
peak=    3.527 closest distance to " CD  ARG A  66 " =    2.556
peak=    3.526 closest distance to " O   HOH Z  80 " =    1.591
peak=    3.524 closest distance to " O   HOH Z  40 " =    1.851
peak=    3.518 closest distance to " O   HOH Z  90 " =    2.195
peak=    3.511 closest distance to " O   HOH Z 196 " =    1.424
peak=    3.510 closest distance to " CG1 ILE A  49 " =    1.538
peak=    3.506 closest distance to " OG BSER A 164 " =    2.264
peak=    3.503 closest distance to " CB  HIS A 108 " =    0.821
peak=    3.500 closest distance to " O   PHE A 192 " =    1.347
peak=    3.499 closest distance to " O   HOH Z 193 " =    1.120
peak=    3.498 closest distance to " CB  GLN A  88 " =    1.258
peak=    3.498 closest distance to " O   HOH Z 197 " =    3.230
peak=    3.488 closest distance to " CG  PRO A 213 " =    1.149
peak=    3.485 closest distance to " CB  ARG A  79 " =    0.930
peak=    3.474 closest distance to " CZ  PHE A  38 " =    1.156
peak=    3.472 closest distance to " OG1 THR A 279 " =    1.413
peak=    3.471 closest distance to " O   HOH Z 299 " =    4.415
peak=    3.468 closest distance to " CB  LEU A 300 " =    0.930
peak=    3.467 closest distance to " CB  TRP A 179 " =    1.463
peak=    3.465 closest distance to " CB  GLN A  89 " =    1.297
peak=    3.461 closest distance to " CA  MET A 105 " =    0.986
peak=    3.455 closest distance to " N   ASP A 162 " =    1.079
peak=    3.454 closest distance to " NE2 HIS A 207 " =    1.224
peak=    3.451 closest distance to " NZ  LYS A 117 " =    3.016
peak=    3.449 closest distance to " CD1 ILE A  33 " =    1.832
peak=    3.441 closest distance to " CG1 VAL A 153 " =    0.900
peak=    3.441 closest distance to " OG BSER A  99 " =    2.160
peak=    3.439 closest distance to " O   HOH Z 368 " =    3.473
peak=    3.430 closest distance to " O   HOH Z  85 " =    2.253
peak=    3.428 closest distance to " CB  SER A   3 " =    1.446
peak=    3.427 closest distance to " CB  ASP A 298 " =    1.160
peak=    3.427 closest distance to " O   THR A 182 " =    1.459
peak=    3.426 closest distance to " NZ  LYS A  48 " =    1.190
peak=    3.425 closest distance to " O   HOH Z 167 " =    1.675
peak=    3.424 closest distance to " OG ASER A 258 " =    3.026
peak=    3.423 closest distance to " CB  MET A  47 " =    1.139
peak=    3.422 closest distance to " CA  ASN A 127 " =    1.059
peak=    3.421 closest distance to " N   SER A 135 " =    1.325
peak=    3.419 closest distance to " O   HOH Z 281 " =    2.540
peak=    3.419 closest distance to " O   HOH Z 394 " =    3.709
peak=    3.419 closest distance to " O   HOH Z 207 " =    1.108
peak=    3.418 closest distance to " O   HOH Z  68 " =    2.266
peak=    3.418 closest distance to " CE1 TYR A 186 " =    1.212
peak=    3.417 closest distance to " O   HOH Z 403 " =    1.536
peak=    3.417 closest distance to " CB  ALA A 114 " =    1.337
peak=    3.417 closest distance to " CA  ARG A 102 " =    1.153
peak=    3.413 closest distance to " CG  ARG A 138 " =    1.280
peak=    3.410 closest distance to " ND2 ASN A 249 " =    0.870
peak=    3.408 closest distance to " CG2 ILE A  20 " =    1.577
peak=    3.407 closest distance to " O   HOH Z 216 " =    3.596
peak=    3.404 closest distance to " CA  ARG A  36 " =    1.056
peak=    3.399 closest distance to " CB  TYR A 116 " =    0.886
peak=    3.396 closest distance to " CB  ASN A 110 " =    1.192
peak=    3.396 closest distance to " O   HOH Z 329 " =    4.248
peak=    3.391 closest distance to " CA  ASP A 162 " =    1.034
peak=    3.388 closest distance to " N   ASN A 127 " =    1.299
peak=    3.383 closest distance to " CB  SER A 212 " =    1.291
peak=    3.382 closest distance to " CD2 TYR A 186 " =    1.126
peak=    3.375 closest distance to " CB  PRO A  90 " =    1.164
peak=    3.367 closest distance to " O   HOH Z 143 " =    1.343
peak=    3.365 closest distance to " CG  MET A 185 " =    1.307
peak=    3.361 closest distance to " NH2AARG A 145 " =    1.185
peak=    3.361 closest distance to " O   HOH Z  20 " =    1.428
peak=    3.361 closest distance to " CA  TYR A  30 " =    1.079
peak=    3.352 closest distance to " OG  SER A  62 " =    2.952
peak=    3.351 closest distance to " O   HOH Z   1 " =    1.597
peak=    3.350 closest distance to " CA  ALA A 158 " =    1.368
peak=    3.344 closest distance to " CD1 LEU A   5 " =    1.418
peak=    3.342 closest distance to " CD  ARG A 195 " =    3.537
peak=    3.342 closest distance to " O   HOH Z  21 " =    1.750
peak=    3.341 closest distance to " CG1 ILE A 151 " =    1.098
