# Date 2008-01-16 Time 02:53:58 PST -0800 (1200480838.62 s)
#phil __OFF__

Command line arguments: "../1019.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4092
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1019

-------------------------------------------------------------------------------
  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: (71.3037, 46.6953, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.99287
Completeness in resolution range: 0.956354
Completeness with d_max=infinity: 0.953468

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   1.9929

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: (71.3037, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.99287
Completeness in resolution range: 0.956354
Completeness with d_max=infinity: 0.953468

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.2649 [2153/2178]  1938   215  10.0%
  bin  2:  4.2649 -  3.3976 [2053/2073]  1848   205  10.0%
  bin  3:  3.3976 -  2.9717 [2057/2076]  1848   209  10.2%
  bin  4:  2.9717 -  2.7017 [2007/2037]  1810   197   9.8%
  bin  5:  2.7017 -  2.5090 [2023/2042]  1824   199   9.8%
  bin  6:  2.5090 -  2.3616 [1997/2022]  1790   207  10.4%
  bin  7:  2.3616 -  2.2437 [1981/2009]  1785   196   9.9%
  bin  8:  2.2437 -  2.1463 [1988/2024]  1792   196   9.9%
  bin  9:  2.1463 -  2.0639 [1963/2005]  1763   200  10.2%
  bin 10:  2.0639 -  1.9929 [1367/2017]  1232   135   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1019/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 10
        2.42 -     3.04: 2172
        3.04 -     3.66: 4634
        3.66 -     4.28: 8944
        4.28 -     4.90: 12274
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.154 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.154 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28029 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_1019/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1019/model_refine_001.geo

CPU time processing inputs: 9.28


============================ 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 = 71.30375 46.69535 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4471   r_free= 0.4325   ksol= 0.00   Bsol= 0.00   scale= 0.808    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.242577                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7571 0.99   1397  155 0.3745 0.3432      6.5553      6.4681|
|  2:  4.7571 -  3.7952 0.99   1345  152 0.3403 0.3568      6.6795      6.7093|
|  3:  3.7952 -  3.3212 0.99   1318  141 0.3935 0.3517      6.5793      6.5682|
|  4:  3.3212 -  3.0201 0.99   1314  152 0.4292 0.3872       6.479      6.3882|
|  5:  3.0201 -  2.8051 0.99   1305  147 0.4694 0.4655      6.3333      6.3469|
|  6:  2.8051 -  2.6406 0.99   1301  136 0.4652 0.4881      6.2339      6.1635|
|  7:  2.6406 -  2.5090 0.99   1288  142 0.5103 0.5098      6.2273      6.2501|
|  8:  2.5090 -  2.4002 0.98   1274  145 0.4963 0.4581      6.1546      6.1365|
|  9:  2.4002 -  2.3081 0.98   1260  147 0.4792 0.5086      6.0865      6.1462|
| 10:  2.3081 -  2.2287 1.00   1300  142 0.5199 0.4309       6.104      6.0298|
| 11:  2.2287 -  2.1592 0.98   1276  138 0.5034 0.4761       6.016      6.0173|
| 12:  2.1592 -  2.0977 0.98   1250  139 0.5040 0.5121      5.9735      6.0104|
| 13:  2.0977 -  2.0426 0.99   1282  142 0.5095 0.4952      5.8712      5.7885|
| 14:  2.0426 -  1.9929 0.55    720   81 0.5119 0.4550      5.8594      5.7411|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7571  1397   155  0.74  30.97   0.80     0.77      58979.49|
|  2:  4.7571 -  3.7952  1345   152  0.77  28.88   0.90     0.82      77379.05|
|  3:  3.7952 -  3.3212  1318   141  0.69  35.81   0.86     0.79      81337.10|
|  4:  3.3212 -  3.0201  1314   152  0.63  41.38   0.82     0.71      73458.85|
|  5:  3.0201 -  2.8051  1305   147  0.54  48.72   0.75     0.62      64393.85|
|  6:  2.8051 -  2.6406  1301   136  0.50  52.24   0.75     0.55      59266.83|
|  7:  2.6406 -  2.5090  1288   142  0.44  56.59   0.74     0.50      57548.08|
|  8:  2.5090 -  2.4002  1274   145  0.42  58.08   0.74     0.48      53498.85|
|  9:  2.4002 -  2.3081  1260   147  0.44  56.74   0.74     0.50      48135.52|
| 10:  2.3081 -  2.2287  1300   142  0.44  56.75   0.76     0.51      42650.67|
| 11:  2.2287 -  2.1592  1276   138  0.44  56.97   0.76     0.52      39787.49|
| 12:  2.1592 -  2.0977  1250   139  0.44  57.34   0.77     0.52      37037.34|
| 13:  2.0977 -  2.0426  1282   142  0.43  57.99   0.72     0.51      31584.56|
| 14:  2.0426 -  1.9929   720    81  0.49  53.13   0.73     0.52      24008.32|
|alpha:            min =        0.48 max =            0.82 mean =         0.60|
|beta:             min =    24008.32 max =        81337.10 mean =     54711.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.99 mean =        49.03|
|phase err.(test): min =        0.00 max =           89.96 mean =        48.98|
|-----------------------------------------------------------------------------|

