# Date 2008-01-16 Time 02:57:06 PST -0800 (1200481026.67 s)
#phil __OFF__

Command line arguments: "../1039.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15319
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1039

-------------------------------------------------------------------------------
  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, 47.1647, 86.39, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00103
Completeness in resolution range: 0.967788
Completeness with d_max=infinity: 0.964833

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1569
                             d_min =   2.0010

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, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00103
Completeness in resolution range: 0.967788
Completeness with d_max=infinity: 0.964833

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1573 -  4.2817 [2117/2143]  1907   210   9.9%
  bin  2:  4.2817 -  3.4113 [2048/2067]  1842   206  10.1%
  bin  3:  3.4113 -  2.9838 [2011/2030]  1807   204  10.1%
  bin  4:  2.9838 -  2.7127 [1998/2028]  1804   194   9.7%
  bin  5:  2.7127 -  2.5192 [1981/2000]  1784   197   9.9%
  bin  6:  2.5192 -  2.3713 [1969/1994]  1768   201  10.2%
  bin  7:  2.3713 -  2.2529 [1970/1998]  1770   200  10.2%
  bin  8:  2.2529 -  2.1551 [1955/1991]  1764   191   9.8%
  bin  9:  2.1551 -  2.0724 [1965/2007]  1771   194   9.9%
  bin 10:  2.0724 -  2.0010 [1575/1983]  1413   162  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1039/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:
        1.79 -     2.41: 7
        2.41 -     3.03: 2096
        3.03 -     3.65: 4568
        3.65 -     4.28: 9021
        4.28 -     4.90: 12299
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.785 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.360 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27986 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_1039/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1039/model_refine_001.geo

CPU time processing inputs: 9.24


============================ 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 47.16465 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4301   r_free= 0.4160   ksol= 0.00   Bsol= 0.00   scale= 0.817    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.224850                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7756 0.99   1382  154 0.3631 0.3386      6.5282       6.406|
|  2:  4.7756 -  3.8104 0.99   1334  146 0.3219 0.3439      6.6364      6.7029|
|  3:  3.8104 -  3.3346 0.99   1292  144 0.3688 0.3445      6.5526      6.5477|
|  4:  3.3346 -  3.0323 0.99   1291  146 0.4097 0.3594      6.4541      6.3497|
|  5:  3.0323 -  2.8165 0.99   1292  142 0.4486 0.4308      6.3126      6.3479|
|  6:  2.8165 -  2.6514 0.99   1281  144 0.4527 0.4868      6.2322      6.2044|
|  7:  2.6514 -  2.5192 0.99   1272  135 0.4849 0.4676      6.2122      6.1899|
|  8:  2.5192 -  2.4100 0.98   1266  150 0.4855 0.4335      6.1525      6.1114|
|  9:  2.4100 -  2.3176 0.98   1270  137 0.4645 0.4928      6.0824      6.0971|
| 10:  2.3176 -  2.2378 0.99   1257  140 0.4870 0.4723      6.0863      6.0797|
| 11:  2.2378 -  2.1681 0.98   1261  136 0.4843 0.4550      6.0271      5.9982|
| 12:  2.1681 -  2.1063 0.97   1244  142 0.4890 0.4915      5.9649       6.019|
| 13:  2.1063 -  2.0510 1.00   1258  140 0.5115 0.5039      5.8914      5.8639|
| 14:  2.0510 -  2.0010 0.72    930  103 0.4926 0.4346      5.8427      5.6688|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7756  1382   154  0.75  30.19   0.81     0.77      55420.30|
|  2:  4.7756 -  3.8104  1334   146  0.79  27.49   0.91     0.82      70228.06|
|  3:  3.8104 -  3.3346  1292   144  0.72  33.79   0.86     0.79      74324.29|
|  4:  3.3346 -  3.0323  1291   146  0.65  39.94   0.83     0.71      69148.41|
|  5:  3.0323 -  2.8165  1292   142  0.55  47.86   0.76     0.63      62367.26|
|  6:  2.8165 -  2.6514  1281   144  0.52  50.40   0.77     0.58      57032.08|
|  7:  2.6514 -  2.5192  1272   135  0.50  51.99   0.74     0.56      52550.16|
|  8:  2.5192 -  2.4100  1266   150  0.49  53.27   0.75     0.56      48115.93|
|  9:  2.4100 -  2.3176  1270   137  0.50  51.94   0.75     0.55      42430.59|
| 10:  2.3176 -  2.2378  1257   140  0.50  52.14   0.77     0.56      38595.09|
| 11:  2.2378 -  2.1681  1261   136  0.49  53.32   0.77     0.55      35954.09|
| 12:  2.1681 -  2.1063  1244   142  0.47  54.67   0.77     0.54      35052.98|
| 13:  2.1063 -  2.0510  1258   140  0.46  55.21   0.74     0.55      29776.47|
| 14:  2.0510 -  2.0010   930   103  0.56  47.93   0.72     0.60      21436.52|
|alpha:            min =        0.54 max =            0.82 mean =         0.63|
|beta:             min =    21436.52 max =        74324.29 mean =     50238.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.99 mean =        46.19|
|phase err.(test): min =        0.00 max =           89.96 mean =        46.16|
|-----------------------------------------------------------------------------|