peak=    3.339 closest distance to " O   HOH Z 261 " =    1.592
peak=    3.337 closest distance to " O   HOH Z 227 " =    1.937
peak=    3.336 closest distance to " CA  LEU A  83 " =    1.161
peak=    3.332 closest distance to " O   HOH Z 171 " =    4.017
peak=    3.325 closest distance to " O   HOH Z 325 " =    2.116
peak=    3.325 closest distance to " CA  ASN A  74 " =    1.310
peak=    3.322 closest distance to " CA  TYR A 116 " =    1.412
peak=    3.321 closest distance to " CD  LYS A 166 " =    1.429
peak=    3.321 closest distance to " O   HOH Z 133 " =    2.924
peak=    3.320 closest distance to " O   HOH Z  69 " =    2.134
peak=    3.319 closest distance to " O   HOH Z 405 " =    1.284
peak=    3.318 closest distance to " CA  LEU A 282 " =    1.148
peak=    3.316 closest distance to " O   HOH Z 213 " =    2.780
peak=    3.316 closest distance to " O   HOH Z 417 " =    3.540
peak=    3.316 closest distance to " CZ3 TRP A  92 " =    1.272
peak=    3.315 closest distance to " O   HOH Z 294 " =    1.556
peak=    3.314 closest distance to " O   HOH Z 343 " =    3.164
peak=    3.313 closest distance to " CB  ALA A 248 " =    1.025
peak=    3.312 closest distance to " O   ASP A 124 " =    1.098
peak=    3.308 closest distance to " CB  SER A 273 " =    0.890
peak=    3.304 closest distance to " CG2 VAL A 197 " =    1.031
peak=    3.296 closest distance to " O   HOH Z 357 " =    2.122
peak=    3.294 closest distance to " CE  LYS A  48 " =    1.090
peak=    3.292 closest distance to " CD1 ILE A 199 " =    1.096
peak=    3.289 closest distance to " O   HOH Z 145 " =    1.364
peak=    3.286 closest distance to " N   SER A 271 " =    1.036
peak=    3.285 closest distance to " CG  GLN A  89 " =    1.470
peak=    3.285 closest distance to " CG  GLN A 278 " =    1.283
peak=    3.281 closest distance to " CA  ALA A 129 " =    1.384
peak=    3.276 closest distance to " O   HOH Z  40 " =    1.942
peak=    3.275 closest distance to " O   HOH Z 305 " =    3.482
peak=    3.274 closest distance to " O   HOH Z 258 " =    1.077
peak=    3.273 closest distance to " CG2AVAL A  72 " =    1.617
peak=    3.261 closest distance to " CA  ASN A 215 " =    1.070
peak=    3.260 closest distance to " CB  ALA A  43 " =    0.824
peak=    3.259 closest distance to " CA  SER A 146 " =    1.723
peak=    3.259 closest distance to " CG  GLN A  77 " =    0.997
peak=    3.259 closest distance to " CB  PRO A 243 " =    1.848
peak=    3.256 closest distance to " CB  ALA A   1 " =    4.950
peak=    3.254 closest distance to " CB  ARG A 156 " =    1.063
peak=    3.251 closest distance to " CA  PHE A  59 " =    0.999
peak=    3.250 closest distance to " O   HOH Z 193 " =    1.126
peak=    3.250 closest distance to " CD1 LEU A 300 " =    1.054
peak=    3.247 closest distance to " CB  ALA A   9 " =    1.596
peak=    3.245 closest distance to " O   HOH Z   2 " =    1.584
peak=    3.245 closest distance to " O   HOH Z 128 " =    2.083
peak=    3.244 closest distance to " O   PHE A  61 " =    1.383
peak=    3.243 closest distance to " O   HOH Z 357 " =    2.614
peak=    3.241 closest distance to " CA  ARG A 159 " =    1.225
peak=    3.241 closest distance to " CD  ARG A  66 " =    2.939
peak=    3.241 closest distance to " NE2 GLN A  73 " =    1.399
peak=    3.237 closest distance to " CD  ARG A 195 " =    1.005
peak=    3.235 closest distance to " O   HOH Z  97 " =    2.071
peak=    3.234 closest distance to " CA  ALA A  21 " =    1.184
peak=    3.233 closest distance to " OG  SER A 135 " =    1.227
peak=    3.227 closest distance to " OE1 GLN A 240 " =    1.494
peak=    3.226 closest distance to " CA  ALA A 233 " =    1.265
peak=    3.223 closest distance to " CB  PHE A 204 " =    0.889
peak=    3.221 closest distance to " CA  ARG A 156 " =    1.056
peak=    3.220 closest distance to " O   HOH Z  61 " =    1.617
peak=    3.218 closest distance to " O   HOH Z 263 " =    1.685
peak=    3.216 closest distance to " O   HOH Z 421 " =    2.336
peak=    3.216 closest distance to " CG2 ILE A 120 " =    1.399
peak=    3.216 closest distance to " CB  LEU A 261 " =    0.818
peak=    3.212 closest distance to " O   HOH Z  76 " =    1.084
peak=    3.208 closest distance to " CB  SER A  26 " =    1.815
peak=    3.205 closest distance to " CG  GLU A  37 " =    0.957
peak=    3.205 closest distance to " CB  ASP A 171 " =    1.166
peak=    3.203 closest distance to " CA  ARG A 139 " =    1.050
peak=    3.201 closest distance to " CA  ASN A 217 " =    1.200
peak=    3.199 closest distance to " O   HOH Z 403 " =    1.476