============================== 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 = 8.595246              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.709   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.763282              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.195   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 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:     1475 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2606 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3883 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5033 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6489 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7678 |
|-----------------------------------------------------------------------------|
|-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 |       54.150 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.637 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4546   r_free= 0.4401   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.246091                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4397   r_free= 0.4222   ksol= 0.33   Bsol= 20.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.61,7.72,9.29,0.00,0.00,0.00); trace/3= 8.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.236615                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.026269              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.273   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.719939              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.438   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4397      final r-factor (work) = 0.3345          |
| start r-factor (free) = 0.4222      final r-factor (free) = 0.3505          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 79.2284 = 8.03 * 0.50 * 6.2492 + 1.00 * 54.1496                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.6125 = 8.03 * 0.50 * 6.1023 + 1.00 * 0.1232                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3345      final r-factor (work) = 0.2762          |
| start r-factor (free) = 0.3505      final r-factor (free) = 0.3132          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4080 = 0.72 * 1.00 * 6.1023 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2933 = 0.72 * 1.00 * 5.9460 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    60.18   10.75    None  None   None       |
|    all(noH): 2823   0      0.00    60.18   10.75    None  None   None       |
|    Sol.    : 438    0      0.00    60.18   26.29    None  None   None       |
|    Mac.    : 2385   0      0.00    50.73   7.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.018: 1164   |   5:    30.092 -  36.110:  100        |
|      1:     6.018 -  12.037:  805   |   6:    36.110 -  42.129:   63        |
|      2:    12.037 -  18.055:  347   |   7:    42.129 -  48.147:   32        |
|      3:    18.055 -  24.074:  172   |   8:    48.147 -  54.165:   14        |
|      4:    24.074 -  30.092:  125   |   9:    54.165 -  60.184:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2762 r_free = 0.3132             target_work(ml) = 5.899         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2757 r_free = 0.3138             target_work(ml) = 5.898         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2757   r_free= 0.3138   ksol= 0.33   Bsol= 20.00   scale= 1.086   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.61,7.72,9.29,0.00,0.00,0.00); trace/3= 8.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.898289                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2716   r_free= 0.3091   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.20,4.08,5.90,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.897123                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.216372              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.337   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.433343              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.472  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2716      final r-factor (work) = 0.1799          |
| start r-factor (free) = 0.3091      final r-factor (free) = 0.2243          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6665 = 4.22 * 0.50 * 5.9499 + 1.00 * 0.1231                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1394 = 4.22 * 0.50 * 5.7249 + 1.00 * 0.0702                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1799      final r-factor (work) = 0.1595          |
| start r-factor (free) = 0.2243      final r-factor (free) = 0.2052          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4935 = 0.43 * 1.00 * 5.7249 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3856 = 0.43 * 1.00 * 5.4777 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.10   11.57    None  None   None       |
|    all(noH): 2823   0      0.00    68.10   11.57    None  None   None       |
|    Sol.    : 438    0      0.00    68.10   33.20    None  None   None       |
|    Mac.    : 2385   0      0.00    59.01   7.60     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 -   6.810: 1444   |   5:    34.050 -  40.860:   98        |
|      1:     6.810 -  13.620:  688   |   6:    40.860 -  47.670:   93        |
|      2:    13.620 -  20.430:  206   |   7:    47.670 -  54.480:   57        |
|      3:    20.430 -  27.240:  122   |   8:    54.480 -  61.290:   21        |
|      4:    27.240 -  34.050:   90   |   9:    61.290 -  68.100:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1595 r_free = 0.2052             target_work(ml) = 5.437         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1594 r_free = 0.2052             target_work(ml) = 5.436         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1594   r_free= 0.2052   ksol= 0.33   Bsol= 50.00   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.20,4.08,5.90,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.436186                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1585   r_free= 0.2043   ksol= 0.31   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.46,3.00,4.62,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.437751                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.785360              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.628   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.970633              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.574  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1585      final r-factor (work) = 0.1294          |
| start r-factor (free) = 0.2043      final r-factor (free) = 0.1758          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7118 = 2.79 * 0.50 * 5.4870 + 1.00 * 0.0702                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5195 = 2.79 * 0.50 * 5.3497 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1294      final r-factor (work) = 0.1239          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1717          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2044 = 0.97 * 1.00 * 5.3497 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1075 = 0.97 * 1.00 * 5.2479 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.09   12.09    None  None   None       |
|    all(noH): 2823   0      0.00    76.09   12.09    None  None   None       |
|    Sol.    : 438    0      0.54    76.09   35.65    None  None   None       |
|    Mac.    : 2385   0      0.00    68.80   7.76     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.609: 1577   |   5:    38.043 -  45.651:   88        |
|      1:     7.609 -  15.217:  615   |   6:    45.651 -  53.260:   84        |
|      2:    15.217 -  22.826:  179   |   7:    53.260 -  60.868:   49        |
|      3:    22.826 -  30.434:  110   |   8:    60.868 -  68.477:   18        |
|      4:    30.434 -  38.043:   95   |   9:    68.477 -  76.085:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1239 r_free = 0.1717             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1239 r_free = 0.1718             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1239   r_free= 0.1718   ksol= 0.31   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.46,3.00,4.62,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.235019                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1239   r_free= 0.1713   ksol= 0.33   Bsol= 57.09   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,2.80,4.35,0.00,0.00,0.00); trace/3= 3.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.233972                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.995719              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.803  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.283200              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.266  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1239      final r-factor (work) = 0.1201          |
| start r-factor (free) = 0.1713      final r-factor (free) = 0.1681          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3053 = 2.00 * 0.50 * 5.2475 + 1.00 * 0.0690                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2782 = 2.00 * 0.50 * 5.2223 + 1.00 * 0.0671                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1201      final r-factor (work) = 0.1205          |
| start r-factor (free) = 0.1681      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4926 = 0.28 * 1.00 * 5.2223 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4887 = 0.28 * 1.00 * 5.2164 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.13   11.79    None  None   None       |
|    all(noH): 2823   0      0.00    75.13   11.79    None  None   None       |