============================== 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 = 8.118243              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.538   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.608461              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.928   (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:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      673 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1497 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2593 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3876 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4980 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6577 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7618 |
|-----------------------------------------------------------------------------|
|-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 |       54.205 |
| 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 |       1.615 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.163)------------------------------------------|
|    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 = 12.163)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4374   r_free= 0.4224   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.229199                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4227   r_free= 0.4032   ksol= 0.34   Bsol= 28.30   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.67,8.19,7.78,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.219790                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.533912              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.432   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.598232              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.182   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4227      final r-factor (work) = 0.3114          |
| start r-factor (free) = 0.4032      final r-factor (free) = 0.3385          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.7008 = 7.53 * 0.50 * 6.2374 + 1.00 * 54.2047                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9318 = 7.53 * 0.50 * 6.0558 + 1.00 * 0.1199                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3114      final r-factor (work) = 0.2500          |
| start r-factor (free) = 0.3385      final r-factor (free) = 0.2859          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6375 = 0.60 * 1.00 * 6.0558 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5332 = 0.60 * 1.00 * 5.8876 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.163)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    55.41   9.87     None  None   None       |
|    all(noH): 2823   0      0.00    55.41   9.87     None  None   None       |
|    Sol.    : 438    0      0.00    55.41   26.03    None  None   None       |
|    Mac.    : 2385   0      0.00    49.97   6.90     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 -   5.541: 1283   |   5:    27.707 -  33.248:  111        |
|      1:     5.541 -  11.083:  746   |   6:    33.248 -  38.790:   66        |
|      2:    11.083 -  16.624:  291   |   7:    38.790 -  44.331:   49        |
|      3:    16.624 -  22.166:  124   |   8:    44.331 -  49.872:   23        |
|      4:    22.166 -  27.707:  123   |   9:    49.872 -  55.414:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2500 r_free = 0.2859             target_work(ml) = 5.817         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2493 r_free = 0.2858             target_work(ml) = 5.816         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2493   r_free= 0.2858   ksol= 0.34   Bsol= 28.30   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.67,8.19,7.78,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.816273                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2455   r_free= 0.2810   ksol= 0.32   Bsol= 46.81   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.48,4.98,5.20,0.00,0.00,0.00); trace/3= 5.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.815390                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.739006              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.698   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.355378              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.652  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2455      final r-factor (work) = 0.1676          |
| start r-factor (free) = 0.2810      final r-factor (free) = 0.2097          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1364 = 3.74 * 0.50 * 5.8929 + 1.00 * 0.1196                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6283 = 3.74 * 0.50 * 5.6488 + 1.00 * 0.0679                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1676      final r-factor (work) = 0.1538          |
| start r-factor (free) = 0.2097      final r-factor (free) = 0.1985          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0366 = 0.36 * 1.00 * 5.6488 + 1.00 * 0.0291                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0295 = 0.36 * 1.00 * 5.4319 + 1.00 * 0.0992                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.163)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.74   10.38    None  None   None       |
|    all(noH): 2823   0      0.00    80.74   10.38    None  None   None       |
|    Sol.    : 438    0      0.60    55.49   29.13    None  None   None       |
|    Mac.    : 2385   0      0.00    80.74   6.93     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.074: 1740   |   5:    40.368 -  48.442:   59        |
|      1:     8.074 -  16.147:  528   |   6:    48.442 -  56.516:   21        |
|      2:    16.147 -  24.221:  174   |   7:    56.516 -  64.589:    0        |
|      3:    24.221 -  32.295:  152   |   8:    64.589 -  72.663:    0        |
|      4:    32.295 -  40.368:  148   |   9:    72.663 -  80.736:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1538 r_free = 0.1985             target_work(ml) = 5.405         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1536 r_free = 0.1985             target_work(ml) = 5.405         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1536   r_free= 0.1985   ksol= 0.32   Bsol= 46.81   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.48,4.98,5.20,0.00,0.00,0.00); trace/3= 5.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.404671                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1530   r_free= 0.1976   ksol= 0.33   Bsol= 50.96   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.87,3.83,4.49,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.404573                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.867252              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.716  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.066006              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.450   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1530      final r-factor (work) = 0.1319          |
| start r-factor (free) = 0.1976      final r-factor (free) = 0.1758          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1464 = 1.87 * 0.50 * 5.4395 + 1.00 * 0.0679                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0455 = 1.87 * 0.50 * 5.3380 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1319      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0453 = 2.07 * 1.00 * 5.3380 + 1.00 * 0.0169                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8641 = 2.07 * 1.00 * 5.2506 + 1.00 * 0.0164                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.163)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.63   11.67    None  None   None       |
|    all(noH): 2823   0      0.00    79.63   11.67    None  None   None       |
|    Sol.    : 438    0      0.00    79.63   35.43    None  None   None       |
|    Mac.    : 2385   0      0.00    77.85   7.31     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.963: 1697   |   5:    39.815 -  47.778:   78        |
|      1:     7.963 -  15.926:  540   |   6:    47.778 -  55.741:   81        |
|      2:    15.926 -  23.889:  159   |   7:    55.741 -  63.704:   45        |
|      3:    23.889 -  31.852:  108   |   8:    63.704 -  71.667:   13        |
|      4:    31.852 -  39.815:   93   |   9:    71.667 -  79.630:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1244 r_free = 0.1703             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1244 r_free = 0.1702             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1702   ksol= 0.33   Bsol= 50.96   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.87,3.83,4.49,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.235598                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1702   ksol= 0.32   Bsol= 50.96   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,3.68,4.49,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.235152                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.746385              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.590  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.260500              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.263  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1641          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2706 = 2.75 * 0.50 * 5.2497 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2159 = 2.75 * 0.50 * 5.2021 + 1.00 * 0.0724                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1641      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3713 = 0.26 * 1.00 * 5.2021 + 1.00 * 0.0162                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3661 = 0.26 * 1.00 * 5.1826 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.163)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.93   11.37    None  None   None       |