peak=    3.197 closest distance to " O   ASN A  74 " =    1.415
peak=    3.191 closest distance to " CA  ILE A 234 " =    1.069
peak=    3.190 closest distance to " CG  GLN A  55 " =    2.424
peak=    3.189 closest distance to " CA  GLY A 267 " =    1.025
peak=    3.187 closest distance to " CB  MET A  40 " =    0.799
peak=    3.187 closest distance to " O   HOH Z 265 " =    2.280
peak=    3.186 closest distance to " O   ASP A 191 " =    1.564
peak=    3.182 closest distance to " O   HOH Z  88 " =    3.412
peak=    3.180 closest distance to " N   GLN A 278 " =    1.457
peak=    3.180 closest distance to " CD1 ILE A 106 " =    0.917
peak=    3.179 closest distance to " O   HOH Z 156 " =    3.353
peak=    3.173 closest distance to " CA  TRP A 150 " =    1.125
peak=    3.167 closest distance to " O   HOH Z 189 " =    3.113
peak=    3.167 closest distance to " OG  SER A  62 " =    2.769
peak=    3.165 closest distance to " O   HOH Z 437 " =    2.164
peak=    3.159 closest distance to " CB  SER A  62 " =    0.933
peak=    3.157 closest distance to " O   HOH Z 172 " =    3.190
peak=    3.153 closest distance to " NH2AARG A 275 " =    3.439
peak=    3.151 closest distance to " CG  GLN A  88 " =    1.113
peak=    3.151 closest distance to " N   GLY A 133 " =    3.841
peak=    3.149 closest distance to " CG2BVAL A 121 " =    0.773
peak=    3.139 closest distance to " O   ALA A   1 " =    1.700
peak=    3.133 closest distance to " CE AMET A  47 " =    1.473
peak=    3.127 closest distance to " O   HOH Z  44 " =    1.557
peak=    3.125 closest distance to " CB  THR A 157 " =    1.132
peak=    3.125 closest distance to " O   HOH Z 246 " =    1.075
peak=    3.125 closest distance to " O   HOH Z 213 " =    2.259
peak=    3.124 closest distance to " CG1 VAL A 126 " =    1.316
peak=    3.111 closest distance to " O   HOH Z 153 " =    3.759
peak=    3.102 closest distance to " CD  ARG A 138 " =    0.869
peak=    3.101 closest distance to " O   HOH Z 285 " =    2.105
peak=    3.099 closest distance to " O   THR A 220 " =    1.348
peak=    3.098 closest distance to " O   HOH Z 116 " =    3.203
peak=    3.092 closest distance to " CB  ALA A  34 " =    1.274
peak=    3.072 closest distance to " CG  LEU A 281 " =    1.045
peak=    3.071 closest distance to " CB  ALA A 227 " =    1.036
peak=    3.068 closest distance to " CG  ARG A 159 " =    0.836
peak=    3.063 closest distance to " CZ3 TRP A 177 " =    1.054
peak=    3.058 closest distance to " O   HOH Z 438 " =    2.620
peak=    3.050 closest distance to " N   ALA A   7 " =    1.230
peak=    3.049 closest distance to " CB  LEU A  96 " =    1.376
peak=    3.047 closest distance to " O   HOH Z 423 " =    2.352
peak=    3.043 closest distance to " OD2 ASP A  50 " =    2.880
peak=    3.041 closest distance to " CB  ALA A 160 " =    1.482
peak=    3.034 closest distance to " O   HOH Z   4 " =    1.447
peak=    3.026 closest distance to " O   SER A 164 " =    1.284

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.688 - 5.600
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 214
   mapped sites are within: 0.804 - 5.600

peak=   -4.617 closest distance to " CD  ARG A  14 " =    3.255
peak=   -4.482 closest distance to " CB  PRO A 243 " =    2.712
peak=   -4.377 closest distance to " CD  ARG A 156 " =    2.062
peak=   -4.326 closest distance to " CZ2 TRP A  92 " =    2.836
peak=   -4.239 closest distance to " OG BSER A 134 " =    1.303
peak=   -4.209 closest distance to " O   HOH Z 131 " =    4.023
peak=   -4.181 closest distance to " O   VAL A  67 " =    2.527
peak=   -4.172 closest distance to " O   HOH Z 231 " =    2.015
peak=   -4.134 closest distance to " CG2 VAL A 230 " =    0.804
peak=   -4.063 closest distance to " CD1 LEU A 101 " =    2.363
peak=   -4.049 closest distance to " O   HOH Z 193 " =    1.033
peak=   -4.047 closest distance to " CG  GLN A 223 " =    2.323
peak=   -4.042 closest distance to " CB  VAL A 230 " =    1.130
peak=   -3.986 closest distance to " CG2 VAL A 202 " =    2.716
peak=   -3.982 closest distance to " CB  ALA A  43 " =    2.615
peak=   -3.960 closest distance to " O   HOH Z 411 " =    5.450
peak=   -3.955 closest distance to " C   HIS A 108 " =    1.252
peak=   -3.940 closest distance to " O   HOH Z  69 " =    1.724
peak=   -3.915 closest distance to " O   HOH Z  44 " =    2.385
peak=   -3.876 closest distance to " CG1 VAL A 112 " =    2.623
peak=   -3.865 closest distance to " CB  PHE A 192 " =    1.906
peak=   -3.861 closest distance to " CG  GLN A  58 " =    1.072
peak=   -3.855 closest distance to " O   PRO A 198 " =    1.249