|    Sol.    : 438    0      1.12    75.13   34.50    None  None   None       |
|    Mac.    : 2385   0      0.00    70.37   7.62     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.513: 1594   |   5:    37.565 -  45.078:   78        |
|      1:     7.513 -  15.026:  618   |   6:    45.078 -  52.591:   83        |
|      2:    15.026 -  22.539:  172   |   7:    52.591 -  60.104:   39        |
|      3:    22.539 -  30.052:  106   |   8:    60.104 -  67.617:   19        |
|      4:    30.052 -  37.565:  105   |   9:    67.617 -  75.130:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1205 r_free = 0.1662             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1205 r_free = 0.1662             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1662   ksol= 0.33   Bsol= 57.09   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,2.80,4.35,0.00,0.00,0.00); trace/3= 3.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207815                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1662   ksol= 0.33   Bsol= 57.09   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,2.79,4.28,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207829                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.018312              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.294  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.371354              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 160.289  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1205      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1662      final r-factor (free) = 0.1626          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3309 = 2.02 * 0.50 * 5.2160 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3081 = 2.02 * 0.50 * 5.1931 + 1.00 * 0.0675                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1166      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1626      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9398 = 0.37 * 1.00 * 5.1931 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9369 = 0.37 * 1.00 * 5.1805 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.28   11.69    None  None   None       |
|    all(noH): 2823   0      0.00    75.28   11.69    None  None   None       |
|    Sol.    : 438    0      1.50    75.28   34.14    None  None   None       |
|    Mac.    : 2385   0      0.00    72.56   7.57     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 -   7.528: 1624   |   5:    37.639 -  45.167:   72        |
|      1:     7.528 -  15.056:  586   |   6:    45.167 -  52.695:   86        |
|      2:    15.056 -  22.583:  179   |   7:    52.695 -  60.222:   34        |
|      3:    22.583 -  30.111:  104   |   8:    60.222 -  67.750:   17        |
|      4:    30.111 -  37.639:  112   |   9:    67.750 -  75.278:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1623             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1158 r_free = 0.1623             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1623   ksol= 0.33   Bsol= 57.09   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,2.79,4.28,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.179839                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7571 0.99   1397  155 0.1007 0.1326      5.3963      5.5375|
|  2:  4.7571 -  3.7952 0.99   1345  152 0.0888 0.1163      5.4623      5.6565|
|  3:  3.7952 -  3.3212 0.99   1318  141 0.1090 0.1500      5.5025      5.8495|
|  4:  3.3212 -  3.0201 0.99   1314  152 0.1230 0.1713       5.473      5.6452|
|  5:  3.0201 -  2.8051 0.99   1305  147 0.1412 0.1783      5.3661      5.5874|
|  6:  2.8051 -  2.6406 0.99   1301  136 0.1251 0.1961      5.2272      5.4872|
|  7:  2.6406 -  2.5090 0.99   1288  142 0.1325 0.1667      5.2104      5.3827|
|  8:  2.5090 -  2.4002 0.98   1274  145 0.1222 0.1735      5.1106      5.3494|
|  9:  2.4002 -  2.3081 0.98   1260  147 0.1237 0.1877      5.0856      5.3585|
| 10:  2.3081 -  2.2287 1.00   1300  142 0.1191 0.1690      4.9964      5.2196|
| 11:  2.2287 -  2.1592 0.98   1276  138 0.1195 0.1900      4.9886       5.297|
| 12:  2.1592 -  2.0977 0.98   1250  139 0.1144 0.1812      4.9043      5.2172|
| 13:  2.0977 -  2.0426 0.99   1282  142 0.1185 0.1756      4.8204      5.0817|
| 14:  2.0426 -  1.9929 0.55    720   81 0.1071 0.1643      4.7044      4.9123|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7571  1397   155  0.94   9.11   0.97     0.95       7340.40|
|  2:  4.7571 -  3.7952  1345   152  0.95   8.14   1.00     0.99       9352.78|
|  3:  3.7952 -  3.3212  1318   141  0.93  11.68   1.02     1.01      10930.97|
|  4:  3.3212 -  3.0201  1314   152  0.92  13.95   1.00     0.98      10771.58|
|  5:  3.0201 -  2.8051  1305   147  0.90  16.47   0.99     0.97       8865.98|
|  6:  2.8051 -  2.6406  1301   136  0.89  16.64   0.98     0.95       7357.32|
|  7:  2.6406 -  2.5090  1288   142  0.90  16.06   0.98     0.95       6589.91|
|  8:  2.5090 -  2.4002  1274   145  0.90  16.00   0.98     0.96       5717.47|
|  9:  2.4002 -  2.3081  1260   147  0.90  16.30   1.00     0.96       5531.60|
| 10:  2.3081 -  2.2287  1300   142  0.90  16.44   0.99     0.96       4707.67|
| 11:  2.2287 -  2.1592  1276   138  0.90  16.75   0.99     0.94       4678.03|
| 12:  2.1592 -  2.0977  1250   139  0.91  15.72   1.00     0.99       4225.96|
| 13:  2.0977 -  2.0426  1282   142  0.89  17.20   0.99     0.97       3617.22|
| 14:  2.0426 -  1.9929   720    81  0.91  14.86   0.97     0.94       2772.95|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2772.95 max =        10930.97 mean =      6765.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.59|
|phase err.(test): min =        0.00 max =           87.58 mean =        14.00|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1623   ksol= 0.33   Bsol= 60.48   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,-0.56,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.179864                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1623   ksol= 0.33   Bsol= 60.48   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,-0.56,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.179864                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7571 0.99   1397  155 0.1007 0.1326      5.3964      5.5376|
|  2:  4.7571 -  3.7952 0.99   1345  152 0.0888 0.1163      5.4623      5.6565|
|  3:  3.7952 -  3.3212 0.99   1318  141 0.1090 0.1500      5.5024      5.8495|
|  4:  3.3212 -  3.0201 0.99   1314  152 0.1230 0.1714       5.473      5.6452|
|  5:  3.0201 -  2.8051 0.99   1305  147 0.1412 0.1783      5.3662      5.5874|
|  6:  2.8051 -  2.6406 0.99   1301  136 0.1251 0.1961      5.2272      5.4873|
|  7:  2.6406 -  2.5090 0.99   1288  142 0.1325 0.1667      5.2104      5.3827|
|  8:  2.5090 -  2.4002 0.98   1274  145 0.1222 0.1735      5.1106      5.3494|
|  9:  2.4002 -  2.3081 0.98   1260  147 0.1237 0.1878      5.0856      5.3587|
| 10:  2.3081 -  2.2287 1.00   1300  142 0.1192 0.1690      4.9964      5.2193|
| 11:  2.2287 -  2.1592 0.98   1276  138 0.1195 0.1899      4.9886       5.297|
| 12:  2.1592 -  2.0977 0.98   1250  139 0.1144 0.1812      4.9043      5.2171|
| 13:  2.0977 -  2.0426 0.99   1282  142 0.1185 0.1757      4.8205      5.0818|
| 14:  2.0426 -  1.9929 0.55    720   81 0.1071 0.1643      4.7046      4.9126|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7571  1397   155  0.94   9.11   0.97     0.95       7341.88|
|  2:  4.7571 -  3.7952  1345   152  0.95   8.14   1.00     0.99       9353.26|
|  3:  3.7952 -  3.3212  1318   141  0.93  11.68   1.02     1.01      10929.71|
|  4:  3.3212 -  3.0201  1314   152  0.92  13.95   1.00     0.98      10772.18|
|  5:  3.0201 -  2.8051  1305   147  0.90  16.48   0.99     0.97       8867.34|
|  6:  2.8051 -  2.6406  1301   136  0.89  16.64   0.98     0.95       7357.74|
|  7:  2.6406 -  2.5090  1288   142  0.90  16.06   0.98     0.95       6590.19|
|  8:  2.5090 -  2.4002  1274   145  0.90  16.00   0.98     0.96       5717.71|
|  9:  2.4002 -  2.3081  1260   147  0.90  16.30   1.00     0.96       5531.95|
| 10:  2.3081 -  2.2287  1300   142  0.90  16.44   1.00     0.96       4706.98|
| 11:  2.2287 -  2.1592  1276   138  0.90  16.75   0.99     0.94       4677.04|
| 12:  2.1592 -  2.0977  1250   139  0.91  15.72   1.01     0.99       4225.24|
| 13:  2.0977 -  2.0426  1282   142  0.89  17.20   0.99     0.97       3617.81|
| 14:  2.0426 -  1.9929   720    81  0.91  14.86   0.97     0.94       2774.58|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2774.58 max =        10929.71 mean =      6766.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.59|
|phase err.(test): min =        0.00 max =           87.58 mean =        14.00|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.39    78.67   15.08    None  None   None       |
|    all(noH): 2823   0      3.39    78.67   15.08    None  None   None       |
|    Sol.    : 438    0      4.89    78.67   37.53    None  None   None       |
|    Mac.    : 2385   0      3.39    75.95   10.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.390 -  10.918: 1624   |   5:    41.029 -  48.557:   72        |
|      1:    10.918 -  18.446:  586   |   6:    48.557 -  56.085:   86        |
|      2:    18.446 -  25.973:  179   |   7:    56.085 -  63.612:   34        |
|      3:    25.973 -  33.501:  104   |   8:    63.612 -  71.140:   17        |
|      4:    33.501 -  41.029:  112   |   9:    71.140 -  78.668:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 321         
Filter by distance & map next to the model:
   mapped sites are within: 0.328 - 4.813
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 315 from: 321
   mapped sites are within: 0.709 - 4.813