|    all(noH): 2823   0      0.00    76.93   11.37    None  None   None       |
|    Sol.    : 438    0      0.64    76.13   34.19    None  None   None       |
|    Mac.    : 2385   0      0.00    76.93   7.18     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.693: 1710   |   5:    38.467 -  46.161:   69        |
|      1:     7.693 -  15.387:  528   |   6:    46.161 -  53.854:   84        |
|      2:    15.387 -  23.080:  162   |   7:    53.854 -  61.547:   41        |
|      3:    23.080 -  30.774:  103   |   8:    61.547 -  69.241:   14        |
|      4:    30.774 -  38.467:  103   |   9:    69.241 -  76.934:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1153 r_free = 0.1615             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1152 r_free = 0.1614             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1614   ksol= 0.32   Bsol= 50.96   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,3.68,4.49,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171880                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1613   ksol= 0.32   Bsol= 50.96   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,3.68,4.49,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.172158                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.950742              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.319  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.666986              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.154  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1155      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1274 = 1.95 * 0.50 * 5.1827 + 1.00 * 0.0724                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1088 = 1.95 * 0.50 * 5.1731 + 1.00 * 0.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1604      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4657 = 0.67 * 1.00 * 5.1731 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4669 = 0.67 * 1.00 * 5.1670 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.163)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.73   11.35    None  None   None       |
|    all(noH): 2823   0      0.00    79.73   11.35    None  None   None       |
|    Sol.    : 438    0      0.63    75.97   34.11    None  None   None       |
|    Mac.    : 2385   0      0.00    79.73   7.18     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.973: 1735   |   5:    39.865 -  47.838:   81        |
|      1:     7.973 -  15.946:  516   |   6:    47.838 -  55.811:   71        |
|      2:    15.946 -  23.919:  150   |   7:    55.811 -  63.783:   28        |
|      3:    23.919 -  31.892:  118   |   8:    63.783 -  71.756:   12        |
|      4:    31.892 -  39.865:  104   |   9:    71.756 -  79.729:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1610             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1145 r_free = 0.1610             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1610   ksol= 0.32   Bsol= 50.96   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,3.68,4.49,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170825                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7756 0.99   1382  154 0.1012 0.1358      5.3971      5.5423|
|  2:  4.7756 -  3.8104 0.99   1334  146 0.0885 0.1091       5.459      5.6294|
|  3:  3.8104 -  3.3346 0.99   1292  144 0.1058 0.1536      5.4837      5.8739|
|  4:  3.3346 -  3.0323 0.99   1291  146 0.1223 0.1535      5.4762      5.6072|
|  5:  3.0323 -  2.8165 0.99   1292  142 0.1366 0.1805       5.359      5.5876|
|  6:  2.8165 -  2.6514 0.99   1281  144 0.1236 0.1913      5.2428      5.4696|
|  7:  2.6514 -  2.5192 0.99   1272  135 0.1301 0.1673      5.1999      5.4109|
|  8:  2.5192 -  2.4100 0.98   1266  150 0.1222 0.1783      5.1055       5.383|
|  9:  2.4100 -  2.3176 0.98   1270  137 0.1209 0.1829      5.0763      5.3274|
| 10:  2.3176 -  2.2378 0.99   1257  140 0.1161 0.1718      4.9916       5.259|
| 11:  2.2378 -  2.1681 0.98   1261  136 0.1175 0.1741      4.9729      5.2478|
| 12:  2.1681 -  2.1063 0.97   1244  142 0.1113 0.1732      4.8878      5.2121|
| 13:  2.1063 -  2.0510 1.00   1258  140 0.1196 0.1795      4.8311      5.1139|
| 14:  2.0510 -  2.0010 0.72    930  103 0.1123 0.1866      4.7291      4.9635|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7756  1382   154  0.94   9.20   0.97     0.95       7291.38|
|  2:  4.7756 -  3.8104  1334   146  0.95   8.05   1.01     0.99       9172.04|
|  3:  3.8104 -  3.3346  1292   144  0.93  11.37   1.02     1.01      10660.86|
|  4:  3.3346 -  3.0323  1291   146  0.92  13.95   1.00     0.99      10763.72|
|  5:  3.0323 -  2.8165  1292   142  0.89  16.61   0.99     0.96       8865.14|
|  6:  2.8165 -  2.6514  1281   144  0.90  16.15   0.98     0.96       7592.59|
|  7:  2.6514 -  2.5192  1272   135  0.90  16.04   0.99     0.96       6580.89|
|  8:  2.5192 -  2.4100  1266   150  0.90  15.79   0.99     0.96       5702.68|
|  9:  2.4100 -  2.3176  1270   137  0.90  15.90   1.00     0.97       5421.18|
| 10:  2.3176 -  2.2378  1257   140  0.90  15.79   1.00     0.95       4542.96|
| 11:  2.2378 -  2.1681  1261   136  0.89  16.84   0.99     0.95       4593.19|
| 12:  2.1681 -  2.1063  1244   142  0.92  14.69   1.00     0.99       3972.92|
| 13:  2.1063 -  2.0510  1258   140  0.90  16.78   1.00     0.98       3651.47|
| 14:  2.0510 -  2.0010   930   103  0.90  16.03   0.97     0.93       2920.97|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2920.97 max =        10763.72 mean =      6658.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.42|
|phase err.(test): min =        0.00 max =           89.14 mean =        13.91|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1610   ksol= 0.32   Bsol= 54.90   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,-0.26,0.55,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170825                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1610   ksol= 0.32   Bsol= 54.90   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,-0.26,0.55,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170825                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7756 0.99   1382  154 0.1012 0.1358      5.3971      5.5423|
|  2:  4.7756 -  3.8104 0.99   1334  146 0.0885 0.1091       5.459      5.6294|
|  3:  3.8104 -  3.3346 0.99   1292  144 0.1058 0.1536      5.4837      5.8739|
|  4:  3.3346 -  3.0323 0.99   1291  146 0.1223 0.1535      5.4762      5.6072|
|  5:  3.0323 -  2.8165 0.99   1292  142 0.1366 0.1805       5.359      5.5876|
|  6:  2.8165 -  2.6514 0.99   1281  144 0.1236 0.1913      5.2428      5.4696|
|  7:  2.6514 -  2.5192 0.99   1272  135 0.1301 0.1673      5.1999      5.4109|
|  8:  2.5192 -  2.4100 0.98   1266  150 0.1222 0.1783      5.1055       5.383|
|  9:  2.4100 -  2.3176 0.98   1270  137 0.1209 0.1829      5.0763      5.3274|
| 10:  2.3176 -  2.2378 0.99   1257  140 0.1161 0.1718      4.9916       5.259|
| 11:  2.2378 -  2.1681 0.98   1261  136 0.1175 0.1741      4.9729      5.2478|
| 12:  2.1681 -  2.1063 0.97   1244  142 0.1113 0.1732      4.8878      5.2121|
| 13:  2.1063 -  2.0510 1.00   1258  140 0.1196 0.1795      4.8311      5.1139|
| 14:  2.0510 -  2.0010 0.72    930  103 0.1123 0.1866      4.7291      4.9635|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7756  1382   154  0.94   9.20   0.97     0.95       7291.38|
|  2:  4.7756 -  3.8104  1334   146  0.95   8.05   1.01     0.99       9172.04|
|  3:  3.8104 -  3.3346  1292   144  0.93  11.37   1.02     1.01      10660.86|
|  4:  3.3346 -  3.0323  1291   146  0.92  13.95   1.00     0.99      10763.72|
|  5:  3.0323 -  2.8165  1292   142  0.89  16.61   0.99     0.96       8865.14|
|  6:  2.8165 -  2.6514  1281   144  0.90  16.15   0.98     0.96       7592.59|
|  7:  2.6514 -  2.5192  1272   135  0.90  16.04   0.99     0.96       6580.89|
|  8:  2.5192 -  2.4100  1266   150  0.90  15.79   0.99     0.96       5702.68|
|  9:  2.4100 -  2.3176  1270   137  0.90  15.90   1.00     0.97       5421.18|
| 10:  2.3176 -  2.2378  1257   140  0.90  15.79   1.00     0.95       4542.96|
| 11:  2.2378 -  2.1681  1261   136  0.89  16.84   0.99     0.95       4593.19|
| 12:  2.1681 -  2.1063  1244   142  0.92  14.69   1.00     0.99       3972.92|
| 13:  2.1063 -  2.0510  1258   140  0.90  16.78   1.00     0.98       3651.47|
| 14:  2.0510 -  2.0010   930   103  0.90  16.03   0.97     0.93       2920.97|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2920.97 max =        10763.72 mean =      6658.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.42|
|phase err.(test): min =        0.00 max =           89.14 mean =        13.91|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.163)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.94    83.66   15.29    None  None   None       |
|    all(noH): 2823   0      3.94    83.66   15.29    None  None   None       |
|    Sol.    : 438    0      4.56    79.91   38.04    None  None   None       |
|    Mac.    : 2385   0      3.94    83.66   11.11    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:     3.936 -  11.909: 1735   |   5:    43.800 -  51.773:   81        |
|      1:    11.909 -  19.882:  516   |   6:    51.773 -  59.746:   71        |
|      2:    19.882 -  27.854:  150   |   7:    59.746 -  67.719:   28        |
|      3:    27.854 -  35.827:  118   |   8:    67.719 -  75.692:   12        |
|      4:    35.827 -  43.800:  104   |   9:    75.692 -  83.665:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.320 - 4.764
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 317
   mapped sites are within: 0.715 - 4.764