peak=   -3.842 closest distance to " OG  SER A  62 " =    4.378
peak=   -3.841 closest distance to " O   HOH Z 394 " =    1.564
peak=   -3.822 closest distance to " OG  SER A  97 " =    2.365
peak=   -3.794 closest distance to " O   HOH Z  52 " =    1.468
peak=   -3.779 closest distance to " O   PRO A 163 " =    2.037
peak=   -3.738 closest distance to " O   HOH Z  73 " =    2.343
peak=   -3.716 closest distance to " O   HOH Z 147 " =    2.015
peak=   -3.705 closest distance to " O   HOH Z 185 " =    2.254
peak=   -3.701 closest distance to " CD1 LEU A 255 " =    2.874
peak=   -3.693 closest distance to " CA  ASP A 298 " =    1.096
peak=   -3.687 closest distance to " CB  PRO A 280 " =    2.122
peak=   -3.675 closest distance to " CE3 TRP A 150 " =    2.328
peak=   -3.658 closest distance to " O   VAL A 189 " =    2.663
peak=   -3.646 closest distance to " CG1 VAL A 250 " =    2.744
peak=   -3.641 closest distance to " ND2 ASN A 187 " =    1.465
peak=   -3.638 closest distance to " OG  SER A  87 " =    1.371
peak=   -3.634 closest distance to " CB  ALA A 244 " =    2.108
peak=   -3.629 closest distance to " CA  ASP A  27 " =    2.481
peak=   -3.626 closest distance to " CD2 LEU A 237 " =    2.731
peak=   -3.623 closest distance to " CE BMET A  47 " =    1.401
peak=   -3.618 closest distance to " ND2 ASN A  45 " =    2.049
peak=   -3.607 closest distance to " CG1 VAL A 112 " =    2.904
peak=   -3.596 closest distance to " CG2 VAL A 296 " =    1.761
peak=   -3.593 closest distance to " O   HOH Z 231 " =    1.133
peak=   -3.583 closest distance to " O   HOH Z 429 " =    1.989
peak=   -3.579 closest distance to " O   HOH Z 115 " =    1.683
peak=   -3.570 closest distance to " ND2 ASN A 249 " =    2.152
peak=   -3.564 closest distance to " O   HOH Z 295 " =    1.708
peak=   -3.561 closest distance to " CG2 ILE A  20 " =    2.991
peak=   -3.556 closest distance to " O   HOH Z 191 " =    5.600
peak=   -3.553 closest distance to " CB  PRO A 163 " =    2.395
peak=   -3.543 closest distance to " CD2 TYR A 293 " =    1.979
peak=   -3.542 closest distance to " O   HOH Z 198 " =    2.001
peak=   -3.538 closest distance to " O   HOH Z 149 " =    2.107
peak=   -3.537 closest distance to " O   HOH Z 357 " =    2.018
peak=   -3.528 closest distance to " CB  ALA A 161 " =    2.518
peak=   -3.517 closest distance to " O   HOH Z 123 " =    2.494
peak=   -3.499 closest distance to " O   HOH Z 292 " =    1.622
peak=   -3.499 closest distance to " O   HOH Z 359 " =    3.047
peak=   -3.493 closest distance to " O   HOH Z 103 " =    1.748
peak=   -3.486 closest distance to " O   HOH Z 412 " =    4.334
peak=   -3.482 closest distance to " CB  GLN A  11 " =    1.839
peak=   -3.479 closest distance to " CG  TRP A 266 " =    1.912
peak=   -3.468 closest distance to " NH2 ARG A  79 " =    2.112
peak=   -3.465 closest distance to " O   HOH Z 389 " =    1.561
peak=   -3.457 closest distance to " CD2 HIS A 207 " =    2.225
peak=   -3.456 closest distance to " CD2 PHE A 225 " =    1.149
peak=   -3.455 closest distance to " CG2 THR A  18 " =    2.847
peak=   -3.447 closest distance to " CZ2 TRP A 274 " =    0.925
peak=   -3.438 closest distance to " CA  GLY A 203 " =    2.540
peak=   -3.433 closest distance to " O   HOH Z 111 " =    1.745
peak=   -3.432 closest distance to " N   ALA A  43 " =    2.673
peak=   -3.428 closest distance to " O   HOH Z 364 " =    2.549
peak=   -3.425 closest distance to " O   HOH Z   9 " =    3.280
peak=   -3.415 closest distance to " N   THR A  52 " =    1.688
peak=   -3.415 closest distance to " CA  GLY A 241 " =    2.362
peak=   -3.413 closest distance to " O   PHE A 218 " =    1.542
peak=   -3.412 closest distance to " CA  ASN A 127 " =    1.154
peak=   -3.409 closest distance to " O   HOH Z  63 " =    1.784
peak=   -3.398 closest distance to " O   HOH Z 174 " =    2.467
peak=   -3.392 closest distance to " O   SER A  22 " =    2.323
peak=   -3.391 closest distance to " O   HOH Z 351 " =    1.653
peak=   -3.385 closest distance to " NE2 GLN A 194 " =    1.840
peak=   -3.385 closest distance to " CG1 VAL A 257 " =    2.370
peak=   -3.384 closest distance to " O   HOH Z 189 " =    2.502
peak=   -3.382 closest distance to " O   HOH Z 216 " =    1.378
peak=   -3.381 closest distance to " O   HOH Z 134 " =    4.080
peak=   -3.380 closest distance to " N   ALA A 226 " =    1.990
peak=   -3.375 closest distance to " ND2 ASN A 173 " =    1.723
peak=   -3.359 closest distance to " O   SER A 276 " =    1.632
peak=   -3.357 closest distance to " CB  ALA A 248 " =    2.271