peak=   10.810 closest distance to " CB  VAL A 230 " =    1.499
peak=    7.125 closest distance to " CG2 VAL A 296 " =    1.126
peak=    6.022 closest distance to " CG  LEU A   5 " =    1.244
peak=    6.006 closest distance to " O   HOH Z 111 " =    2.191
peak=    5.912 closest distance to " CD2 LEU A   5 " =    1.220
peak=    5.814 closest distance to " CG  ARG A 138 " =    1.047
peak=    5.529 closest distance to " CB  GLN A 223 " =    1.391
peak=    5.427 closest distance to " CG  LEU A 228 " =    1.171
peak=    5.294 closest distance to " NH1 ARG A 138 " =    1.010
peak=    5.187 closest distance to " O   HOH Z 232 " =    2.251
peak=    5.152 closest distance to " NE2 GLN A  11 " =    1.164
peak=    5.121 closest distance to " O   HOH Z 142 " =    1.904
peak=    4.994 closest distance to " CB  GLN A 183 " =    1.232
peak=    4.931 closest distance to " CG  PRO A 198 " =    1.253
peak=    4.780 closest distance to " O   HOH Z 265 " =    2.447
peak=    4.661 closest distance to " O   HOH Z 369 " =    2.067
peak=    4.589 closest distance to " O   HOH Z 298 " =    1.869
peak=    4.528 closest distance to " O   HOH Z 126 " =    2.035
peak=    4.525 closest distance to " CB  TRP A 266 " =    1.007
peak=    4.511 closest distance to " CB  ASN A 148 " =    1.349
peak=    4.492 closest distance to " O   HOH Z 427 " =    3.024
peak=    4.479 closest distance to " O   PRO A 198 " =    1.587
peak=    4.469 closest distance to " O   HOH Z 272 " =    1.861
peak=    4.459 closest distance to " CB  SER A  63 " =    1.261
peak=    4.450 closest distance to " CG  PRO A 213 " =    1.257
peak=    4.444 closest distance to " CB  ASP A 124 " =    0.709
peak=    4.430 closest distance to " CB  ARG A 275 " =    0.895
peak=    4.413 closest distance to " O   HOH Z 425 " =    1.468
peak=    4.401 closest distance to " ND2 ASN A 187 " =    1.498
peak=    4.391 closest distance to " CZ  PHE A 218 " =    1.084
peak=    4.389 closest distance to " CG  PRO A 243 " =    1.145
peak=    4.368 closest distance to " O   HOH Z 236 " =    2.138
peak=    4.359 closest distance to " CB  VAL A 296 " =    1.100
peak=    4.290 closest distance to " CD1AILE A 234 " =    1.024
peak=    4.265 closest distance to " NH1AARG A 145 " =    1.193
peak=    4.253 closest distance to " O   HOH Z 303 " =    2.154
peak=    4.239 closest distance to " O   HOH Z 368 " =    2.125
peak=    4.197 closest distance to " CG  LEU A 167 " =    1.188
peak=    4.174 closest distance to " CD  ARG A 159 " =    0.737
peak=    4.166 closest distance to " O   HOH Z 234 " =    3.808
peak=    4.152 closest distance to " O   HOH Z 261 " =    2.089
peak=    4.149 closest distance to " CD2 LEU A 228 " =    1.194
peak=    4.149 closest distance to " CB  ASN A  39 " =    0.910
peak=    4.113 closest distance to " CB  ARG A  79 " =    1.542
peak=    4.111 closest distance to " CB  ASP A 140 " =    0.922
peak=    4.089 closest distance to " CB  GLU A 152 " =    1.158
peak=    4.089 closest distance to " CB  VAL A 230 " =    1.205
peak=    4.081 closest distance to " O   HOH Z 346 " =    1.631
peak=    4.080 closest distance to " CB  VAL A 265 " =    1.303
peak=    4.042 closest distance to " O   HOH Z 316 " =    3.053
peak=    3.995 closest distance to " CB  LEU A 228 " =    1.244
peak=    3.991 closest distance to " O   HOH Z 158 " =    3.144
peak=    3.957 closest distance to " O   HOH Z  61 " =    1.620
peak=    3.939 closest distance to " O   HOH Z 411 " =    3.634
peak=    3.924 closest distance to " O   HOH Z 209 " =    2.284
peak=    3.921 closest distance to " CD  LYS A 166 " =    1.302
peak=    3.897 closest distance to " O   HOH Z   9 " =    1.352
peak=    3.896 closest distance to " CB  GLU A 277 " =    3.644
peak=    3.879 closest distance to " CB  SER A 212 " =    1.255
peak=    3.873 closest distance to " CB  GLN A  88 " =    1.261
peak=    3.863 closest distance to " CD  ARG A 138 " =    1.219
peak=    3.843 closest distance to " CG2 THR A 221 " =    1.019
peak=    3.831 closest distance to " O   SER A  87 " =    2.194
peak=    3.799 closest distance to " CB AVAL A  41 " =    1.285
peak=    3.799 closest distance to " CB  SER A 216 " =    0.867
peak=    3.798 closest distance to " CA  TYR A  30 " =    0.990
peak=    3.794 closest distance to " CB  ARG A 190 " =    1.537
peak=    3.793 closest distance to " CA  SER A  87 " =    0.943
peak=    3.790 closest distance to " CB  LEU A 143 " =    1.184
peak=    3.789 closest distance to " N   PHE A 130 " =    1.244
peak=    3.786 closest distance to " O   HOH Z  78 " =    1.603
peak=    3.782 closest distance to " OG  SER A  97 " =    2.989
peak=    3.782 closest distance to " CB  ASN A 142 " =    0.995
peak=    3.781 closest distance to " O   HOH Z  88 " =    3.219
peak=    3.768 closest distance to " CB  SER A   3 " =    1.380
peak=    3.766 closest distance to " OD1 ASN A  69 " =    2.599
peak=    3.760 closest distance to " CD  ARG A  66 " =    2.344
peak=    3.749 closest distance to " CA  ALA A  51 " =    0.977
peak=    3.745 closest distance to " O   HOH Z 214 " =    2.132
peak=    3.742 closest distance to " CB  GLU A 128 " =    1.001
peak=    3.740 closest distance to " CB  MET A  40 " =    0.843
peak=    3.736 closest distance to " CB  THR A  82 " =    1.308
peak=    3.726 closest distance to " CA  LYS A 117 " =    1.181
peak=    3.717 closest distance to " CB  ALA A 104 " =    0.795
peak=    3.710 closest distance to " O   HOH Z 403 " =    1.652
peak=    3.694 closest distance to " CG  MET A 185 " =    1.196
peak=    3.689 closest distance to " O   HOH Z 353 " =    2.602
peak=    3.684 closest distance to " ND2 ASN A 249 " =    1.903
peak=    3.676 closest distance to " O   HOH Z 193 " =    1.995
peak=    3.676 closest distance to " CB  GLU A  46 " =    0.967
peak=    3.671 closest distance to " CA  ARG A 195 " =    1.228
peak=    3.671 closest distance to " CG  GLN A  88 " =    1.071
peak=    3.654 closest distance to " CA  THR A 264 " =    0.762
peak=    3.652 closest distance to " O   HOH Z 193 " =    1.913
peak=    3.646 closest distance to " O   HOH Z 147 " =    1.690
peak=    3.642 closest distance to " CG2 VAL A 257 " =    0.939
peak=    3.638 closest distance to " N   SER A 135 " =    1.411
peak=    3.628 closest distance to " O   HOH Z   9 " =    1.896
peak=    3.626 closest distance to " CB  ALA A   9 " =    1.616
peak=    3.624 closest distance to " O   HOH Z 184 " =    1.445
peak=    3.622 closest distance to " CB  ASN A 187 " =    1.118
peak=    3.617 closest distance to " CG1 VAL A 153 " =    0.943
peak=    3.614 closest distance to " CB  VAL A 202 " =    1.617
peak=    3.611 closest distance to " CA  ALA A  21 " =    1.183
peak=    3.610 closest distance to " OD2 ASP A 286 " =    2.836
peak=    3.609 closest distance to " CB  SER A 210 " =    0.806
peak=    3.608 closest distance to " CE1 TYR A 186 " =    1.345
peak=    3.592 closest distance to " O   HOH Z 313 " =    1.840
peak=    3.584 closest distance to " CB  ASN A 110 " =    1.155
peak=    3.579 closest distance to " CZ  PHE A 192 " =    0.972
peak=    3.578 closest distance to " O   HOH Z 368 " =    3.593
peak=    3.557 closest distance to " CE  LYS A  76 " =    0.875
peak=    3.556 closest distance to " O   HOH Z  92 " =    2.540
peak=    3.551 closest distance to " O   HOH Z 273 " =    2.807
peak=    3.550 closest distance to " CD  ARG A 269 " =    0.939
peak=    3.548 closest distance to " O   HOH Z 193 " =    1.693
peak=    3.546 closest distance to " O   HOH Z 171 " =    3.960
peak=    3.543 closest distance to " O   HOH Z 290 " =    1.143
peak=    3.535 closest distance to " CG1 ILE A 151 " =    1.211
peak=    3.534 closest distance to " CG1 ILE A  49 " =    1.482
peak=    3.532 closest distance to " CD BLYS A 290 " =    1.009
peak=    3.529 closest distance to " O   HOH Z 313 " =    1.663
peak=    3.527 closest distance to " O   HOH Z 248 " =    1.693
peak=    3.519 closest distance to " O   HOH Z  30 " =    1.439
peak=    3.513 closest distance to " O   MET A 105 " =    1.750
peak=    3.509 closest distance to " CA  ARG A  36 " =    1.187
peak=    3.507 closest distance to " O   HOH Z  78 " =    2.250
peak=    3.499 closest distance to " O   HOH Z 371 " =    3.011
peak=    3.497 closest distance to " CA  ALA A 295 " =    1.117
peak=    3.495 closest distance to " O   HOH Z 109 " =    2.620
peak=    3.493 closest distance to " CB  ALA A 291 " =    1.333
peak=    3.492 closest distance to " O   HOH Z 185 " =    2.313
peak=    3.490 closest distance to " CB  ILE A 120 " =    1.338
peak=    3.489 closest distance to " O   HOH Z 180 " =    2.125
peak=    3.482 closest distance to " O   HOH Z   3 " =    1.973
peak=    3.478 closest distance to " CA  ASN A 215 " =    1.115
peak=    3.476 closest distance to " O   HOH Z 305 " =    3.434
peak=    3.474 closest distance to " CB  ALA A  34 " =    0.924
peak=    3.467 closest distance to " O   HOH Z  10 " =    1.805
peak=    3.465 closest distance to " CB  PRO A  54 " =    0.866
peak=    3.452 closest distance to " CG  MET A 185 " =    1.019
peak=    3.449 closest distance to " CB  HIS A 108 " =    0.825
peak=    3.445 closest distance to " CD1 LEU A 300 " =    1.106
peak=    3.443 closest distance to " CB  GLN A 103 " =    1.102
peak=    3.441 closest distance to " CG1BVAL A  72 " =    1.690
peak=    3.428 closest distance to " O   ALA A 158 " =    1.389
peak=    3.426 closest distance to " CB  TRP A 150 " =    1.428
peak=    3.425 closest distance to " CG BARG A 275 " =    1.510
peak=    3.422 closest distance to " CG BARG A 102 " =    1.834
peak=    3.421 closest distance to " O   HOH Z 280 " =    3.077
peak=    3.421 closest distance to " ND1 HIS A  81 " =    1.738
peak=    3.420 closest distance to " O   HOH Z 423 " =    1.712
peak=    3.415 closest distance to " O   HOH Z 422 " =    2.711
peak=    3.415 closest distance to " O   HOH Z  21 " =    1.740
peak=    3.414 closest distance to " O   HOH Z 185 " =    1.881
peak=    3.412 closest distance to " NZ  LYS A 117 " =    3.193
peak=    3.412 closest distance to " CA  GLY A 267 " =    0.915
peak=    3.412 closest distance to " CA  LEU A 282 " =    1.018