peak=   10.455 closest distance to " CG2 VAL A 230 " =    1.386
peak=    7.664 closest distance to " CG2 VAL A 296 " =    1.148
peak=    6.234 closest distance to " NH2 ARG A  56 " =    2.284
peak=    6.178 closest distance to " CG  LEU A   5 " =    1.238
peak=    5.960 closest distance to " CB  GLN A 223 " =    1.429
peak=    5.639 closest distance to " CD2 LEU A   5 " =    1.181
peak=    5.468 closest distance to " CG  LEU A 228 " =    1.163
peak=    4.948 closest distance to " CB  SER A  63 " =    1.325
peak=    4.825 closest distance to " CB  VAL A 230 " =    1.231
peak=    4.785 closest distance to " CG  PRO A 213 " =    1.214
peak=    4.767 closest distance to " O   HOH Z 232 " =    2.343
peak=    4.766 closest distance to " CB  GLN A 183 " =    1.275
peak=    4.706 closest distance to " CG  PRO A 198 " =    1.253
peak=    4.618 closest distance to " NE2 GLN A  11 " =    1.114
peak=    4.566 closest distance to " CG  PRO A 243 " =    1.137
peak=    4.550 closest distance to " CB  VAL A 296 " =    1.075
peak=    4.483 closest distance to " O   HOH Z 369 " =    2.095
peak=    4.443 closest distance to " CZ  PHE A 218 " =    1.053
peak=    4.417 closest distance to " CB  ARG A 275 " =    0.881
peak=    4.410 closest distance to " O   HOH Z 298 " =    1.797
peak=    4.389 closest distance to " C   PRO A 198 " =    1.539
peak=    4.385 closest distance to " CB  ASN A 148 " =    1.360
peak=    4.378 closest distance to " O   HOH Z 126 " =    1.935
peak=    4.351 closest distance to " CB  GLU A 128 " =    1.089
peak=    4.335 closest distance to " CB  TRP A 266 " =    0.948
peak=    4.329 closest distance to " OD1 ASN A  69 " =    2.639
peak=    4.328 closest distance to " O   HOH Z 427 " =    3.076
peak=    4.290 closest distance to " O   HOH Z  54 " =    2.371
peak=    4.263 closest distance to " O   HOH Z 316 " =    3.141
peak=    4.245 closest distance to " O   HOH Z  78 " =    1.706
peak=    4.234 closest distance to " O   HOH Z 368 " =    2.253
peak=    4.149 closest distance to " CD2 LEU A 228 " =    1.179
peak=    4.138 closest distance to " O   HOH Z 272 " =    1.880
peak=    4.117 closest distance to " O   HOH Z  43 " =    2.012
peak=    4.112 closest distance to " CB  ARG A  79 " =    1.459
peak=    4.098 closest distance to " O   HOH Z 261 " =    1.991
peak=    4.096 closest distance to " CB  SER A   3 " =    1.315
peak=    4.092 closest distance to " CA  TYR A  30 " =    0.952
peak=    4.080 closest distance to " CB  ASP A 140 " =    0.913
peak=    4.080 closest distance to " NH1AARG A 145 " =    1.149
peak=    4.071 closest distance to " O   HOH Z 236 " =    1.911
peak=    4.063 closest distance to " CB  ASP A 124 " =    0.721
peak=    4.056 closest distance to " O   HOH Z 423 " =    1.707
peak=    4.045 closest distance to " O   HOH Z 142 " =    1.555
peak=    4.044 closest distance to " O   HOH Z 303 " =    2.087
peak=    4.027 closest distance to " CZ  PHE A 192 " =    0.995
peak=    4.017 closest distance to " CB  PRO A  54 " =    0.809
peak=    4.017 closest distance to " CB  VAL A 265 " =    1.315
peak=    4.012 closest distance to " CB  GLU A 277 " =    3.669
peak=    4.004 closest distance to " O   HOH Z 158 " =    3.088
peak=    4.002 closest distance to " O   HOH Z 403 " =    1.709
peak=    3.992 closest distance to " CB  GLU A 152 " =    1.152
peak=    3.977 closest distance to " CD  ARG A 159 " =    0.775
peak=    3.959 closest distance to " CB  ARG A 190 " =    1.624
peak=    3.951 closest distance to " CB  ASN A  39 " =    0.880
peak=    3.949 closest distance to " NH2 ARG A 156 " =    1.135
peak=    3.928 closest distance to " O   HOH Z  61 " =    1.663
peak=    3.924 closest distance to " ND2 ASN A 187 " =    1.460
peak=    3.919 closest distance to " CD BLYS A 290 " =    1.027
peak=    3.917 closest distance to " O   SER A  87 " =    2.295
peak=    3.906 closest distance to " O   HOH Z 189 " =    2.897
peak=    3.899 closest distance to " O   HOH Z 346 " =    1.597
peak=    3.888 closest distance to " O   HOH Z 425 " =    1.397
peak=    3.883 closest distance to " CB  VAL A 202 " =    1.624
peak=    3.863 closest distance to " CA  THR A 264 " =    0.745
peak=    3.857 closest distance to " O   HOH Z 203 " =    1.767
peak=    3.854 closest distance to " CD  ARG A  66 " =    2.558
peak=    3.851 closest distance to " O   HOH Z 234 " =    3.778
peak=    3.851 closest distance to " ND2 ASN A 249 " =    1.892
peak=    3.850 closest distance to " O   HOH Z  88 " =    3.260
peak=    3.848 closest distance to " O   HOH Z  63 " =    1.952
peak=    3.843 closest distance to " CA  ALA A  51 " =    1.002
peak=    3.838 closest distance to " O   HOH Z 411 " =    3.691
peak=    3.830 closest distance to " CG  MET A 185 " =    1.231
peak=    3.818 closest distance to " CD  ARG A 269 " =    0.978
peak=    3.805 closest distance to " CB  LEU A 143 " =    1.191
peak=    3.804 closest distance to " O   MET A 105 " =    1.825
peak=    3.799 closest distance to " O   HOH Z  15 " =    2.111
peak=    3.792 closest distance to " CB  SER A 216 " =    0.856
peak=    3.790 closest distance to " O   HOH Z 214 " =    2.090
peak=    3.787 closest distance to " CD1 LEU A 300 " =    1.150
peak=    3.782 closest distance to " N   ASN A  39 " =    1.205
peak=    3.760 closest distance to " O   HOH Z 280 " =    2.943
peak=    3.758 closest distance to " CA  ASN A 215 " =    1.221
peak=    3.755 closest distance to " CB  LEU A 228 " =    1.227
peak=    3.754 closest distance to " CB AVAL A  41 " =    1.199
peak=    3.751 closest distance to " O   HOH Z  68 " =    2.054
peak=    3.743 closest distance to " CB  ALA A   9 " =    1.607
peak=    3.740 closest distance to " O   HOH Z 247 " =    1.355
peak=    3.729 closest distance to " CG1 VAL A 153 " =    0.974
peak=    3.725 closest distance to " CG2 THR A 221 " =    1.083
peak=    3.725 closest distance to " CA  SER A  87 " =    0.999
peak=    3.721 closest distance to " O   HOH Z  44 " =    2.127
peak=    3.719 closest distance to " CB  ASN A 187 " =    1.204
peak=    3.717 closest distance to " CB  TRP A 179 " =    1.448
peak=    3.707 closest distance to " CG2 VAL A 257 " =    0.895
peak=    3.697 closest distance to " CB  ALA A 291 " =    1.366
peak=    3.691 closest distance to " O   HOH Z 193 " =    2.049
peak=    3.683 closest distance to " CA  ALA A 295 " =    1.110
peak=    3.673 closest distance to " O   HOH Z 402 " =    1.498
peak=    3.667 closest distance to " CG  LEU A 167 " =    1.164
peak=    3.658 closest distance to " O   HOH Z  80 " =    1.681
peak=    3.657 closest distance to " O   TRP A 274 " =    1.883
peak=    3.647 closest distance to " O   HOH Z 112 " =    1.661
peak=    3.638 closest distance to " CA  ALA A  21 " =    1.186
peak=    3.638 closest distance to " O   HOH Z  19 " =    2.420
peak=    3.635 closest distance to " O   HOH Z  97 " =    2.091
peak=    3.633 closest distance to " CB  SER A 212 " =    1.182
peak=    3.623 closest distance to " CD  LYS A 166 " =    1.308
peak=    3.622 closest distance to " N   VAL A 126 " =    1.422
peak=    3.615 closest distance to " OD2 ASP A 286 " =    2.836
peak=    3.611 closest distance to " CG1BVAL A  72 " =    1.696
peak=    3.601 closest distance to " CA  ARG A 195 " =    1.231
peak=    3.600 closest distance to " O   HOH Z  21 " =    1.728
peak=    3.600 closest distance to " O   HOH Z 193 " =    1.872
peak=    3.583 closest distance to " CB  ASN A 142 " =    1.060
peak=    3.578 closest distance to " CA  LYS A 117 " =    1.245
peak=    3.577 closest distance to " O   ASP A 124 " =    1.091
peak=    3.577 closest distance to " CG1 ILE A  49 " =    1.485
peak=    3.576 closest distance to " O   HOH Z 193 " =    1.673
peak=    3.573 closest distance to " O   HOH Z 126 " =    1.601
peak=    3.573 closest distance to " CB  GLU A  46 " =    0.994
peak=    3.562 closest distance to " CG1 ILE A  33 " =    1.265
peak=    3.562 closest distance to " O   HOH Z 180 " =    2.116
peak=    3.561 closest distance to " O   HOH Z  48 " =    1.729
peak=    3.546 closest distance to " O   HOH Z 285 " =    3.058
peak=    3.543 closest distance to " CA  THR A 221 " =    0.907
peak=    3.538 closest distance to " CA  MET A  40 " =    1.134
peak=    3.534 closest distance to " O   HOH Z 437 " =    1.867
peak=    3.531 closest distance to " O   HOH Z  20 " =    1.706
peak=    3.529 closest distance to " CB  MET A  40 " =    0.801
peak=    3.526 closest distance to " O   HOH Z 290 " =    1.081
peak=    3.524 closest distance to " CA  TYR A  30 " =    1.063
peak=    3.520 closest distance to " ND1 HIS A  81 " =    1.677
peak=    3.518 closest distance to " O   HOH Z 128 " =    2.163
peak=    3.518 closest distance to " CA  LEU A 282 " =    1.034
peak=    3.517 closest distance to " O   HOH Z 163 " =    1.573
peak=    3.516 closest distance to " O   HOH Z 263 " =    1.631
peak=    3.514 closest distance to " CG2 THR A 220 " =    0.940
peak=    3.509 closest distance to " CE  LYS A  76 " =    0.844
peak=    3.508 closest distance to " CA  ALA A 158 " =    1.205
peak=    3.504 closest distance to " CB  ALA A 248 " =    1.380
peak=    3.502 closest distance to " CG1 VAL A 296 " =    1.222
peak=    3.502 closest distance to " CD  ARG A  66 " =    2.427
peak=    3.501 closest distance to " O   HOH Z 128 " =    2.153
peak=    3.498 closest distance to " O   HOH Z 245 " =    1.346
peak=    3.491 closest distance to " O   HOH Z 313 " =    1.780
peak=    3.491 closest distance to " O   HOH Z 133 " =    2.359
peak=    3.488 closest distance to " O   HOH Z 135 " =    1.927
peak=    3.486 closest distance to " O   HOH Z 102 " =    1.309
peak=    3.479 closest distance to " O   HOH Z 344 " =    3.052
peak=    3.477 closest distance to " O   HOH Z  97 " =    2.534
peak=    3.477 closest distance to " O   HOH Z 134 " =    1.456
peak=    3.475 closest distance to " CB  THR A  82 " =    1.417