peak=   -3.355 closest distance to " CE2 TYR A  30 " =    2.635
peak=   -3.353 closest distance to " OE2 GLU A 152 " =    1.269
peak=   -3.353 closest distance to " CA  GLY A 241 " =    3.169
peak=   -3.340 closest distance to " O   ALA A 227 " =    1.453
peak=   -3.339 closest distance to " CE2 TRP A  70 " =    2.300
peak=   -3.335 closest distance to " NH2 ARG A 219 " =    1.620
peak=   -3.333 closest distance to " NH2AARG A 275 " =    5.210
peak=   -3.332 closest distance to " O   HOH Z 371 " =    2.407
peak=   -3.332 closest distance to " CG  GLU A 277 " =    1.305
peak=   -3.327 closest distance to " O   HOH Z  11 " =    1.845
peak=   -3.319 closest distance to " O   HOH Z 410 " =    2.200
peak=   -3.313 closest distance to " O   HOH Z 252 " =    3.793
peak=   -3.311 closest distance to " O   HOH Z 275 " =    1.544
peak=   -3.308 closest distance to " O   HOH Z 243 " =    2.036
peak=   -3.308 closest distance to " C   MET A 188 " =    1.411
peak=   -3.308 closest distance to " CB  PRO A 213 " =    2.245
peak=   -3.306 closest distance to " ND2 ASN A  60 " =    1.601
peak=   -3.304 closest distance to " O   HOH Z 100 " =    1.174
peak=   -3.304 closest distance to " O   HOH Z 165 " =    2.142
peak=   -3.299 closest distance to " O   HOH Z 275 " =    1.853
peak=   -3.297 closest distance to " CG  ARG A 269 " =    2.363
peak=   -3.297 closest distance to " O   HOH Z  64 " =    1.447
peak=   -3.295 closest distance to " CG2BVAL A  72 " =    2.272
peak=   -3.294 closest distance to " CB  LYS A 289 " =    3.140
peak=   -3.293 closest distance to " C   LEU A 143 " =    1.075
peak=   -3.291 closest distance to " O   HOH Z 140 " =    1.497
peak=   -3.290 closest distance to " CD2 PHE A  61 " =    2.004
peak=   -3.288 closest distance to " O   HOH Z  68 " =    1.371
peak=   -3.286 closest distance to " CA  ALA A 158 " =    1.253
peak=   -3.278 closest distance to " O   GLN A 144 " =    1.405
peak=   -3.276 closest distance to " O   SER A 135 " =    1.489
peak=   -3.276 closest distance to " O   HOH Z 426 " =    1.755
peak=   -3.275 closest distance to " CA  GLY A  98 " =    1.939
peak=   -3.273 closest distance to " O   HOH Z  65 " =    1.663
peak=   -3.269 closest distance to " O   HOH Z 108 " =    1.449
peak=   -3.260 closest distance to " O   HOH Z 390 " =    2.302
peak=   -3.258 closest distance to " NE2 GLN A 278 " =    1.829
peak=   -3.256 closest distance to " O   HOH Z 435 " =    2.920
peak=   -3.255 closest distance to " CD  LYS A 289 " =    2.369
peak=   -3.249 closest distance to " CB  ALA A  10 " =    2.264
peak=   -3.249 closest distance to " OH  TYR A 172 " =    1.812
peak=   -3.248 closest distance to " O   HOH Z 350 " =    1.735
peak=   -3.246 closest distance to " CG2 VAL A 296 " =    1.156
peak=   -3.242 closest distance to " O   GLY A  17 " =    1.173
peak=   -3.241 closest distance to " O   HOH Z 411 " =    1.074
peak=   -3.241 closest distance to " N   THR A 157 " =    1.507
peak=   -3.239 closest distance to " O   GLY A 203 " =    2.500
peak=   -3.235 closest distance to " O   HOH Z 102 " =    1.636
peak=   -3.234 closest distance to " CB  ASP A 132 " =    2.379
peak=   -3.232 closest distance to " O   HOH Z 166 " =    2.290
peak=   -3.230 closest distance to " O   HOH Z  51 " =    0.889
peak=   -3.225 closest distance to " CE  MET A 105 " =    2.349
peak=   -3.224 closest distance to " O   HOH Z 285 " =    2.016
peak=   -3.221 closest distance to " O   HOH Z 368 " =    1.764
peak=   -3.220 closest distance to " O   ALA A  51 " =    1.240
peak=   -3.220 closest distance to " O   HOH Z 407 " =    2.879
peak=   -3.217 closest distance to " CD2 LEU A   5 " =    1.167
peak=   -3.214 closest distance to " CD1 TRP A 274 " =    0.971
peak=   -3.212 closest distance to " OG BSER A 134 " =    1.783
peak=   -3.210 closest distance to " O   HOH Z  70 " =    2.092
peak=   -3.207 closest distance to " CG  GLN A 103 " =    2.407
peak=   -3.206 closest distance to " O   HOH Z 251 " =    5.085
peak=   -3.206 closest distance to " O   HOH Z  43 " =    1.764
peak=   -3.205 closest distance to " O   HOH Z 281 " =    2.749
peak=   -3.203 closest distance to " OD2 ASP A 191 " =    1.294
peak=   -3.197 closest distance to " O   HOH Z 286 " =    1.682
peak=   -3.192 closest distance to " CB  HIS A  81 " =    0.969
peak=   -3.191 closest distance to " CG2 ILE A 263 " =    2.379
peak=   -3.189 closest distance to " O   HOH Z 106 " =    1.702
peak=   -3.187 closest distance to " CB  VAL A 189 " =    2.323
peak=   -3.185 closest distance to " O   HOH Z 250 " =    1.746