peak=    3.410 closest distance to " CB  ALA A 242 " =    0.830
peak=    3.406 closest distance to " O   HOH Z 286 " =    2.407
peak=    3.406 closest distance to " CA  ALA A 299 " =    0.971
peak=    3.404 closest distance to " O   HOH Z 263 " =    1.679
peak=    3.401 closest distance to " CB  TRP A 179 " =    1.465
peak=    3.398 closest distance to " O   HOH Z   1 " =    1.884
peak=    3.394 closest distance to " ND1 HIS A  86 " =    1.685
peak=    3.392 closest distance to " CA  ALA A 291 " =    0.885
peak=    3.391 closest distance to " CD1 LEU A  96 " =    0.759
peak=    3.385 closest distance to " O   TYR A 116 " =    1.224
peak=    3.383 closest distance to " NE2 GLN A  77 " =    3.352
peak=    3.382 closest distance to " NH1 ARG A  14 " =    0.913
peak=    3.381 closest distance to " CD2 TRP A 179 " =    1.326
peak=    3.377 closest distance to " CB  ALA A 248 " =    1.090
peak=    3.375 closest distance to " O   HOH Z 437 " =    1.647
peak=    3.372 closest distance to " N   ASN A  39 " =    1.169
peak=    3.372 closest distance to " O   HOH Z 197 " =    3.279
peak=    3.371 closest distance to " CB  LEU A 237 " =    0.834
peak=    3.370 closest distance to " N   ASN A 127 " =    1.255
peak=    3.369 closest distance to " O   HOH Z 213 " =    2.069
peak=    3.364 closest distance to " CA  MET A  40 " =    1.137
peak=    3.361 closest distance to " CZ  PHE A  38 " =    1.168
peak=    3.360 closest distance to " O   HOH Z 352 " =    1.784
peak=    3.359 closest distance to " CD  GLN A 240 " =    1.598
peak=    3.358 closest distance to " CD1 LEU A   5 " =    1.335
peak=    3.353 closest distance to " O   HOH Z  63 " =    1.872
peak=    3.351 closest distance to " O   HOH Z 166 " =    3.635
peak=    3.350 closest distance to " O   HOH Z 392 " =    1.310
peak=    3.349 closest distance to " O   HOH Z 172 " =    3.300
peak=    3.348 closest distance to " CB  LYS A 117 " =    1.231
peak=    3.345 closest distance to " O   HOH Z 409 " =    2.951
peak=    3.341 closest distance to " NE2 HIS A 207 " =    1.267
peak=    3.341 closest distance to " CB  VAL A 250 " =    1.112
peak=    3.341 closest distance to " CA  ALA A 158 " =    1.155
peak=    3.339 closest distance to " O   TRP A 274 " =    1.820
peak=    3.339 closest distance to " NH2 ARG A 156 " =    1.089
peak=    3.337 closest distance to " CA  ALA A 154 " =    1.058
peak=    3.337 closest distance to " O   HOH Z  43 " =    1.961
peak=    3.336 closest distance to " O   HOH Z 128 " =    2.154
peak=    3.334 closest distance to " O   THR A 251 " =    1.170
peak=    3.330 closest distance to " CA  TYR A 116 " =    1.432
peak=    3.329 closest distance to " CA  THR A 221 " =    0.904
peak=    3.328 closest distance to " CG2 ILE A  20 " =    1.507
peak=    3.327 closest distance to " CG1 ILE A  33 " =    1.321
peak=    3.326 closest distance to " CD2 LEU A 255 " =    1.692
peak=    3.325 closest distance to " O   HOH Z 294 " =    1.535
peak=    3.323 closest distance to " O   HOH Z 156 " =    2.892
peak=    3.323 closest distance to " O   HOH Z 132 " =    2.642
peak=    3.318 closest distance to " N   ALA A 256 " =    1.074
peak=    3.315 closest distance to " O   HOH Z 215 " =    2.967
peak=    3.315 closest distance to " O   HOH Z 116 " =    1.797
peak=    3.314 closest distance to " O   HOH Z 344 " =    2.963
peak=    3.312 closest distance to " O   HOH Z   1 " =    1.851
peak=    3.311 closest distance to " CA  ASN A 217 " =    1.346
peak=    3.309 closest distance to " CD1 LEU A 228 " =    2.043
peak=    3.304 closest distance to " O   HOH Z 227 " =    1.697
peak=    3.302 closest distance to " O   HOH Z 285 " =    2.748
peak=    3.300 closest distance to " CB  VAL A 268 " =    0.856
peak=    3.298 closest distance to " O   HOH Z   2 " =    1.539
peak=    3.297 closest distance to " O   PHE A 192 " =    1.425
peak=    3.295 closest distance to " O   HOH Z  58 " =    1.484
peak=    3.293 closest distance to " OH  TYR A 214 " =    1.237
peak=    3.290 closest distance to " CD1 ILE A  33 " =    1.755
peak=    3.288 closest distance to " O   HOH Z 302 " =    1.877
peak=    3.280 closest distance to " CZ3 TRP A 266 " =    1.085
peak=    3.280 closest distance to " O   HOH Z 148 " =    3.441
peak=    3.273 closest distance to " O   HOH Z 291 " =    1.653
peak=    3.268 closest distance to " O  BHOH Z 338 " =    2.413
peak=    3.268 closest distance to " CB  PRO A 243 " =    1.440
peak=    3.264 closest distance to " CB  THR A 157 " =    1.097
peak=    3.263 closest distance to " ND2 ASN A 249 " =    0.887
peak=    3.263 closest distance to " O   HOH Z  68 " =    2.059
peak=    3.262 closest distance to " O   ASP A 124 " =    1.066
peak=    3.260 closest distance to " CG1 VAL A 296 " =    1.247
peak=    3.254 closest distance to " CA  ASP A 162 " =    0.932
peak=    3.249 closest distance to " OG BSER A 212 " =    2.495
peak=    3.248 closest distance to " N   SER A 271 " =    0.969
peak=    3.246 closest distance to " O   HOH Z 350 " =    1.578
peak=    3.246 closest distance to " CD1 ILE A 106 " =    0.864
peak=    3.245 closest distance to " O   HOH Z 133 " =    1.740
peak=    3.244 closest distance to " CB  MET A  47 " =    0.914
peak=    3.241 closest distance to " OG  SER A  62 " =    2.946
peak=    3.237 closest distance to " NE AARG A 275 " =    1.338
peak=    3.237 closest distance to " CE3 TRP A 150 " =    0.968
peak=    3.235 closest distance to " O   HOH Z  88 " =    3.372
peak=    3.233 closest distance to " CG2 ILE A 234 " =    0.897
peak=    3.233 closest distance to " OG BSER A 164 " =    2.259
peak=    3.230 closest distance to " CB  LEU A  83 " =    0.778
peak=    3.230 closest distance to " CB  THR A 235 " =    1.213
peak=    3.227 closest distance to " CG  ARG A 269 " =    1.792
peak=    3.225 closest distance to " OG  SER A  62 " =    3.009
peak=    3.222 closest distance to " CB  ASP A 298 " =    1.189
peak=    3.219 closest distance to " CA  ILE A 234 " =    0.909
peak=    3.216 closest distance to " N   VAL A 126 " =    1.343
peak=    3.216 closest distance to " O   HOH Z 260 " =    1.520
peak=    3.215 closest distance to " CB  ASN A 173 " =    1.065
peak=    3.215 closest distance to " CB  ALA A 227 " =    0.931
peak=    3.211 closest distance to " NZ  LYS A  48 " =    1.363
peak=    3.210 closest distance to " OG  SER A  22 " =    2.885
peak=    3.205 closest distance to " CG1 VAL A 174 " =    1.105
peak=    3.203 closest distance to " CB  ALA A 248 " =    1.280
peak=    3.200 closest distance to " N   SER A  12 " =    1.640
peak=    3.199 closest distance to " CB  PHE A 283 " =    0.717
peak=    3.197 closest distance to " CA  ALA A 100 " =    1.040
peak=    3.196 closest distance to " O   HOH Z 126 " =    1.577
peak=    3.194 closest distance to " C   GLN A  88 " =    1.511
peak=    3.194 closest distance to " CG  ARG A 159 " =    1.013
peak=    3.192 closest distance to " CA  GLY A 211 " =    1.349
peak=    3.188 closest distance to " O   HOH Z  97 " =    2.083
peak=    3.187 closest distance to " CA  TYR A  30 " =    1.066
peak=    3.187 closest distance to " O   HOH Z 162 " =    3.986
peak=    3.185 closest distance to " O   HOH Z 188 " =    1.946
peak=    3.185 closest distance to " CB  GLN A  89 " =    1.210
peak=    3.183 closest distance to " OG BSER A 134 " =    3.027
peak=    3.175 closest distance to " O   HOH Z 148 " =    2.183
peak=    3.171 closest distance to " OE2 GLU A   2 " =    1.791
peak=    3.170 closest distance to " CA  VAL A  41 " =    0.847
peak=    3.167 closest distance to " CA  ILE A 106 " =    0.768
peak=    3.166 closest distance to " N   TYR A  15 " =    0.788
peak=    3.165 closest distance to " O   HOH Z 329 " =    4.007
peak=    3.163 closest distance to " O   HOH Z   4 " =    1.660
peak=    3.161 closest distance to " CB  ALA A 114 " =    1.155
peak=    3.153 closest distance to " CA  LYS A 290 " =    1.315
peak=    3.152 closest distance to " O   HOH Z 438 " =    2.916
peak=    3.150 closest distance to " O   HOH Z 406 " =    1.511
peak=    3.149 closest distance to " CZ3 TRP A  92 " =    1.380
peak=    3.146 closest distance to " CB  ALA A   1 " =    4.813
peak=    3.145 closest distance to " CB  TYR A 247 " =    0.956
peak=    3.141 closest distance to " O   HOH Z 250 " =    1.288
peak=    3.141 closest distance to " CB  ASN A 224 " =    1.015
peak=    3.134 closest distance to " CB  THR A  31 " =    1.599
peak=    3.121 closest distance to " O   HOH Z 301 " =    1.795
peak=    3.120 closest distance to " CA  ASN A 127 " =    1.068
peak=    3.120 closest distance to " O   HOH Z 303 " =    2.529
peak=    3.117 closest distance to " CB  PHE A 204 " =    0.860
peak=    3.114 closest distance to " O   HOH Z 130 " =    2.138
peak=    3.111 closest distance to " O   HOH Z 213 " =    2.619
peak=    3.111 closest distance to " NH2BARG A 145 " =    2.036
peak=    3.099 closest distance to " O   HOH Z  80 " =    1.554
peak=    3.099 closest distance to " O   HOH Z 124 " =    1.869
peak=    3.093 closest distance to " O   HOH Z 128 " =    2.311
peak=    3.092 closest distance to " O   HOH Z  40 " =    1.473
peak=    3.092 closest distance to " OG  SER A 206 " =    1.178
peak=    3.086 closest distance to " O   PRO A  90 " =    1.510
peak=    3.084 closest distance to " O   PHE A  61 " =    1.400
peak=    3.084 closest distance to " CG  GLN A  89 " =    1.526
peak=    3.081 closest distance to " CA  ASP A 191 " =    0.848
peak=    3.079 closest distance to " CB  TYR A 116 " =    0.882
peak=    3.076 closest distance to " O   HOH Z 175 " =    2.133
peak=    3.076 closest distance to " O   HOH Z  89 " =    1.837
peak=    3.071 closest distance to " O   HOH Z  57 " =    1.229
peak=    3.070 closest distance to " CB  SER A 245 " =    3.211
peak=    3.054 closest distance to " O   HOH Z 271 " =    2.076
peak=    3.047 closest distance to " OE1 GLU A  37 " =    1.198
peak=    3.044 closest distance to " O   HOH Z 134 " =    2.833
peak=    3.020 closest distance to " O   GLY A 203 " =    1.470
peak=    3.018 closest distance to " CB  SER A  62 " =    1.103

