# Date 2008-01-16 Time 01:27:15 PST -0800 (1200475635.35 s)
#phil __OFF__

Command line arguments: "../418.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5968
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 418

-------------------------------------------------------------------------------
  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: (69.5475, 46.93, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.80, per 1000 atoms: 0.99


================================== 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: (69.5475, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.782 1.95128
Completeness in resolution range: 0.949355
Completeness with d_max=infinity: 0.94642

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7820
                             d_min =   1.9513

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: (69.5475, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.782 1.95128
Completeness in resolution range: 0.949355
Completeness with d_max=infinity: 0.94642

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7824 -  4.1753 [2172/2200]  1956   216   9.9%
  bin  2:  4.1753 -  3.3265 [2067/2090]  1860   207  10.0%
  bin  3:  3.3265 -  2.9096 [2053/2075]  1844   209  10.2%
  bin  4:  2.9096 -  2.6453 [2044/2063]  1847   197   9.6%
  bin  5:  2.6453 -  2.4566 [2027/2056]  1818   209  10.3%
  bin  6:  2.4566 -  2.3123 [2000/2042]  1803   197   9.8%
  bin  7:  2.3123 -  2.1969 [1983/2019]  1783   200  10.1%
  bin  8:  2.1969 -  2.1016 [2006/2043]  1808   198   9.9%
  bin  9:  2.1016 -  2.0209 [2000/2032]  1801   199   9.9%
  bin 10:  2.0209 -  1.9513 [1237/2014]  1110   127  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_418/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: 0.12 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:
        1.41 -     2.11: 23
        2.11 -     2.81: 814
        2.81 -     3.50: 4552
        3.50 -     4.20: 9481
        4.20 -     4.90: 13970
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.412 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.542 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.641 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.701 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.773 3.120 -x,y-1/2,-z+1/2
  ... (remaining 28835 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_418/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_418/model_refine_001.geo

CPU time processing inputs: 8.21


============================ 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 = 69.5475 46.93 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4700   r_free= 0.4739   ksol= 0.00   Bsol= 0.00   scale= 0.810    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.271818                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6569 0.99   1404  154 0.3897 0.3784      6.5819      6.5763|
|  2:  4.6569 -  3.7157 0.99   1362  150 0.3904 0.3773      6.7578      6.7703|
|  3:  3.7157 -  3.2517 0.99   1322  154 0.4237 0.4326      6.6573      6.7429|
|  4:  3.2517 -  2.9570 0.99   1324  142 0.4406 0.4929      6.5026      6.4966|
|  5:  2.9570 -  2.7465 0.99   1304  147 0.4880 0.4928      6.3724      6.3722|
|  6:  2.7465 -  2.5854 0.98   1297  146 0.4916 0.5445      6.2585      6.2137|
|  7:  2.5854 -  2.4566 0.99   1312  145 0.5085 0.4688      6.2457      6.1796|
|  8:  2.4566 -  2.3501 0.99   1285  143 0.5152 0.5304      6.1632      6.1796|
|  9:  2.3501 -  2.2599 0.98   1295  141 0.5176 0.4895      6.1241      6.0887|
| 10:  2.2599 -  2.1822 0.98   1275  141 0.5366 0.5182      6.1057       6.111|
| 11:  2.1822 -  2.1142 0.98   1284  145 0.5332 0.5379      6.0451      6.0486|
| 12:  2.1142 -  2.0539 0.99   1281  139 0.5081 0.5413      5.9631      5.9933|
| 13:  2.0539 -  2.0000 0.97   1263  142 0.5333 0.5154      5.8785      5.8476|
| 14:  2.0000 -  1.9513 0.48    622   70 0.5409 0.5299      5.8438      5.7161|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6569  1404   154  0.68  36.04   0.81     0.71      75443.60|
|  2:  4.6569 -  3.7157  1362   150  0.69  36.39   0.89     0.77     110110.19|
|  3:  3.7157 -  3.2517  1322   154  0.59  44.78   0.86     0.72     118716.75|
|  4:  3.2517 -  2.9570  1324   142  0.51  51.16   0.82     0.62     104444.69|
|  5:  2.9570 -  2.7465  1304   147  0.42  57.85   0.76     0.53      84588.98|
|  6:  2.7465 -  2.5854  1297   146  0.41  59.28   0.75     0.48      70507.47|
|  7:  2.5854 -  2.4566  1312   145  0.40  59.75   0.74     0.46      62757.21|
|  8:  2.4566 -  2.3501  1285   143  0.39  60.59   0.74     0.47      56521.54|
|  9:  2.3501 -  2.2599  1295   141  0.39  60.42   0.75     0.47      51226.13|
| 10:  2.2599 -  2.1822  1275   141  0.37  62.11   0.76     0.46      47676.03|
| 11:  2.1822 -  2.1142  1284   145  0.34  64.49   0.78     0.43      45959.03|
| 12:  2.1142 -  2.0539  1281   139  0.31  66.56   0.77     0.40      44904.55|
| 13:  2.0539 -  2.0000  1263   142  0.29  68.11   0.75     0.39      38244.45|
| 14:  2.0000 -  1.9513   622    70  0.35  63.79   0.72     0.40      28707.59|
|alpha:            min =        0.39 max =            0.77 mean =         0.53|
|beta:             min =    28707.59 max =       118716.75 mean =     69067.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.98 mean =        55.98|
|phase err.(test): min =        0.00 max =           89.99 mean =        56.53|
|-----------------------------------------------------------------------------|