peak=    3.475 closest distance to " CA  ARG A  36 " =    1.151
peak=    3.474 closest distance to " O   HOH Z 248 " =    1.733
peak=    3.473 closest distance to " NZ  LYS A 117 " =    3.293
peak=    3.472 closest distance to " O   ALA A 158 " =    1.447
peak=    3.464 closest distance to " O   HOH Z 197 " =    3.023
peak=    3.463 closest distance to " O   HOH Z 133 " =    1.727
peak=    3.462 closest distance to " CG  GLN A  88 " =    1.060
peak=    3.458 closest distance to " O   HOH Z 147 " =    1.722
peak=    3.455 closest distance to " O   HOH Z 368 " =    3.583
peak=    3.453 closest distance to " CA  VAL A  41 " =    0.855
peak=    3.452 closest distance to " CD1 ILE A 106 " =    0.972
peak=    3.444 closest distance to " CZ  PHE A  38 " =    1.168
peak=    3.444 closest distance to " O   HOH Z 371 " =    3.242
peak=    3.444 closest distance to " O   HOH Z 273 " =    2.711
peak=    3.443 closest distance to " CB  ARG A  79 " =    0.907
peak=    3.442 closest distance to " CE1 TYR A 186 " =    1.285
peak=    3.442 closest distance to " CB  ALA A 242 " =    0.825
peak=    3.439 closest distance to " O   HOH Z 426 " =    1.568
peak=    3.437 closest distance to " CG BARG A 275 " =    1.445
peak=    3.433 closest distance to " N   PHE A 130 " =    1.237
peak=    3.430 closest distance to " CG1 ILE A 151 " =    1.039
peak=    3.424 closest distance to " N   SER A 135 " =    1.417
peak=    3.423 closest distance to " CB  THR A 157 " =    1.149
peak=    3.420 closest distance to " OG  SER A  22 " =    2.840
peak=    3.418 closest distance to " O   HOH Z 184 " =    1.343
peak=    3.417 closest distance to " O   HOH Z 171 " =    3.849
peak=    3.415 closest distance to " CG  MET A 185 " =    1.090
peak=    3.415 closest distance to " CB  ASN A 110 " =    1.234
peak=    3.411 closest distance to " CB  SER A 273 " =    0.875
peak=    3.410 closest distance to " CD1 LEU A   5 " =    1.348
peak=    3.409 closest distance to " O   HOH Z 383 " =    2.103
peak=    3.408 closest distance to " O   HOH Z 250 " =    1.368
peak=    3.407 closest distance to " CD1 ILE A  33 " =    1.611
peak=    3.393 closest distance to " CB  ALA A  34 " =    0.774
peak=    3.391 closest distance to " CD2 LEU A   5 " =    0.760
peak=    3.389 closest distance to " CA  ALA A 291 " =    0.924
peak=    3.387 closest distance to " N   ARG A 190 " =    1.057
peak=    3.386 closest distance to " CG  ARG A 138 " =    1.163
peak=    3.385 closest distance to " O   HOH Z 227 " =    1.676
peak=    3.376 closest distance to " O   HOH Z 145 " =    1.966
peak=    3.372 closest distance to " CB  MET A  47 " =    1.078
peak=    3.371 closest distance to " CB  ILE A 120 " =    1.333
peak=    3.371 closest distance to " OG BSER A 164 " =    2.210
peak=    3.364 closest distance to " CB  PRO A 198 " =    1.018
peak=    3.357 closest distance to " CB  TRP A 150 " =    1.392
peak=    3.356 closest distance to " O   HOH Z 305 " =    3.654
peak=    3.354 closest distance to " CB  ALA A 104 " =    0.780
peak=    3.350 closest distance to " CA  ALA A 154 " =    0.982
peak=    3.346 closest distance to " O   HOH Z 295 " =    1.490
peak=    3.346 closest distance to " CD2 TRP A 179 " =    1.371
peak=    3.346 closest distance to " OH  TYR A 214 " =    1.228
peak=    3.345 closest distance to " CB  THR A  31 " =    1.708
peak=    3.341 closest distance to " CA  LYS A 181 " =    1.040
peak=    3.337 closest distance to " O   HOH Z 141 " =    1.660
peak=    3.334 closest distance to " CB  GLN A  89 " =    1.181
peak=    3.333 closest distance to " O   HOH Z  62 " =    2.325
peak=    3.333 closest distance to " CB  ALA A 161 " =    0.897
peak=    3.328 closest distance to " O   HOH Z 353 " =    2.704
peak=    3.323 closest distance to " CB  VAL A 268 " =    0.842
peak=    3.320 closest distance to " CB  ARG A 139 " =    0.842
peak=    3.318 closest distance to " O   HOH Z 422 " =    2.693
peak=    3.313 closest distance to " CG  PRO A 280 " =    0.715
peak=    3.311 closest distance to " CA  ASP A 140 " =    1.245
peak=    3.309 closest distance to " O   HOH Z 132 " =    2.721
peak=    3.302 closest distance to " CA  ASP A 191 " =    0.741
peak=    3.301 closest distance to " NE2 HIS A 207 " =    1.347
peak=    3.294 closest distance to " O   HOH Z 291 " =    1.620
peak=    3.293 closest distance to " CB  ALA A 248 " =    1.117
peak=    3.293 closest distance to " CA  LYS A 290 " =    1.269
peak=    3.289 closest distance to " O   HOH Z 155 " =    3.363
peak=    3.288 closest distance to " O   HOH Z 327 " =    2.362
peak=    3.283 closest distance to " O   HOH Z 345 " =    3.458
peak=    3.282 closest distance to " O   HOH Z 172 " =    3.697
peak=    3.282 closest distance to " O   HOH Z 435 " =    2.013
peak=    3.280 closest distance to " CB  HIS A 108 " =    0.787
peak=    3.280 closest distance to " O   HOH Z  59 " =    2.194
peak=    3.274 closest distance to " CG BARG A 102 " =    1.849
peak=    3.274 closest distance to " CB  ALA A   1 " =    4.764
peak=    3.264 closest distance to " O   GLN A 278 " =    1.546
peak=    3.261 closest distance to " CE1 HIS A 108 " =    1.177
peak=    3.261 closest distance to " C   TYR A 214 " =    1.499
peak=    3.259 closest distance to " O   HOH Z 185 " =    2.323
peak=    3.256 closest distance to " O   HOH Z 329 " =    3.873
peak=    3.248 closest distance to " CA  ALA A 233 " =    1.527
peak=    3.248 closest distance to " O   HOH Z   4 " =    1.854
peak=    3.242 closest distance to " CD1 LEU A 228 " =    1.915
peak=    3.237 closest distance to " O   HOH Z 409 " =    3.226
peak=    3.236 closest distance to " O   HOH Z  10 " =    1.782
peak=    3.235 closest distance to " O   HOH Z 302 " =    1.940
peak=    3.234 closest distance to " C   ALA A 299 " =    0.979
peak=    3.233 closest distance to " O   HOH Z 420 " =    1.869
peak=    3.233 closest distance to " ND1 HIS A  86 " =    1.719
peak=    3.233 closest distance to " CB  ALA A 114 " =    1.173
peak=    3.231 closest distance to " O   HOH Z 350 " =    1.652
peak=    3.229 closest distance to " CB  ARG A 138 " =    0.980
peak=    3.228 closest distance to " CA  ASN A 127 " =    1.073
peak=    3.228 closest distance to " O   HOH Z 116 " =    1.813
peak=    3.223 closest distance to " CA  GLY A 211 " =    1.297
peak=    3.223 closest distance to " CB  ALA A 137 " =    1.080
peak=    3.223 closest distance to " O   HOH Z 425 " =    2.025
peak=    3.222 closest distance to " C   SER A  32 " =    1.052
peak=    3.222 closest distance to " N   ASN A 127 " =    1.212
peak=    3.221 closest distance to " OD1 ASN A 217 " =    1.654
peak=    3.219 closest distance to " CD1 TRP A 266 " =    1.116
peak=    3.218 closest distance to " O  BHOH Z 338 " =    2.435
peak=    3.213 closest distance to " N   GLN A 278 " =    1.075
peak=    3.211 closest distance to " O   HOH Z 250 " =    1.343
peak=    3.208 closest distance to " O   HOH Z 294 " =    1.587
peak=    3.205 closest distance to " O   HOH Z  63 " =    1.201
peak=    3.204 closest distance to " CE2 TYR A  30 " =    0.787
peak=    3.202 closest distance to " CB  TYR A 116 " =    0.852
peak=    3.198 closest distance to " O   HOH Z 403 " =    1.387
peak=    3.195 closest distance to " CG2 VAL A 202 " =    1.147
peak=    3.195 closest distance to " N   TYR A  15 " =    0.783
peak=    3.194 closest distance to " N   SER A 146 " =    1.718
peak=    3.189 closest distance to " CA  ILE A 106 " =    0.783
peak=    3.185 closest distance to " O   HOH Z 359 " =    1.307
peak=    3.184 closest distance to " CB  LYS A 117 " =    1.166
peak=    3.183 closest distance to " O   HOH Z 365 " =    2.983
peak=    3.180 closest distance to " CD2 LEU A 255 " =    1.713
peak=    3.176 closest distance to " CG2 VAL A 197 " =    1.086
peak=    3.176 closest distance to " O   HOH Z 313 " =    1.785
peak=    3.173 closest distance to " O   HOH Z 417 " =    2.071
peak=    3.168 closest distance to " O   HOH Z 271 " =    2.465
peak=    3.166 closest distance to " CD  LYS A 119 " =    1.833
peak=    3.156 closest distance to " ND2 ASN A 110 " =    1.624
peak=    3.156 closest distance to " NZ  LYS A  48 " =    1.414
peak=    3.154 closest distance to " NH2 ARG A  79 " =    1.425
peak=    3.141 closest distance to " CD2 HIS A  81 " =    1.009
peak=    3.136 closest distance to " CB  ALA A 227 " =    1.013
peak=    3.134 closest distance to " CZ3 TRP A  85 " =    1.057
peak=    3.129 closest distance to " CB  PRO A 243 " =    1.219
peak=    3.126 closest distance to " CA  ASN A 176 " =    1.136
peak=    3.122 closest distance to " CA  MET A 105 " =    0.985
peak=    3.116 closest distance to " CG  ARG A 159 " =    1.047
peak=    3.112 closest distance to " CG  GLU A  37 " =    0.809
peak=    3.109 closest distance to " N   ARG A 156 " =    1.401
peak=    3.108 closest distance to " O   HOH Z 213 " =    1.886
peak=    3.093 closest distance to " O   HOH Z 293 " =    1.920
peak=    3.091 closest distance to " CD1 ILE A 199 " =    0.817
peak=    3.089 closest distance to " CG1 VAL A 174 " =    1.126
peak=    3.078 closest distance to " CB  LYS A 193 " =    1.064
peak=    3.075 closest distance to " O   HOH Z 327 " =    1.868
peak=    3.068 closest distance to " CB  ALA A 100 " =    1.258
peak=    3.065 closest distance to " OG  SER A 206 " =    1.164
peak=    3.060 closest distance to " O   HOH Z  49 " =    2.793
peak=    3.059 closest distance to " O   HOH Z 326 " =    2.282
peak=    3.056 closest distance to " CB  GLN A 278 " =    0.878
peak=    3.054 closest distance to " CA  ALA A 248 " =    1.224
peak=    3.049 closest distance to " O   HOH Z 417 " =    2.765
peak=    3.042 closest distance to " CZ3 TRP A 266 " =    1.109
peak=    3.035 closest distance to " CB  ALA A  43 " =    0.852
peak=    3.035 closest distance to " CB  ASN A 215 " =    1.167
peak=    3.031 closest distance to " O   HOH Z 128 " =    1.953