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.537 - 5.496
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 211
   mapped sites are within: 0.746 - 5.496

peak=   -5.264 closest distance to " CG2 VAL A 230 " =    0.749
peak=   -4.415 closest distance to " O   HOH Z  52 " =    1.311
peak=   -4.321 closest distance to " CD  ARG A  14 " =    3.255
peak=   -4.266 closest distance to " CD  ARG A 156 " =    2.097
peak=   -4.255 closest distance to " CG1 VAL A 112 " =    2.654
peak=   -4.183 closest distance to " O   HOH Z 162 " =    2.619
peak=   -4.106 closest distance to " O   HOH Z 290 " =    1.268
peak=   -4.084 closest distance to " CD  GLN A 223 " =    2.189
peak=   -4.034 closest distance to " O   HOH Z 266 " =    5.454
peak=   -4.017 closest distance to " O   HOH Z 231 " =    1.816
peak=   -4.015 closest distance to " OG BSER A 134 " =    1.301
peak=   -3.982 closest distance to " OG  SER A  97 " =    2.298
peak=   -3.973 closest distance to " O   HOH Z 211 " =    1.288
peak=   -3.968 closest distance to " CD  GLN A  58 " =    0.990
peak=   -3.968 closest distance to " CG  ARG A 138 " =    0.960
peak=   -3.944 closest distance to " CG2 ILE A  49 " =    2.838
peak=   -3.919 closest distance to " CA  GLY A 241 " =    2.337
peak=   -3.912 closest distance to " O   HOH Z 351 " =    1.456
peak=   -3.907 closest distance to " CG2 VAL A 296 " =    1.063
peak=   -3.861 closest distance to " CG1 VAL A 296 " =    1.351
peak=   -3.852 closest distance to " O   PRO A 198 " =    1.199
peak=   -3.848 closest distance to " OE1 GLN A  88 " =    0.935
peak=   -3.842 closest distance to " C   ALA A 158 " =    1.395
peak=   -3.817 closest distance to " O   GLY A 203 " =    2.386
peak=   -3.810 closest distance to " O   HOH Z 196 " =    2.370
peak=   -3.803 closest distance to " O   HOH Z 435 " =    2.802
peak=   -3.795 closest distance to " O   VAL A  67 " =    2.588
peak=   -3.743 closest distance to " O   VAL A 189 " =    2.573
peak=   -3.736 closest distance to " O   GLY A  17 " =    1.338
peak=   -3.733 closest distance to " O   HOH Z  73 " =    2.129
peak=   -3.722 closest distance to " CG  TRP A 266 " =    1.815
peak=   -3.722 closest distance to " CB  ALA A 161 " =    2.639
peak=   -3.718 closest distance to " ND2 ASN A  45 " =    1.235
peak=   -3.717 closest distance to " CE2 TYR A  30 " =    2.765
peak=   -3.702 closest distance to " CZ3 TRP A 179 " =    1.150
peak=   -3.701 closest distance to " CB  PRO A 163 " =    2.499
peak=   -3.697 closest distance to " N   ALA A  43 " =    2.442
peak=   -3.667 closest distance to " CA  GLY A 241 " =    3.135
peak=   -3.666 closest distance to " O   HOH Z 394 " =    1.525
peak=   -3.665 closest distance to " N   THR A 157 " =    1.449
peak=   -3.664 closest distance to " CB  ALA A  43 " =    2.601
peak=   -3.660 closest distance to " CD2 LEU A 237 " =    2.792
peak=   -3.653 closest distance to " CB  PHE A 192 " =    1.915
peak=   -3.648 closest distance to " CG  MET A 105 " =    0.996
peak=   -3.636 closest distance to " C   HIS A 108 " =    1.211
peak=   -3.634 closest distance to " CD1 LEU A 228 " =    2.388
peak=   -3.632 closest distance to " CE3 TRP A 150 " =    2.219
peak=   -3.631 closest distance to " NH2AARG A 275 " =    5.411
peak=   -3.629 closest distance to " CG1 VAL A 112 " =    2.934
peak=   -3.621 closest distance to " O   HOH Z 377 " =    1.977
peak=   -3.608 closest distance to " CB  VAL A 230 " =    1.083
peak=   -3.605 closest distance to " SD BMET A  47 " =    0.968
peak=   -3.593 closest distance to " O   GLY A 211 " =    1.344
peak=   -3.588 closest distance to " N   ALA A 226 " =    2.185
peak=   -3.587 closest distance to " O   HOH Z  38 " =    1.589
peak=   -3.586 closest distance to " O   HOH Z 359 " =    3.127
peak=   -3.576 closest distance to " O   HOH Z 185 " =    2.348
peak=   -3.573 closest distance to " CG  ASP A 231 " =    0.768
peak=   -3.569 closest distance to " CB  ALA A 248 " =    2.126
peak=   -3.564 closest distance to " O   HOH Z 389 " =    2.065
peak=   -3.562 closest distance to " C   LEU A 222 " =    0.895
peak=   -3.543 closest distance to " O   GLY A  80 " =    2.535
peak=   -3.543 closest distance to " O   HOH Z 176 " =    0.746
peak=   -3.542 closest distance to " CE BMET A  47 " =    1.604
peak=   -3.531 closest distance to " CD1 LEU A 101 " =    2.373
peak=   -3.522 closest distance to " OG  SER A  87 " =    1.492
peak=   -3.518 closest distance to " CD2 LEU A 167 " =    1.879
peak=   -3.513 closest distance to " CA  ASP A 298 " =    1.086
peak=   -3.505 closest distance to " O   PRO A 163 " =    2.072
peak=   -3.499 closest distance to " O   HOH Z  43 " =    1.738
peak=   -3.493 closest distance to " O   HOH Z  11 " =    1.900
peak=   -3.481 closest distance to " O   SER A 271 " =    2.281
peak=   -3.478 closest distance to " O   HOH Z 231 " =    1.122
peak=   -3.465 closest distance to " CB  ALA A 248 " =    2.484
peak=   -3.465 closest distance to " CA  ASP A  27 " =    2.448
peak=   -3.464 closest distance to " CG  HIS A  86 " =    1.088
peak=   -3.454 closest distance to " CD1 TYR A 247 " =    2.826
peak=   -3.453 closest distance to " O   HOH Z  44 " =    2.217
peak=   -3.447 closest distance to " CG1 VAL A 265 " =    2.444
peak=   -3.442 closest distance to " O   HOH Z 166 " =    1.588
peak=   -3.441 closest distance to " O   HOH Z 417 " =    2.986
peak=   -3.440 closest distance to " O   HOH Z 295 " =    1.594
peak=   -3.436 closest distance to " C   MET A 188 " =    1.465
peak=   -3.436 closest distance to " C   ASN A 285 " =    2.418
peak=   -3.436 closest distance to " CD  PRO A 213 " =    2.109
peak=   -3.429 closest distance to " O   HOH Z 166 " =    1.986
peak=   -3.425 closest distance to " O   VAL A  67 " =    2.636
peak=   -3.422 closest distance to " O   HOH Z  51 " =    1.240
peak=   -3.417 closest distance to " CD  ARG A 138 " =    1.270
peak=   -3.415 closest distance to " O   LEU A 101 " =    2.850
peak=   -3.414 closest distance to " O   HOH Z 281 " =    2.552
peak=   -3.405 closest distance to " O   HOH Z  10 " =    1.506
peak=   -3.405 closest distance to " O   HOH Z  60 " =    2.283
peak=   -3.401 closest distance to " O   HOH Z 426 " =    1.651
peak=   -3.395 closest distance to " N   SER A   3 " =    2.091
peak=   -3.392 closest distance to " CE  MET A 105 " =    2.374
peak=   -3.387 closest distance to " O   HOH Z 103 " =    1.852
peak=   -3.384 closest distance to " OG  SER A 206 " =    1.709
peak=   -3.380 closest distance to " N   ALA A 248 " =    1.710
peak=   -3.379 closest distance to " O   HOH Z 241 " =    1.203
peak=   -3.371 closest distance to " CZ  TYR A 172 " =    1.806
peak=   -3.370 closest distance to " O   HOH Z 350 " =    1.783
peak=   -3.363 closest distance to " CD2 TYR A 293 " =    1.931