peak=   -3.183 closest distance to " ND2 ASN A  60 " =    1.277
peak=   -3.181 closest distance to " O   HOH Z 117 " =    2.036
peak=   -3.181 closest distance to " ND2 ASN A  69 " =    1.931
peak=   -3.178 closest distance to " CZ  TYR A 169 " =    1.770
peak=   -3.176 closest distance to " OH  TYR A 214 " =    1.233
peak=   -3.175 closest distance to " CG2 THR A  42 " =    1.805
peak=   -3.175 closest distance to " O   HOH Z 110 " =    1.336
peak=   -3.172 closest distance to " O   HOH Z 290 " =    1.296
peak=   -3.168 closest distance to " O   HOH Z 200 " =    2.968
peak=   -3.166 closest distance to " CZ3 TRP A 179 " =    1.243
peak=   -3.165 closest distance to " CE1 PHE A 218 " =    2.679
peak=   -3.162 closest distance to " N   ALA A 248 " =    1.582
peak=   -3.161 closest distance to " CE1 TYR A 247 " =    2.675
peak=   -3.161 closest distance to " O   HOH Z  83 " =    1.586
peak=   -3.159 closest distance to " CD1 ILE A 151 " =    2.493
peak=   -3.159 closest distance to " CG2 VAL A 189 " =    1.847
peak=   -3.158 closest distance to " O   HOH Z 253 " =    3.898
peak=   -3.158 closest distance to " O   HOH Z 152 " =    4.965
peak=   -3.155 closest distance to " O   ASP A  27 " =    1.846
peak=   -3.154 closest distance to " O   HOH Z 166 " =    1.517
peak=   -3.154 closest distance to " O   HOH Z 352 " =    1.384
peak=   -3.151 closest distance to " O   HOH Z 431 " =    1.866
peak=   -3.144 closest distance to " OD1 ASP A 171 " =    1.642
peak=   -3.143 closest distance to " O   HOH Z 346 " =    1.790
peak=   -3.143 closest distance to " O   HOH Z 318 " =    1.989
peak=   -3.138 closest distance to " O   HOH Z 426 " =    2.391
peak=   -3.128 closest distance to " O   LYS A 117 " =    1.682
peak=   -3.124 closest distance to " O   SER A 271 " =    2.136
peak=   -3.122 closest distance to " O   HOH Z  60 " =    2.171
peak=   -3.121 closest distance to " O   HOH Z 262 " =    2.527
peak=   -3.116 closest distance to " O   HOH Z 278 " =    1.797
peak=   -3.115 closest distance to " CB  TYR A  15 " =    2.238
peak=   -3.114 closest distance to " CD  GLN A  77 " =    1.412
peak=   -3.105 closest distance to " OD1 ASP A 200 " =    1.602
peak=   -3.102 closest distance to " O   HOH Z 111 " =    4.510
peak=   -3.089 closest distance to " O   HOH Z  20 " =    1.330
peak=   -3.072 closest distance to " CG  GLN A  88 " =    0.810
peak=   -3.070 closest distance to " CG  PHE A 283 " =    2.646
peak=   -3.068 closest distance to " CD2 TYR A 247 " =    2.477
peak=   -3.061 closest distance to " N   ALA A 248 " =    2.403
peak=   -3.056 closest distance to " OXT GLY A 302 " =    3.202
peak=   -3.056 closest distance to " OG  SER A  63 " =    1.261
peak=   -3.055 closest distance to " N   ALA A 248 " =    1.868
peak=   -3.052 closest distance to " N   SER A 276 " =    1.429
peak=   -3.045 closest distance to " O   HOH Z 116 " =    1.922
peak=   -3.041 closest distance to " CB  ALA A 244 " =    2.302
peak=   -3.008 closest distance to " O   ALA A 292 " =    2.028

================= 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    :  0.4831 0.4689   6.284141e+00   6.264347e+00
   1_bss:  0.4739 0.4560   6.276963e+00   6.254114e+00
   1_xyz:  0.3921 0.4150   6.170119e+00   6.192483e+00
   1_adp:  0.3468 0.3981   6.089600e+00   6.166567e+00
   1_occ:  0.3460 0.3987   6.089196e+00   6.168300e+00
   2_bss:  0.3437 0.3956   6.090483e+00   6.167948e+00
   2_xyz:  0.2468 0.3065   5.813499e+00   5.969860e+00
   2_adp:  0.2149 0.2754   5.703390e+00   5.885031e+00
   2_occ:  0.2149 0.2751   5.703158e+00   5.884900e+00
   3_bss:  0.2126 0.2750   5.703254e+00   5.885969e+00
   3_xyz:  0.1700 0.2250   5.505679e+00   5.712748e+00
   3_adp:  0.1585 0.2143   5.451009e+00   5.667466e+00
   3_occ:  0.1584 0.2142   5.450426e+00   5.667040e+00
   4_bss:  0.1582 0.2141   5.450206e+00   5.667314e+00
   4_xyz:  0.1327 0.1849   5.301481e+00   5.534988e+00
   4_adp:  0.1295 0.1784   5.270988e+00   5.499129e+00
   4_occ:  0.1293 0.1783   5.270498e+00   5.498921e+00
   5_bss:  0.1295 0.1783   5.270624e+00   5.498204e+00
   5_xyz:  0.1187 0.1661   5.199125e+00   5.439505e+00
   5_adp:  0.1158 0.1659   5.187468e+00   5.437519e+00
   5_occ:  0.1157 0.1658   5.187309e+00   5.437478e+00
   5_bss:  0.1157 0.1659   5.187375e+00   5.437590e+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:  0.348  20.000   6.436   7.973  12.065   0.000   0.000   0.000
   1_xyz:  0.348  20.000   6.436   7.973  12.065   0.000   0.000   0.000
   1_adp:  0.348  20.000   6.436   7.973  12.065   0.000   0.000   0.000
   1_occ:  0.348  20.000   6.436   7.973  12.065   0.000   0.000   0.000