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.782 - 5.527
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 206
   mapped sites are within: 0.782 - 5.527

peak=   -5.187 closest distance to " CG2 VAL A 230 " =    0.814
peak=   -4.424 closest distance to " CD  ARG A 156 " =    2.024
peak=   -4.258 closest distance to " O   HOH Z 266 " =    5.124
peak=   -4.141 closest distance to " CD  ARG A  14 " =    3.228
peak=   -4.140 closest distance to " CB  PRO A 243 " =    2.666
peak=   -4.084 closest distance to " CB  ALA A 161 " =    2.602
peak=   -4.057 closest distance to " OE1 GLN A 223 " =    2.117
peak=   -4.000 closest distance to " O   HOH Z  52 " =    1.620
peak=   -3.984 closest distance to " CD  GLN A  58 " =    1.020
peak=   -3.908 closest distance to " O   HOH Z 196 " =    2.195
peak=   -3.877 closest distance to " O   HOH Z 118 " =    3.250
peak=   -3.861 closest distance to " CG  ASP A 231 " =    0.782
peak=   -3.859 closest distance to " C   HIS A 108 " =    1.147
peak=   -3.834 closest distance to " CG2BVAL A  41 " =    2.611
peak=   -3.833 closest distance to " CG2 VAL A 296 " =    1.465
peak=   -3.832 closest distance to " O   HOH Z 351 " =    1.473
peak=   -3.817 closest distance to " NH2AARG A 275 " =    5.333
peak=   -3.810 closest distance to " O   HOH Z  11 " =    1.941
peak=   -3.809 closest distance to " O   HOH Z 231 " =    1.999
peak=   -3.805 closest distance to " CG1 VAL A 112 " =    2.643
peak=   -3.803 closest distance to " CG1 VAL A 296 " =    1.363
peak=   -3.801 closest distance to " CD2 LEU A 300 " =    2.791
peak=   -3.799 closest distance to " N   ALA A 226 " =    2.133
peak=   -3.798 closest distance to " O   HOH Z 394 " =    1.538
peak=   -3.793 closest distance to " O   HOH Z 290 " =    1.247
peak=   -3.787 closest distance to " O   HOH Z 166 " =    1.907
peak=   -3.787 closest distance to " CE2 TYR A  30 " =    2.798
peak=   -3.772 closest distance to " CZ3 TRP A 179 " =    1.180
peak=   -3.770 closest distance to " OG BSER A 134 " =    1.162
peak=   -3.752 closest distance to " OG  SER A  97 " =    2.294
peak=   -3.738 closest distance to " CG1 VAL A 250 " =    2.723
peak=   -3.699 closest distance to " OXT GLY A 302 " =    3.011
peak=   -3.696 closest distance to " CG1 VAL A 112 " =    2.997
peak=   -3.691 closest distance to " CA  GLY A 241 " =    3.073
peak=   -3.682 closest distance to " O   VAL A 189 " =    2.605
peak=   -3.668 closest distance to " O   HOH Z 426 " =    1.660
peak=   -3.667 closest distance to " O   HOH Z 435 " =    2.784
peak=   -3.662 closest distance to " O   HOH Z 103 " =    1.837
peak=   -3.660 closest distance to " CG1 VAL A 265 " =    2.447
peak=   -3.649 closest distance to " CD1 LEU A 228 " =    2.390
peak=   -3.648 closest distance to " CA  ASP A 298 " =    1.044
peak=   -3.646 closest distance to " O   PRO A 163 " =    2.165
peak=   -3.635 closest distance to " C   ALA A 158 " =    1.298
peak=   -3.633 closest distance to " NE2 GLN A  88 " =    2.085
peak=   -3.617 closest distance to " O   VAL A  67 " =    2.647
peak=   -3.609 closest distance to " O   HOH Z 389 " =    1.930
peak=   -3.602 closest distance to " ND2 ASN A  45 " =    1.114
peak=   -3.601 closest distance to " O   HOH Z 241 " =    1.207
peak=   -3.583 closest distance to " OD1 ASN A 148 " =    1.480
peak=   -3.579 closest distance to " O   HOH Z 350 " =    1.713
peak=   -3.578 closest distance to " O   HOH Z 185 " =    2.400
peak=   -3.569 closest distance to " CB  PHE A 192 " =    1.905
peak=   -3.569 closest distance to " OG  SER A  87 " =    1.540
peak=   -3.566 closest distance to " CB  ALA A  43 " =    2.589
peak=   -3.563 closest distance to " O   PRO A 198 " =    1.230
peak=   -3.560 closest distance to " O   GLY A 203 " =    2.350
peak=   -3.551 closest distance to " O   HOH Z  19 " =    2.341
peak=   -3.550 closest distance to " O   HOH Z  73 " =    2.168
peak=   -3.536 closest distance to " CB  PRO A 163 " =    2.587
peak=   -3.535 closest distance to " O   SER A 271 " =    2.246
peak=   -3.533 closest distance to " CG  HIS A  86 " =    0.954
peak=   -3.531 closest distance to " N   ALA A  43 " =    2.529
peak=   -3.528 closest distance to " CE3 TRP A 150 " =    2.100
peak=   -3.521 closest distance to " CG  ARG A 269 " =    2.515
peak=   -3.513 closest distance to " N   THR A  18 " =    1.311
peak=   -3.498 closest distance to " CE  MET A 105 " =    2.207
peak=   -3.491 closest distance to " CG  GLU A 277 " =    1.160
peak=   -3.489 closest distance to " CD1 LEU A 101 " =    2.505
peak=   -3.486 closest distance to " O   HOH Z  10 " =    1.538
peak=   -3.478 closest distance to " O   HOH Z 231 " =    1.502
peak=   -3.474 closest distance to " O   HOH Z 377 " =    1.981
peak=   -3.462 closest distance to " O   HOH Z 275 " =    1.505
peak=   -3.460 closest distance to " CB  ALA A 291 " =    2.215
peak=   -3.458 closest distance to " CG  MET A 105 " =    0.969
peak=   -3.455 closest distance to " OD1 ASN A 187 " =    1.596
peak=   -3.454 closest distance to " CD2 LEU A 167 " =    1.786
peak=   -3.453 closest distance to " O   HOH Z 353 " =    2.164
peak=   -3.444 closest distance to " CB  ALA A 248 " =    2.070
peak=   -3.439 closest distance to " CG  LEU A 101 " =    2.483
peak=   -3.436 closest distance to " ND2 ASN A  45 " =    1.812
peak=   -3.435 closest distance to " CA  GLY A 203 " =    2.449
peak=   -3.431 closest distance to " O   HOH Z  44 " =    2.148
peak=   -3.429 closest distance to " CD  ARG A 139 " =    1.620
peak=   -3.429 closest distance to " CG2 VAL A 112 " =    2.548
peak=   -3.420 closest distance to " O   HOH Z  38 " =    1.518
peak=   -3.415 closest distance to " CD  LYS A 289 " =    2.568
peak=   -3.415 closest distance to " O   GLY A 211 " =    1.404
peak=   -3.414 closest distance to " OG ASER A 134 " =    1.389
peak=   -3.411 closest distance to " NE2 GLN A 194 " =    1.791
peak=   -3.409 closest distance to " O   HOH Z  60 " =    2.232
peak=   -3.408 closest distance to " O   GLY A  80 " =    2.551
peak=   -3.403 closest distance to " O   HOH Z  13 " =    1.441
peak=   -3.403 closest distance to " C   LEU A 222 " =    0.892
peak=   -3.402 closest distance to " O   HOH Z 407 " =    3.183
peak=   -3.401 closest distance to " OG BSER A 134 " =    1.864
peak=   -3.399 closest distance to " O   HOH Z  17 " =    1.538
peak=   -3.397 closest distance to " CA  GLY A 241 " =    2.290
peak=   -3.390 closest distance to " CG1 VAL A 197 " =    2.304
peak=   -3.386 closest distance to " O   HOH Z 211 " =    1.564
peak=   -3.384 closest distance to " CG  TRP A 266 " =    1.823
peak=   -3.383 closest distance to " OD2 ASP A  50 " =    2.373