peak=   -3.355 closest distance to " O   MET A  40 " =    2.840
peak=   -3.347 closest distance to " O   HOH Z 275 " =    1.494
peak=   -3.347 closest distance to " O   HOH Z 262 " =    2.883
peak=   -3.346 closest distance to " O   HOH Z 359 " =    1.611
peak=   -3.344 closest distance to " CE1 TYR A 169 " =    2.551
peak=   -3.342 closest distance to " O   HOH Z 114 " =    3.034
peak=   -3.341 closest distance to " NH2 ARG A  79 " =    2.052
peak=   -3.327 closest distance to " CD1 ILE A  33 " =    2.505
peak=   -3.326 closest distance to " CG  PRO A 163 " =    2.455
peak=   -3.325 closest distance to " N   SER A 276 " =    1.431
peak=   -3.322 closest distance to " CE3 TRP A  70 " =    1.740
peak=   -3.319 closest distance to " CG  LEU A 101 " =    2.489
peak=   -3.315 closest distance to " OXT GLY A 302 " =    3.076
peak=   -3.315 closest distance to " CB  ALA A 291 " =    2.235
peak=   -3.310 closest distance to " CZ2 TRP A 274 " =    0.958
peak=   -3.309 closest distance to " CD  LYS A 289 " =    2.507
peak=   -3.306 closest distance to " CD1 ILE A 239 " =    2.146
peak=   -3.301 closest distance to " OD1 ASN A 148 " =    1.391
peak=   -3.301 closest distance to " CD1 LEU A   5 " =    2.692
peak=   -3.300 closest distance to " O   HOH Z 128 " =    2.652
peak=   -3.292 closest distance to " CD2 LEU A   5 " =    1.135
peak=   -3.290 closest distance to " CD  ARG A 139 " =    1.669
peak=   -3.286 closest distance to " CD2 PHE A 192 " =    2.345
peak=   -3.284 closest distance to " O   HOH Z 140 " =    1.501
peak=   -3.281 closest distance to " CG  GLN A  88 " =    0.845
peak=   -3.277 closest distance to " N   THR A  52 " =    1.698
peak=   -3.276 closest distance to " CB  ALA A 114 " =    2.505
peak=   -3.275 closest distance to " CZ  PHE A 130 " =    1.091
peak=   -3.264 closest distance to " ND2 ASN A 249 " =    2.438
peak=   -3.263 closest distance to " NE2 GLN A 194 " =    1.823
peak=   -3.260 closest distance to " C   ASP A 270 " =    1.490
peak=   -3.258 closest distance to " CG2 VAL A 202 " =    2.696
peak=   -3.255 closest distance to " O   HOH Z 407 " =    3.192
peak=   -3.255 closest distance to " O   HOH Z 100 " =    1.197
peak=   -3.252 closest distance to " OH  TYR A 247 " =    2.024
peak=   -3.252 closest distance to " ND2 ASN A  60 " =    1.597
peak=   -3.244 closest distance to " O   GLN A 240 " =    2.414
peak=   -3.242 closest distance to " O   HOH Z 377 " =    0.814
peak=   -3.239 closest distance to " CA  GLY A 203 " =    2.494
peak=   -3.238 closest distance to " O   HOH Z 174 " =    2.519
peak=   -3.236 closest distance to " CG  GLU A 277 " =    1.240
peak=   -3.235 closest distance to " N   ASN A  60 " =    1.257
peak=   -3.233 closest distance to " CD  GLN A 223 " =    1.475
peak=   -3.231 closest distance to " CB  ALA A   9 " =    2.621
peak=   -3.231 closest distance to " CA  ASN A 127 " =    1.156
peak=   -3.228 closest distance to " CE  LYS A  76 " =    2.585
peak=   -3.226 closest distance to " O   HOH Z 353 " =    2.084
peak=   -3.224 closest distance to " OG ASER A 134 " =    1.563
peak=   -3.223 closest distance to " C   ASP A 231 " =    2.597
peak=   -3.221 closest distance to " C   GLU A 236 " =    0.922
peak=   -3.218 closest distance to " CB  ASN A  69 " =    1.326
peak=   -3.216 closest distance to " CB  TRP A  85 " =    2.531
peak=   -3.214 closest distance to " CD2 PHE A 225 " =    1.192
peak=   -3.214 closest distance to " O   HOH Z  13 " =    1.581
peak=   -3.212 closest distance to " O   HOH Z 216 " =    1.537
peak=   -3.210 closest distance to " OD1 ASP A 171 " =    1.673
peak=   -3.209 closest distance to " OG BSER A 134 " =    1.951
peak=   -3.195 closest distance to " NH2 ARG A  79 " =    1.560
peak=   -3.193 closest distance to " OH  TYR A 247 " =    1.875
peak=   -3.193 closest distance to " CD2 PHE A  61 " =    1.858
peak=   -3.192 closest distance to " O   HOH Z 191 " =    5.496
peak=   -3.191 closest distance to " CG  PHE A 283 " =    2.704
peak=   -3.189 closest distance to " C   LEU A 143 " =    1.182
peak=   -3.187 closest distance to " O   GLY A 196 " =    1.298
peak=   -3.185 closest distance to " OG1 THR A 246 " =    1.482
peak=   -3.180 closest distance to " O   HOH Z 111 " =    2.078
peak=   -3.180 closest distance to " ND2 ASN A  60 " =    1.789
peak=   -3.178 closest distance to " O   HOH Z 372 " =    2.405
peak=   -3.172 closest distance to " CA  SER A 135 " =    1.369
peak=   -3.172 closest distance to " NZ  LYS A 119 " =    3.508
peak=   -3.170 closest distance to " ND2BASN A 224 " =    1.540
peak=   -3.169 closest distance to " O   SER A  22 " =    2.140
peak=   -3.166 closest distance to " CA  ARG A 139 " =    1.020
peak=   -3.163 closest distance to " N   SER A 212 " =    1.944
peak=   -3.160 closest distance to " O   HOH Z 184 " =    1.638
peak=   -3.159 closest distance to " O   ASP A  27 " =    2.081
peak=   -3.155 closest distance to " CH2 TRP A 177 " =    2.239
peak=   -3.154 closest distance to " CB  ASN A 252 " =    1.641
peak=   -3.150 closest distance to " CB  PHE A 130 " =    1.286
peak=   -3.147 closest distance to " CB  ALA A 291 " =    2.176
peak=   -3.145 closest distance to " O   HOH Z 102 " =    1.211
peak=   -3.144 closest distance to " O   HOH Z 177 " =    1.790
peak=   -3.141 closest distance to " CG2 THR A 178 " =    2.185
peak=   -3.140 closest distance to " CD2 TYR A 247 " =    2.444
peak=   -3.139 closest distance to " CD  GLN A 223 " =    0.830
peak=   -3.138 closest distance to " CD  PRO A 243 " =    2.104
peak=   -3.134 closest distance to " O   HOH Z 326 " =    5.145
peak=   -3.133 closest distance to " CB  ASP A 132 " =    2.379
peak=   -3.133 closest distance to " O   HOH Z 368 " =    1.647
peak=   -3.130 closest distance to " O   THR A  18 " =    1.580
peak=   -3.127 closest distance to " O   HOH Z 106 " =    1.984
peak=   -3.126 closest distance to " CG  ARG A 269 " =    2.439
peak=   -3.126 closest distance to " OD2 ASP A  50 " =    2.167
peak=   -3.117 closest distance to " NH2BARG A 275 " =    1.789
peak=   -3.116 closest distance to " O   TRP A  70 " =    1.452
peak=   -3.108 closest distance to " O   PRO A 198 " =    1.394
peak=   -3.101 closest distance to " OD1 ASN A 187 " =    1.494
peak=   -3.095 closest distance to " CD1 TYR A 247 " =    2.321
peak=   -3.092 closest distance to " CA  GLY A 133 " =    2.257
peak=   -3.091 closest distance to " CB  TYR A  15 " =    2.182
peak=   -3.091 closest distance to " N   ALA A 248 " =    2.374
peak=   -3.075 closest distance to " O   HOH Z 390 " =    2.288
peak=   -3.052 closest distance to " NE2 GLN A  88 " =    1.056
peak=   -3.044 closest distance to " CD2 LEU A 300 " =    2.873
peak=   -3.035 closest distance to " O   ALA A 180 " =    1.426