   2_bss:  0.342  50.000   3.368   4.286   8.500   0.000   0.000   0.000
   2_xyz:  0.342  50.000   3.368   4.286   8.500   0.000   0.000   0.000
   2_adp:  0.342  50.000   3.368   4.286   8.500   0.000   0.000   0.000
   2_occ:  0.342  50.000   3.368   4.286   8.500   0.000   0.000   0.000
   3_bss:  0.324  59.515   2.121   2.483   5.318   0.000   0.000   0.000
   3_xyz:  0.324  59.515   2.121   2.483   5.318   0.000   0.000   0.000
   3_adp:  0.324  59.515   2.121   2.483   5.318   0.000   0.000   0.000
   3_occ:  0.324  59.515   2.121   2.483   5.318   0.000   0.000   0.000
   4_bss:  0.330  59.515   1.670   1.971   4.411   0.000   0.000   0.000
   4_xyz:  0.330  59.515   1.670   1.971   4.411   0.000   0.000   0.000
   4_adp:  0.330  59.515   1.670   1.971   4.411   0.000   0.000   0.000
   4_occ:  0.330  59.515   1.670   1.971   4.411   0.000   0.000   0.000
   5_bss:  0.330  59.515   1.602   1.811   4.028   0.000   0.000   0.000
   5_xyz:  0.330  59.515   1.602   1.811   4.028   0.000   0.000   0.000
   5_adp:  0.330  59.515   1.602   1.811   4.028   0.000   0.000   0.000
   5_occ:  0.330  59.515   1.602   1.811   4.028   0.000   0.000   0.000
   5_bss:  0.330  62.122  -0.793  -0.681   1.473   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.682 0.4362  0.5073    67983.168
   1_bss:  56.041 0.4436  0.6673    66010.336
   1_xyz:  47.031 0.5567  0.8146    49477.088
   1_adp:  43.762 0.5973  0.9204    45074.659
   1_occ:  43.937 0.5951  0.9158    45348.897
   2_bss:  43.759 0.5972  0.8153    45128.555
   2_xyz:  31.836 0.7365  0.9715    24477.410
   2_adp:  27.543 0.7848  1.0004    19562.332
   2_occ:  27.547 0.7847  0.9999    19541.152
   3_bss:  27.476 0.7856  0.9307    19566.345
   3_xyz:  21.847 0.8436  0.9768    12981.058
   3_adp:  20.431 0.8579  0.9803    11799.824
   3_occ:  20.416 0.8581  0.9804    11784.647
   4_bss:  20.390 0.8583  0.9591    11770.626
   4_xyz:  17.376 0.8860  0.9732     8886.570
   4_adp:  16.477 0.8943  0.9742     8294.227
   4_occ:  16.470 0.8944  0.9743     8284.984
   5_bss:  16.443 0.8946  0.9673     8272.649
   5_xyz:  15.077 0.9063  0.9747     7211.742
   5_adp:  14.993 0.9071  0.9692     7106.142
   5_occ:  14.993 0.9071  0.9692     7103.821
   5_bss:  14.994 0.9071  0.9736     7107.401
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4020e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4020e+01
   1_xyz:   1.696  0.013  0.107 18.384  0.006  4.109   1.4128e-01
   1_adp:   1.696  0.013  0.107 18.384  0.006  4.109   1.4128e-01
   1_occ:   1.696  0.013  0.107 18.384  0.006  4.109   1.4128e-01
   2_bss:   1.696  0.013  0.107 18.384  0.006  4.109   1.4128e-01
   2_xyz:   1.306  0.011  0.093 16.564  0.006  4.110   1.0284e-01
   2_adp:   1.306  0.011  0.093 16.564  0.006  4.110   1.0284e-01
   2_occ:   1.306  0.011  0.093 16.564  0.006  4.110   1.0284e-01
   3_bss:   1.306  0.011  0.093 16.564  0.006  4.110   1.0284e-01
   3_xyz:   0.971  0.007  0.072 15.882  0.003  4.124   6.1682e-02
   3_adp:   0.971  0.007  0.072 15.882  0.003  4.124   6.1682e-02
   3_occ:   0.971  0.007  0.072 15.882  0.003  4.124   6.1682e-02
   4_bss:   0.971  0.007  0.072 15.882  0.003  4.124   6.1682e-02
   4_xyz:   1.016  0.008  0.076 15.629  0.004  4.113   6.4943e-02
   4_adp:   1.016  0.008  0.076 15.629  0.004  4.113   6.4943e-02
   4_occ:   1.016  0.008  0.076 15.629  0.004  4.113   6.4943e-02
   5_bss:   1.016  0.008  0.076 15.629  0.004  4.113   6.4943e-02
   5_xyz:   1.129  0.010  0.087 15.745  0.004  4.119   7.7922e-02
   5_adp:   1.129  0.010  0.087 15.745  0.004  4.119   7.7922e-02
   5_occ:   1.129  0.010  0.087 15.745  0.004  4.119   7.7922e-02
   5_bss:   1.129  0.010  0.087 15.745  0.004  4.119   7.7922e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0025e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0025e+00
   1_xyz:  13.964  0.174  0.415 85.547  0.031  2.123   1.0124e-01
   1_adp:  13.964  0.174  0.415 85.547  0.031  2.123   1.0124e-01
   1_occ:  13.964  0.174  0.415 85.547  0.031  2.123   1.0124e-01
   2_bss:  13.964  0.174  0.415 85.547  0.031  2.123   1.0124e-01
   2_xyz:   7.138  0.132  0.296 82.305  0.044  2.139   1.0719e-01
   2_adp:   7.138  0.132  0.296 82.305  0.044  2.139   1.0719e-01
   2_occ:   7.138  0.132  0.296 82.305  0.044  2.139   1.0719e-01
   3_bss:   7.138  0.132  0.296 82.305  0.044  2.139   1.0719e-01
   3_xyz:   6.543  0.037  0.279 88.846  0.037  2.346   1.0242e-01
   3_adp:   6.543  0.037  0.279 88.846  0.037  2.346   1.0242e-01
   3_occ:   6.543  0.037  0.279 88.846  0.037  2.346   1.0242e-01