peak=   -3.377 closest distance to " O   HOH Z  43 " =    1.706
peak=   -3.377 closest distance to " O   HOH Z 222 " =    1.548
peak=   -3.375 closest distance to " NE2 GLN A 103 " =    1.805
peak=   -3.375 closest distance to " NH2 ARG A  79 " =    2.017
peak=   -3.372 closest distance to " CD2 TYR A 293 " =    2.053
peak=   -3.368 closest distance to " N   THR A 157 " =    1.527
peak=   -3.364 closest distance to " ND2 ASN A 187 " =    1.694
peak=   -3.362 closest distance to " O   HOH Z 177 " =    1.652
peak=   -3.359 closest distance to " CG  PHE A 283 " =    2.886
peak=   -3.352 closest distance to " C   ASN A 285 " =    2.511
peak=   -3.351 closest distance to " CD1 PHE A  59 " =    1.940
peak=   -3.350 closest distance to " NZ  LYS A 119 " =    3.492
peak=   -3.350 closest distance to " C   MET A 188 " =    1.379
peak=   -3.348 closest distance to " O   HOH Z 184 " =    1.552
peak=   -3.346 closest distance to " CD1 ILE A 239 " =    2.131
peak=   -3.345 closest distance to " CB  ASN A  39 " =    2.240
peak=   -3.343 closest distance to " O   HOH Z 166 " =    1.627
peak=   -3.336 closest distance to " CD1 LEU A 101 " =    2.793
peak=   -3.327 closest distance to " CB  ASP A 132 " =    2.316
peak=   -3.319 closest distance to " O   HOH Z 102 " =    1.653
peak=   -3.313 closest distance to " CE1 TYR A 169 " =    2.421
peak=   -3.311 closest distance to " NH2 ARG A  66 " =    1.960
peak=   -3.308 closest distance to " O   HOH Z  63 " =    1.173
peak=   -3.307 closest distance to " CB  ALA A 248 " =    2.461
peak=   -3.306 closest distance to " CB  VAL A 230 " =    1.072
peak=   -3.304 closest distance to " ND2 ASN A  60 " =    1.420
peak=   -3.304 closest distance to " C   ASN A 187 " =    1.805
peak=   -3.300 closest distance to " O   HOH Z 359 " =    3.106
peak=   -3.295 closest distance to " CB  ASN A  69 " =    1.202
peak=   -3.287 closest distance to " N   GLN A  58 " =    1.684
peak=   -3.287 closest distance to " OG  SER A 206 " =    1.752
peak=   -3.285 closest distance to " OE1 GLN A  88 " =    1.094
peak=   -3.285 closest distance to " O   GLY A 196 " =    1.202
peak=   -3.282 closest distance to " O   HOH Z 388 " =    2.085
peak=   -3.278 closest distance to " NH1 ARG A 195 " =    2.609
peak=   -3.277 closest distance to " O   HOH Z 311 " =    3.786
peak=   -3.273 closest distance to " OG  SER A  62 " =    1.772
peak=   -3.270 closest distance to " O   LEU A 167 " =    1.493
peak=   -3.270 closest distance to " O   HOH Z 231 " =    1.754
peak=   -3.270 closest distance to " CE2 PHE A 218 " =    2.578
peak=   -3.270 closest distance to " CG  GLU A  53 " =    1.529
peak=   -3.267 closest distance to " C   LEU A 143 " =    1.134
peak=   -3.262 closest distance to " O   HOH Z 113 " =    2.088
peak=   -3.259 closest distance to " CE3 TRP A  70 " =    1.788
peak=   -3.257 closest distance to " O   HOH Z 243 " =    1.971
peak=   -3.255 closest distance to " CD2 PHE A  61 " =    2.438
peak=   -3.252 closest distance to " O   HOH Z 165 " =    1.853
peak=   -3.245 closest distance to " O   HOH Z 372 " =    2.416
peak=   -3.243 closest distance to " CA  ASN A 127 " =    1.083
peak=   -3.242 closest distance to " O   HOH Z 234 " =    4.358
peak=   -3.239 closest distance to " O   ASP A 270 " =    1.643
peak=   -3.239 closest distance to " O   HOH Z 191 " =    5.527
peak=   -3.233 closest distance to " O   HOH Z 292 " =    4.635
peak=   -3.232 closest distance to " O   HOH Z 377 " =    1.552
peak=   -3.226 closest distance to " O   VAL A 125 " =    2.330
peak=   -3.224 closest distance to " CD  PRO A 213 " =    2.188
peak=   -3.214 closest distance to " O   HOH Z 252 " =    4.032
peak=   -3.211 closest distance to " N   SER A 212 " =    1.834
peak=   -3.209 closest distance to " O   HOH Z 128 " =    2.565
peak=   -3.203 closest distance to " O   HOH Z 262 " =    2.891
peak=   -3.198 closest distance to " NE2 GLN A  88 " =    1.007
peak=   -3.196 closest distance to " CA  ALA A 248 " =    2.611
peak=   -3.193 closest distance to " CE BMET A  47 " =    1.949
peak=   -3.192 closest distance to " OG  SER A  26 " =    1.345
peak=   -3.192 closest distance to " O   HOH Z 396 " =    1.852
peak=   -3.187 closest distance to " CD2 LEU A 237 " =    2.871
peak=   -3.185 closest distance to " O   HOH Z  90 " =    1.595
peak=   -3.184 closest distance to " CA  GLY A 133 " =    2.298
peak=   -3.182 closest distance to " CH2 TRP A 177 " =    2.157
peak=   -3.181 closest distance to " CD  GLN A  88 " =    0.833
peak=   -3.180 closest distance to " O   HOH Z 123 " =    2.457
peak=   -3.179 closest distance to " N   SER A   3 " =    2.033
peak=   -3.178 closest distance to " CB  ALA A  10 " =    2.214
peak=   -3.177 closest distance to " O   HOH Z 313 " =    1.139
peak=   -3.173 closest distance to " O   MET A  40 " =    2.733
peak=   -3.173 closest distance to " O   HOH Z 417 " =    2.809
peak=   -3.170 closest distance to " O   LYS A 117 " =    1.806
peak=   -3.169 closest distance to " N   SER A 276 " =    1.381
peak=   -3.166 closest distance to " CZ2 TRP A  92 " =    2.834
peak=   -3.161 closest distance to " O   HOH Z 423 " =    2.063
peak=   -3.155 closest distance to " O   HOH Z 111 " =    2.240
peak=   -3.152 closest distance to " CZ  TYR A 169 " =    1.687
peak=   -3.146 closest distance to " CB  ALA A 291 " =    2.210
peak=   -3.143 closest distance to " CD1 TYR A 247 " =    2.360
peak=   -3.143 closest distance to " CG1 VAL A  67 " =    3.037
peak=   -3.143 closest distance to " O   HOH Z 429 " =    2.089
peak=   -3.139 closest distance to " CB  TYR A  15 " =    2.244
peak=   -3.126 closest distance to " CG2 THR A 178 " =    2.222
peak=   -3.108 closest distance to " O   ALA A  10 " =    1.738
peak=   -3.106 closest distance to " C   ASP A 231 " =    2.627
peak=   -3.105 closest distance to " N   ALA A 248 " =    1.750
peak=   -3.100 closest distance to " ND2 ASN A  60 " =    1.856
peak=   -3.097 closest distance to " OXT GLY A 302 " =    3.464
peak=   -3.094 closest distance to " OD2 ASP A 171 " =    1.852
peak=   -3.094 closest distance to " CG1 VAL A 296 " =    1.302
peak=   -3.093 closest distance to " CG2 VAL A 296 " =    1.853
peak=   -3.081 closest distance to " O   HOH Z  51 " =    1.422
peak=   -3.071 closest distance to " CD1 TYR A 247 " =    2.615
peak=   -3.062 closest distance to " CZ  PHE A  38 " =    2.300
peak=   -3.057 closest distance to " CD1 ILE A 199 " =    2.597
peak=   -3.043 closest distance to " N   PHE A  59 " =    2.299
peak=   -3.039 closest distance to " CA  TYR A  68 " =    2.890
peak=   -3.039 closest distance to " O   PRO A 198 " =    1.335
peak=   -3.037 closest distance to " CD  ARG A 195 " =    5.085