============================== 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 = 12.357022             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.146   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.134942              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.611   (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 |  0.864 -  1.267:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.267 -  1.671:        8 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.671 -  2.075:       54 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.075 -  2.478:      404 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.478 -  2.882:     1184 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.882 -  3.285:     2397 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.285 -  3.689:     3958 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.689 -  4.093:     5289 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.093 -  4.496:     7084 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.496 -  4.900:     8421 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.045 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  0.864 |       2.271 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.482)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.482)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4773   r_free= 0.4791   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.274665                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4617   r_free= 0.4619   ksol= 0.36   Bsol= 8.02   scale= 1.007    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.03,7.65,10.02,0.00,0.00,0.00); trace/3= 8.23                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.267725                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.531483             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.831   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.077074              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.540   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4617      final r-factor (work) = 0.3853          |
| start r-factor (free) = 0.4619      final r-factor (free) = 0.4060          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.0735 = 10.53 * 0.50 * 6.2724 + 1.00 * 53.0448                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.6944 = 10.53 * 0.50 * 6.1834 + 1.00 * 0.1343                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3853      final r-factor (work) = 0.3356          |
| start r-factor (free) = 0.4060      final r-factor (free) = 0.3839          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6743 = 1.08 * 1.00 * 6.1834 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5776 = 1.08 * 1.00 * 6.0923 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.482)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.24   12.82    None  None   None       |
|    all(noH): 2823   0      0.00    79.24   12.82    None  None   None       |
|    Sol.    : 438    0      0.00    68.40   26.37    None  None   None       |
|    Mac.    : 2385   0      0.00    79.24   10.33    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 -   7.924: 1242   |   5:    39.622 -  47.547:   66        |
|      1:     7.924 -  15.849:  761   |   6:    47.547 -  55.471:   25        |
|      2:    15.849 -  23.773:  365   |   7:    55.471 -  63.395:   14        |
|      3:    23.773 -  31.698:  217   |   8:    63.395 -  71.320:    6        |
|      4:    31.698 -  39.622:  123   |   9:    71.320 -  79.244:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3356 r_free = 0.3839             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3354 r_free = 0.3837             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3354   r_free= 0.3837   ksol= 0.36   Bsol= 8.02   scale= 1.105    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.03,7.65,10.02,0.00,0.00,0.00); trace/3= 8.23                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.073908                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3311   r_free= 0.3814   ksol= 0.32   Bsol= 25.75   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,3.90,6.79,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.073096                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.085651              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.085   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.516555              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.910  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3311      final r-factor (work) = 0.2508          |
| start r-factor (free) = 0.3814      final r-factor (free) = 0.3077          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7055 = 7.09 * 0.50 * 6.0887 + 1.00 * 0.1343                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.1875 = 7.09 * 0.50 * 5.9579 + 1.00 * 0.0797                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2508      final r-factor (work) = 0.2299          |