   4_bss:   6.543  0.037  0.279 88.846  0.037  2.346   1.0242e-01
   4_xyz:   6.777  0.046  0.351 83.415  0.041  2.305   4.1211e-02
   4_adp:   6.777  0.046  0.351 83.415  0.041  2.305   4.1211e-02
   4_occ:   6.777  0.046  0.351 83.415  0.041  2.305   4.1211e-02
   5_bss:   6.777  0.046  0.351 83.415  0.041  2.305   4.1211e-02
   5_xyz:   6.717  0.065  0.407 84.088  0.045  2.294   5.5864e-02
   5_adp:   6.717  0.065  0.407 84.088  0.045  2.294   5.5864e-02
   5_occ:   6.717  0.065  0.407 84.088  0.045  2.294   5.5864e-02
   5_bss:   6.717  0.065  0.407 84.088  0.045  2.294   5.5864e-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:  60.11   0.00  13.16  53.85   0.00  11.09  60.11   0.00  24.46
   1_occ:  60.11   0.00  13.16  53.85   0.00  11.09  60.11   0.00  24.46
   2_bss:  60.11   0.00  13.16  53.85   0.00  11.09  60.11   0.00  24.46
   2_xyz:  60.11   0.00  13.16  53.85   0.00  11.09  60.11   0.00  24.46
   2_adp:  71.38   0.00  12.82  57.52   0.00   9.18  71.38   0.00  32.63
   2_occ:  71.38   0.00  12.82  57.52   0.00   9.18  71.38   0.00  32.63
   3_bss:  71.38   0.00  12.82  57.52   0.00   9.18  71.38   0.00  32.63
   3_xyz:  71.38   0.00  12.82  57.52   0.00   9.18  71.38   0.00  32.63
   3_adp:  82.37   0.00  13.58  79.14   0.00   9.02  82.37   0.82  38.42
   3_occ:  82.37   0.00  13.58  79.14   0.00   9.02  82.37   0.82  38.42
   4_bss:  82.37   0.00  13.58  79.14   0.00   9.02  82.37   0.82  38.42
   4_xyz:  82.37   0.00  13.58  79.14   0.00   9.02  82.37   0.82  38.42
   4_adp:  81.93   0.00  13.27  79.63   0.00   8.74  81.93   1.76  37.93
   4_occ:  81.93   0.00  13.27  79.63   0.00   8.74  81.93   1.76  37.93
   5_bss:  81.93   0.00  13.27  79.63   0.00   8.74  81.93   1.76  37.93
   5_xyz:  81.93   0.00  13.27  79.63   0.00   8.74  81.93   1.76  37.93
   5_adp:  92.70   0.00  13.47  85.34   0.00   8.77  92.70   1.85  39.08
   5_occ:  92.70   0.00  13.47  85.34   0.00   8.77  92.70   1.85  39.08
   5_bss:  95.31   2.61  16.08  87.95   2.61  11.38  95.31   4.46  41.69
------------------------------------------------------------------------
 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:    1.267    0.013    0.410
   1_adp:    1.267    0.013    0.410
   1_occ:    1.267    0.013    0.410
   2_bss:    1.267    0.013    0.410
   2_xyz:    1.754    0.022    0.618
   2_adp:    1.754    0.022    0.618
   2_occ:    1.754    0.022    0.618
   3_bss:    1.754    0.022    0.618
   3_xyz:    1.721    0.017    0.661
   3_adp:    1.721    0.017    0.661
   3_occ:    1.721    0.017    0.661
   4_bss:    1.721    0.017    0.661
   4_xyz:    1.837    0.063    0.713
   4_adp:    1.837    0.063    0.713
   4_occ:    1.837    0.063    0.713
   5_bss:    1.837    0.063    0.713
   5_xyz:    2.016    0.047    0.734
   5_adp:    2.016    0.047    0.734
   5_occ:    2.016    0.047    0.734
   5_bss:    2.016    0.047    0.734
------------------------------------------------------------------------

CPU time actual refinement: 337.04


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_648/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_648/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_648/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_648/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_648/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.89 
  Macro-tasks:
    bulk solvent and scale       = 43.51  
    individual site refinement   = 140.67 
    weights calculation          = 32.27  
    collect and process          = 6.68   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 223.22 
  Micro-tasks:
    mask                            = 2.21   
    f_calc                          = 103.49 
    alpha_beta                      = 8.69   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 110.07 
    fmodel                         = 7.50   
    r_factors                      = 0.24   
    phase_errors                   = 11.51  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 245.17 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.693 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    649 calls, 103.03 s
gradients_fft:          594 calls,  98.35 s

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

# Date 2008-01-16 Time 02:04:37 PST -0800 (1200477877.50 s)
Start R-work = 0.4831, R-free = 0.4689 (no bulk solvent and anisotropic scale)
Final R-work = 0.1336, R-free = 0.1821 (no bulk solvent and anisotropic scale)

Start R-work = 0.4739, R-free = 0.4560
Final R-work = 0.1157, R-free = 0.1659