================= 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    :  0.4301 0.4160   6.224850e+00   6.199081e+00
   1_bss:  0.4227 0.4032   6.219790e+00   6.186281e+00
   1_xyz:  0.3114 0.3385   6.001869e+00   6.063560e+00
   1_adp:  0.2500 0.2859   5.817379e+00   5.936711e+00
   1_occ:  0.2493 0.2858   5.816273e+00   5.937578e+00
   2_bss:  0.2455 0.2810   5.815390e+00   5.933505e+00
   2_xyz:  0.1676 0.2097   5.476719e+00   5.656859e+00
   2_adp:  0.1538 0.1985   5.405181e+00   5.602618e+00
   2_occ:  0.1536 0.1985   5.404671e+00   5.602727e+00
   3_bss:  0.1530 0.1976   5.404573e+00   5.601345e+00
   3_xyz:  0.1319 0.1758   5.277211e+00   5.497734e+00
   3_adp:  0.1244 0.1703   5.235789e+00   5.468009e+00
   3_occ:  0.1244 0.1702   5.235598e+00   5.467873e+00
   4_bss:  0.1244 0.1702   5.235152e+00   5.467652e+00
   4_xyz:  0.1152 0.1641   5.180171e+00   5.430073e+00
   4_adp:  0.1153 0.1615   5.172144e+00   5.414049e+00
   4_occ:  0.1152 0.1614   5.171880e+00   5.414032e+00
   5_bss:  0.1155 0.1613   5.172158e+00   5.412452e+00
   5_xyz:  0.1154 0.1604   5.171181e+00   5.409458e+00
   5_adp:  0.1145 0.1610   5.170991e+00   5.414054e+00
   5_occ:  0.1145 0.1610   5.170825e+00   5.413971e+00
   5_bss:  0.1145 0.1610   5.170825e+00   5.413971e+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:  0.337  28.298   8.666   8.192   7.780   0.000   0.000   0.000
   1_xyz:  0.337  28.298   8.666   8.192   7.780   0.000   0.000   0.000
   1_adp:  0.337  28.298   8.666   8.192   7.780   0.000   0.000   0.000
   1_occ:  0.337  28.298   8.666   8.192   7.780   0.000   0.000   0.000
   2_bss:  0.322  46.808   5.478   4.977   5.196   0.000   0.000   0.000
   2_xyz:  0.322  46.808   5.478   4.977   5.196   0.000   0.000   0.000
   2_adp:  0.322  46.808   5.478   4.977   5.196   0.000   0.000   0.000
   2_occ:  0.322  46.808   5.478   4.977   5.196   0.000   0.000   0.000
   3_bss:  0.331  50.960   3.869   3.829   4.491   0.000   0.000   0.000
   3_xyz:  0.331  50.960   3.869   3.829   4.491   0.000   0.000   0.000
   3_adp:  0.331  50.960   3.869   3.829   4.491   0.000   0.000   0.000
   3_occ:  0.331  50.960   3.869   3.829   4.491   0.000   0.000   0.000
   4_bss:  0.321  50.960   3.644   3.675   4.487   0.000   0.000   0.000
   4_xyz:  0.321  50.960   3.644   3.675   4.487   0.000   0.000   0.000
   4_adp:  0.321  50.960   3.644   3.675   4.487   0.000   0.000   0.000
   4_occ:  0.321  50.960   3.644   3.675   4.487   0.000   0.000   0.000
   5_bss:  0.324  50.960   3.644   3.675   4.487   0.000   0.000   0.000
   5_xyz:  0.324  50.960   3.644   3.675   4.487   0.000   0.000   0.000
   5_adp:  0.324  50.960   3.644   3.675   4.487   0.000   0.000   0.000
   5_occ:  0.324  50.960   3.644   3.675   4.487   0.000   0.000   0.000
   5_bss:  0.324  54.896  -0.291  -0.260   0.551   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.189 0.5696  0.6289    50239.143
   1_bss:  45.897 0.5713  0.8079    48017.178
   1_xyz:  37.139 0.6754  0.9288    32257.941
   1_adp:  29.374 0.7654  1.0133    21986.670
   1_occ:  29.409 0.7649  1.0125    22019.417
   2_bss:  29.223 0.7669  0.9113    21779.067
   2_xyz:  20.114 0.8607  0.9908    11185.666
   2_adp:  18.642 0.8750  1.0031     9993.821
   2_occ:  18.643 0.8750  1.0029     9995.588
   3_bss:  18.602 0.8754  0.9617     9969.062
   3_xyz:  16.140 0.8975  0.9712     7952.144
   3_adp:  15.501 0.9031  0.9719     7450.582
   3_occ:  15.500 0.9031  0.9719     7447.187
   4_bss:  15.495 0.9031  0.9674     7441.153
   4_xyz:  14.751 0.9091  0.9712     6885.698
   4_adp:  14.360 0.9124  0.9733     6684.026
   4_occ:  14.367 0.9124  0.9732     6683.874
   5_bss:  14.369 0.9123  0.9724     6652.206
   5_xyz:  14.255 0.9133  0.9717     6595.002
   5_adp:  14.373 0.9125  0.9690     6660.191
   5_occ:  14.371 0.9125  0.9689     6658.655
   5_bss:  14.371 0.9125  0.9689     6658.655
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4205e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4205e+01
   1_xyz:   1.529  0.012  0.101 17.925  0.006  4.125   1.1989e-01
   1_adp:   1.529  0.012  0.101 17.925  0.006  4.125   1.1989e-01
   1_occ:   1.529  0.012  0.101 17.925  0.006  4.125   1.1989e-01
   2_bss:   1.529  0.012  0.101 17.925  0.006  4.125   1.1989e-01
   2_xyz:   1.031  0.008  0.074 16.393  0.004  4.130   6.7925e-02
   2_adp:   1.031  0.008  0.074 16.393  0.004  4.130   6.7925e-02
   2_occ:   1.031  0.008  0.074 16.393  0.004  4.130   6.7925e-02
   3_bss:   1.031  0.008  0.074 16.393  0.004  4.130   6.7925e-02
   3_xyz:   0.992  0.007  0.078 16.010  0.003  4.115   6.1763e-02
   3_adp:   0.992  0.007  0.078 16.010  0.003  4.115   6.1763e-02
   3_occ:   0.992  0.007  0.078 16.010  0.003  4.115   6.1763e-02
   4_bss:   0.992  0.007  0.078 16.010  0.003  4.115   6.1763e-02
   4_xyz:   1.076  0.009  0.087 15.899  0.004  4.119   7.2381e-02
   4_adp:   1.076  0.009  0.087 15.899  0.004  4.119   7.2381e-02
   4_occ:   1.076  0.009  0.087 15.899  0.004  4.119   7.2381e-02
   5_bss:   1.076  0.009  0.087 15.899  0.004  4.119   7.2381e-02
   5_xyz:   0.997  0.008  0.080 15.575  0.004  4.121   6.3181e-02
   5_adp:   0.997  0.008  0.080 15.575  0.004  4.121   6.3181e-02
   5_occ:   0.997  0.008  0.080 15.575  0.004  4.121   6.3181e-02
   5_bss:   0.997  0.008  0.080 15.575  0.004  4.121   6.3181e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0286e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0286e+00
   1_xyz:  13.050  0.140  0.416 85.969  0.040  2.264   9.0678e-02
   1_adp:  13.050  0.140  0.416 85.969  0.040  2.264   9.0678e-02
   1_occ:  13.050  0.140  0.416 85.969  0.040  2.264   9.0678e-02
   2_bss:  13.050  0.140  0.416 85.969  0.040  2.264   9.0678e-02
   2_xyz:   7.120  0.085  0.265 84.131  0.037  2.347   6.3874e-02
   2_adp:   7.120  0.085  0.265 84.131  0.037  2.347   6.3874e-02
   2_occ:   7.120  0.085  0.265 84.131  0.037  2.347   6.3874e-02
   3_bss:   7.120  0.085  0.265 84.131  0.037  2.347   6.3874e-02
   3_xyz:   7.542  0.050  0.432 82.509  0.038  2.410   3.5652e-02
   3_adp:   7.542  0.050  0.432 82.509  0.038  2.410   3.5652e-02
   3_occ:   7.542  0.050  0.432 82.509  0.038  2.410   3.5652e-02
   4_bss:   7.542  0.050  0.432 82.509  0.038  2.410   3.5652e-02
   4_xyz:   7.867  0.044  0.562 83.172  0.040  2.286   5.4110e-02
   4_adp:   7.867  0.044  0.562 83.172  0.040  2.286   5.4110e-02
   4_occ:   7.867  0.044  0.562 83.172  0.040  2.286   5.4110e-02
   5_bss:   7.867  0.044  0.562 83.172  0.040  2.286   5.4110e-02
   5_xyz:   7.752  0.045  0.489 82.616  0.039  2.400   4.5467e-02
   5_adp:   7.752  0.045  0.489 82.616  0.039  2.400   4.5467e-02
   5_occ:   7.752  0.045  0.489 82.616  0.039  2.400   4.5467e-02
   5_bss:   7.752  0.045  0.489 82.616  0.039  2.400   4.5467e-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:  55.41   0.00   9.87  49.97   0.00   6.90  55.41   0.00  26.03
   1_occ:  55.41   0.00   9.87  49.97   0.00   6.90  55.41   0.00  26.03
   2_bss:  55.41   0.00   9.87  49.97   0.00   6.90  55.41   0.00  26.03
   2_xyz:  55.41   0.00   9.87  49.97   0.00   6.90  55.41   0.00  26.03
   2_adp:  80.74   0.00  10.38  80.74   0.00   6.93  55.49   0.60  29.13
   2_occ:  80.74   0.00  10.38  80.74   0.00   6.93  55.49   0.60  29.13
   3_bss:  80.74   0.00  10.38  80.74   0.00   6.93  55.49   0.60  29.13
   3_xyz:  80.74   0.00  10.38  80.74   0.00   6.93  55.49   0.60  29.13
   3_adp:  79.63   0.00  11.67  77.85   0.00   7.31  79.63   0.00  35.43
   3_occ:  79.63   0.00  11.67  77.85   0.00   7.31  79.63   0.00  35.43
   4_bss:  79.63   0.00  11.67  77.85   0.00   7.31  79.63   0.00  35.43
   4_xyz:  79.63   0.00  11.67  77.85   0.00   7.31  79.63   0.00  35.43
   4_adp:  76.93   0.00  11.37  76.93   0.00   7.18  76.13   0.64  34.19
   4_occ:  76.93   0.00  11.37  76.93   0.00   7.18  76.13   0.64  34.19
   5_bss:  76.93   0.00  11.37  76.93   0.00   7.18  76.13   0.64  34.19
   5_xyz:  76.93   0.00  11.37  76.93   0.00   7.18  76.13   0.64  34.19
   5_adp:  79.73   0.00  11.35  79.73   0.00   7.18  75.97   0.63  34.11
   5_occ:  79.73   0.00  11.35  79.73   0.00   7.18  75.97   0.63  34.11
   5_bss:  83.66   3.94  15.29  83.66   3.94  11.11  79.91   4.56  38.04
------------------------------------------------------------------------
 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:    1.187    0.017    0.404
   1_adp:    1.187    0.017    0.404
   1_occ:    1.187    0.017    0.404
   2_bss:    1.187    0.017    0.404
   2_xyz:    1.453    0.030    0.509
   2_adp:    1.453    0.030    0.509
   2_occ:    1.453    0.030    0.509
   3_bss:    1.453    0.030    0.509
   3_xyz:    1.495    0.038    0.538
   3_adp:    1.495    0.038    0.538
   3_occ:    1.495    0.038    0.538
   4_bss:    1.495    0.038    0.538
   4_xyz:    1.516    0.035    0.556
   4_adp:    1.516    0.035    0.556
   4_occ:    1.516    0.035    0.556
   5_bss:    1.516    0.035    0.556
   5_xyz:    1.557    0.026    0.566
   5_adp:    1.557    0.026    0.566
   5_occ:    1.557    0.026    0.566
   5_bss:    1.557    0.026    0.566
------------------------------------------------------------------------

CPU time actual refinement: 327.28


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1039/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_1039/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1039/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1039/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1039/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.12 
  Macro-tasks:
    bulk solvent and scale       = 36.45  
    individual site refinement   = 135.76 
    weights calculation          = 33.10  
    collect and process          = 6.75   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 212.21 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 100.50 
    alpha_beta                      = 8.19   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 111.33 
    fmodel                         = 7.19   
    r_factors                      = 0.19   
    phase_errors                   = 10.98  
    foms                           = 0.33   
    TOTAL for micro-tasks          = 241.62 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.614 micro seconds
Total CPU time: 5.68 minutes
from_scatterers_fft:    643 calls, 100.09 s
gradients_fft:          588 calls,  97.97 s

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

# Date 2008-01-16 Time 03:02:47 PST -0800 (1200481367.07 s)
Start R-work = 0.4301, R-free = 0.4160 (no bulk solvent and anisotropic scale)
Final R-work = 0.1312, R-free = 0.1765 (no bulk solvent and anisotropic scale)

Start R-work = 0.4227, R-free = 0.4032
Final R-work = 0.1145, R-free = 0.1610