================= 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    :  0.4471 0.4325   6.242577e+00   6.217747e+00
   1_bss:  0.4397 0.4222   6.236615e+00   6.208998e+00
   1_xyz:  0.3345 0.3505   6.051176e+00   6.090509e+00
   1_adp:  0.2762 0.3132   5.899237e+00   6.005489e+00
   1_occ:  0.2757 0.3138   5.898289e+00   6.006590e+00
   2_bss:  0.2716 0.3091   5.897123e+00   6.002286e+00
   2_xyz:  0.1799 0.2243   5.539642e+00   5.710421e+00
   2_adp:  0.1595 0.2052   5.436897e+00   5.630518e+00
   2_occ:  0.1594 0.2052   5.436186e+00   5.629984e+00
   3_bss:  0.1585 0.2043   5.437751e+00   5.630807e+00
   3_xyz:  0.1294 0.1758   5.267462e+00   5.490478e+00
   3_adp:  0.1239 0.1717   5.235278e+00   5.467152e+00
   3_occ:  0.1239 0.1718   5.235019e+00   5.467246e+00
   4_bss:  0.1239 0.1713   5.233972e+00   5.465262e+00
   4_xyz:  0.1201 0.1681   5.213256e+00   5.448068e+00
   4_adp:  0.1205 0.1662   5.208184e+00   5.435038e+00
   4_occ:  0.1205 0.1662   5.207815e+00   5.434775e+00
   5_bss:  0.1205 0.1662   5.207829e+00   5.434790e+00
   5_xyz:  0.1166 0.1626   5.183388e+00   5.418894e+00
   5_adp:  0.1158 0.1623   5.179925e+00   5.417533e+00
   5_occ:  0.1158 0.1623   5.179839e+00   5.417625e+00
   5_bss:  0.1158 0.1623   5.179864e+00   5.417643e+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:  0.327  20.001   8.606   7.716   9.293   0.000   0.000   0.000
   1_xyz:  0.327  20.001   8.606   7.716   9.293   0.000   0.000   0.000
   1_adp:  0.327  20.001   8.606   7.716   9.293   0.000   0.000   0.000
   1_occ:  0.327  20.001   8.606   7.716   9.293   0.000   0.000   0.000
   2_bss:  0.334  50.004   5.198   4.076   5.896   0.000   0.000   0.000
   2_xyz:  0.334  50.004   5.198   4.076   5.896   0.000   0.000   0.000
   2_adp:  0.334  50.004   5.198   4.076   5.896   0.000   0.000   0.000
   2_occ:  0.334  50.004   5.198   4.076   5.896   0.000   0.000   0.000
   3_bss:  0.314  50.004   3.464   2.999   4.622   0.000   0.000   0.000
   3_xyz:  0.314  50.004   3.464   2.999   4.622   0.000   0.000   0.000
   3_adp:  0.314  50.004   3.464   2.999   4.622   0.000   0.000   0.000
   3_occ:  0.314  50.004   3.464   2.999   4.622   0.000   0.000   0.000
   4_bss:  0.328  57.088   3.139   2.802   4.346   0.000   0.000   0.000
   4_xyz:  0.328  57.088   3.139   2.802   4.346   0.000   0.000   0.000
   4_adp:  0.328  57.088   3.139   2.802   4.346   0.000   0.000   0.000
   4_occ:  0.328  57.088   3.139   2.802   4.346   0.000   0.000   0.000
   5_bss:  0.329  57.088   3.014   2.787   4.283   0.000   0.000   0.000
   5_xyz:  0.329  57.088   3.014   2.787   4.283   0.000   0.000   0.000
   5_adp:  0.329  57.088   3.014   2.787   4.283   0.000   0.000   0.000
   5_occ:  0.329  57.088   3.014   2.787   4.283   0.000   0.000   0.000
   5_bss:  0.329  60.478  -0.354  -0.561   0.915   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.022 0.5337  0.5999    54711.800
   1_bss:  49.227 0.5295  0.7680    53094.710
   1_xyz:  38.760 0.6567  0.9186    34748.092
   1_adp:  32.690 0.7282  1.0063    26785.665
   1_occ:  32.748 0.7275  1.0050    26839.613
   2_bss:  32.464 0.7306  0.8921    26451.213
   2_xyz:  21.727 0.8445  0.9943    12542.671
   2_adp:  19.401 0.8677  1.0108    10571.985
   2_occ:  19.386 0.8678  1.0108    10552.374
   3_bss:  19.406 0.8678  0.9617    10604.445
   3_xyz:  16.238 0.8962  0.9783     7889.904
   3_adp:  15.687 0.9012  0.9793     7556.026
   3_occ:  15.688 0.9012  0.9793     7557.170
   4_bss:  15.659 0.9014  0.9699     7517.060
   4_xyz:  15.251 0.9050  0.9704     7228.879
   4_adp:  14.937 0.9077  0.9699     7067.437
   4_occ:  14.930 0.9078  0.9698     7057.810
   5_bss:  14.930 0.9078  0.9674     7056.919
   5_xyz:  14.570 0.9108  0.9689     6802.602
   5_adp:  14.532 0.9111  0.9662     6768.995
   5_occ:  14.534 0.9110  0.9661     6766.217
   5_bss:  14.535 0.9110  0.9670     6766.454
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4150e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4150e+01
   1_xyz:   1.554  0.012  0.103 18.141  0.006  4.124   1.2323e-01
   1_adp:   1.554  0.012  0.103 18.141  0.006  4.124   1.2323e-01
   1_occ:   1.554  0.012  0.103 18.141  0.006  4.124   1.2323e-01
   2_bss:   1.554  0.012  0.103 18.141  0.006  4.124   1.2323e-01
   2_xyz:   1.037  0.008  0.075 16.491  0.005  4.128   7.0204e-02
   2_adp:   1.037  0.008  0.075 16.491  0.005  4.128   7.0204e-02
   2_occ:   1.037  0.008  0.075 16.491  0.005  4.128   7.0204e-02
   3_bss:   1.037  0.008  0.075 16.491  0.005  4.128   7.0204e-02
   3_xyz:   1.058  0.008  0.083 16.152  0.003  4.140   6.9023e-02
   3_adp:   1.058  0.008  0.083 16.152  0.003  4.140   6.9023e-02
   3_occ:   1.058  0.008  0.083 16.152  0.003  4.140   6.9023e-02
   4_bss:   1.058  0.008  0.083 16.152  0.003  4.140   6.9023e-02
   4_xyz:   1.041  0.008  0.082 16.083  0.003  4.113   6.7074e-02
   4_adp:   1.041  0.008  0.082 16.083  0.003  4.113   6.7074e-02
   4_occ:   1.041  0.008  0.082 16.083  0.003  4.113   6.7074e-02
   5_bss:   1.041  0.008  0.082 16.083  0.003  4.113   6.7074e-02
   5_xyz:   1.051  0.008  0.083 15.850  0.003  4.116   6.7460e-02
   5_adp:   1.051  0.008  0.083 15.850  0.003  4.116   6.7460e-02
   5_occ:   1.051  0.008  0.083 15.850  0.003  4.116   6.7460e-02
   5_bss:   1.051  0.008  0.083 15.850  0.003  4.116   6.7460e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0213e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0213e+00
   1_xyz:  12.605  0.147  0.382 85.800  0.035  2.259   9.2073e-02
   1_adp:  12.605  0.147  0.382 85.800  0.035  2.259   9.2073e-02
   1_occ:  12.605  0.147  0.382 85.800  0.035  2.259   9.2073e-02
   2_bss:  12.605  0.147  0.382 85.800  0.035  2.259   9.2073e-02
   2_xyz:   7.476  0.075  0.264 87.148  0.044  2.356   1.0222e-01
   2_adp:   7.476  0.075  0.264 87.148  0.044  2.356   1.0222e-01
   2_occ:   7.476  0.075  0.264 87.148  0.044  2.356   1.0222e-01
   3_bss:   7.476  0.075  0.264 87.148  0.044  2.356   1.0222e-01
   3_xyz:   8.079  0.062  0.473 81.720  0.034  2.363   8.0224e-02
   3_adp:   8.079  0.062  0.473 81.720  0.034  2.363   8.0224e-02
   3_occ:   8.079  0.062  0.473 81.720  0.034  2.363   8.0224e-02
   4_bss:   8.079  0.062  0.473 81.720  0.034  2.363   8.0224e-02
   4_xyz:   7.929  0.059  0.477 83.004  0.040  2.375   4.6513e-02
   4_adp:   7.929  0.059  0.477 83.004  0.040  2.375   4.6513e-02
   4_occ:   7.929  0.059  0.477 83.004  0.040  2.375   4.6513e-02
   5_bss:   7.929  0.059  0.477 83.004  0.040  2.375   4.6513e-02
   5_xyz:   8.492  0.058  0.505 82.746  0.037  2.355   3.9741e-02
   5_adp:   8.492  0.058  0.505 82.746  0.037  2.355   3.9741e-02
   5_occ:   8.492  0.058  0.505 82.746  0.037  2.355   3.9741e-02
   5_bss:   8.492  0.058  0.505 82.746  0.037  2.355   3.9741e-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:  60.18   0.00  10.75  50.73   0.00   7.89  60.18   0.00  26.29
   1_occ:  60.18   0.00  10.75  50.73   0.00   7.89  60.18   0.00  26.29
   2_bss:  60.18   0.00  10.75  50.73   0.00   7.89  60.18   0.00  26.29
   2_xyz:  60.18   0.00  10.75  50.73   0.00   7.89  60.18   0.00  26.29
   2_adp:  68.10   0.00  11.57  59.01   0.00   7.60  68.10   0.00  33.20
   2_occ:  68.10   0.00  11.57  59.01   0.00   7.60  68.10   0.00  33.20
   3_bss:  68.10   0.00  11.57  59.01   0.00   7.60  68.10   0.00  33.20
   3_xyz:  68.10   0.00  11.57  59.01   0.00   7.60  68.10   0.00  33.20
   3_adp:  76.09   0.00  12.09  68.80   0.00   7.76  76.09   0.54  35.65
   3_occ:  76.09   0.00  12.09  68.80   0.00   7.76  76.09   0.54  35.65
   4_bss:  76.09   0.00  12.09  68.80   0.00   7.76  76.09   0.54  35.65
   4_xyz:  76.09   0.00  12.09  68.80   0.00   7.76  76.09   0.54  35.65
   4_adp:  75.13   0.00  11.79  70.37   0.00   7.62  75.13   1.12  34.50
   4_occ:  75.13   0.00  11.79  70.37   0.00   7.62  75.13   1.12  34.50
   5_bss:  75.13   0.00  11.79  70.37   0.00   7.62  75.13   1.12  34.50
   5_xyz:  75.13   0.00  11.79  70.37   0.00   7.62  75.13   1.12  34.50
   5_adp:  75.28   0.00  11.69  72.56   0.00   7.57  75.28   1.50  34.14
   5_occ:  75.28   0.00  11.69  72.56   0.00   7.57  75.28   1.50  34.14
   5_bss:  78.67   3.39  15.08  75.95   3.39  10.96  78.67   4.89  37.53
------------------------------------------------------------------------
 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:    1.210    0.023    0.403
   1_adp:    1.210    0.023    0.403
   1_occ:    1.210    0.023    0.403
   2_bss:    1.210    0.023    0.403
   2_xyz:    1.427    0.025    0.529
   2_adp:    1.427    0.025    0.529
   2_occ:    1.427    0.025    0.529
   3_bss:    1.427    0.025    0.529
   3_xyz:    1.454    0.034    0.562
   3_adp:    1.454    0.034    0.562
   3_occ:    1.454    0.034    0.562
   4_bss:    1.454    0.034    0.562
   4_xyz:    1.512    0.027    0.570
   4_adp:    1.512    0.027    0.570
   4_occ:    1.512    0.027    0.570
   5_bss:    1.512    0.027    0.570
   5_xyz:    1.611    0.041    0.590
   5_adp:    1.611    0.041    0.590
   5_occ:    1.611    0.041    0.590
   5_bss:    1.611    0.041    0.590
------------------------------------------------------------------------

CPU time actual refinement: 323.25


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1019/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_1019/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1019/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1019/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1019/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.10 
  Macro-tasks:
    bulk solvent and scale       = 40.77  
    individual site refinement   = 132.06 
    weights calculation          = 31.16  
    collect and process          = 6.37   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 210.47 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 98.27  
    alpha_beta                      = 8.06   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 109.21 
    fmodel                         = 7.36   
    r_factors                      = 0.28   
    phase_errors                   = 10.54  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 236.82 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.526 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    652 calls, 97.96 s
gradients_fft:          596 calls, 95.70 s

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

# Date 2008-01-16 Time 02:59:34 PST -0800 (1200481174.34 s)
Start R-work = 0.4471, R-free = 0.4325 (no bulk solvent and anisotropic scale)
Final R-work = 0.1330, R-free = 0.1791 (no bulk solvent and anisotropic scale)

Start R-work = 0.4397, R-free = 0.4222
Final R-work = 0.1158, R-free = 0.1623