| start r-factor (free) = 0.3077      final r-factor (free) = 0.2891          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1003 = 0.52 * 1.00 * 5.9579 + 1.00 * 0.0227                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0061 = 0.52 * 1.00 * 5.7979 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.482)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.92   13.11    None  None   None       |
|    all(noH): 2823   0      0.00    79.92   13.11    None  None   None       |
|    Sol.    : 438    0      0.00    67.90   30.90    None  None   None       |
|    Mac.    : 2385   0      0.00    79.92   9.84     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 -   7.992: 1311   |   5:    39.960 -  47.951:   94        |
|      1:     7.992 -  15.984:  737   |   6:    47.951 -  55.943:   28        |
|      2:    15.984 -  23.976:  293   |   7:    55.943 -  63.935:   15        |
|      3:    23.976 -  31.968:  195   |   8:    63.935 -  71.927:    3        |
|      4:    31.968 -  39.960:  143   |   9:    71.927 -  79.919:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2299 r_free = 0.2891             target_work(ml) = 5.770         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2297 r_free = 0.2896             target_work(ml) = 5.770         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2297   r_free= 0.2896   ksol= 0.32   Bsol= 25.75   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,3.90,6.79,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.770078                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2280   r_free= 0.2877   ksol= 0.31   Bsol= 30.65   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.92,2.55,3.95,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.767609                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.796523              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.961  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.554956              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.051  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2280      final r-factor (work) = 0.1766          |
| start r-factor (free) = 0.2877      final r-factor (free) = 0.2343          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1923 = 2.80 * 0.50 * 5.8019 + 1.00 * 0.0797                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9810 = 2.80 * 0.50 * 5.6639 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1766      final r-factor (work) = 0.1620          |
| start r-factor (free) = 0.2343      final r-factor (free) = 0.2172          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1545 = 0.55 * 1.00 * 5.6639 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0711 = 0.55 * 1.00 * 5.5130 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.482)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.31   13.49    None  None   None       |
|    all(noH): 2823   0      0.00    84.31   13.49    None  None   None       |
|    Sol.    : 438    0      2.27    74.85   36.35    None  None   None       |
|    Mac.    : 2385   0      0.00    84.31   9.29     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 -   8.431: 1479   |   5:    42.156 -  50.587:   98        |
|      1:     8.431 -  16.862:  687   |   6:    50.587 -  59.018:   69        |
|      2:    16.862 -  25.294:  213   |   7:    59.018 -  67.450:   22        |
|      3:    25.294 -  33.725:  114   |   8:    67.450 -  75.881:    6        |
|      4:    33.725 -  42.156:  131   |   9:    75.881 -  84.312:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1620 r_free = 0.2172             target_work(ml) = 5.471         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1618 r_free = 0.2168             target_work(ml) = 5.471         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1618   r_free= 0.2168   ksol= 0.31   Bsol= 30.65   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.92,2.55,3.95,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.470508                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1614   r_free= 0.2159   ksol= 0.32   Bsol= 31.17   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,1.98,2.67,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.468089                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.420430              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.510   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.230914              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.628  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1614      final r-factor (work) = 0.1309          |
| start r-factor (free) = 0.2159      final r-factor (free) = 0.1780          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4945 = 3.42 * 0.50 * 5.5158 + 1.00 * 0.0614                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2700 = 3.42 * 0.50 * 5.3830 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1309      final r-factor (work) = 0.1261          |
| start r-factor (free) = 0.1780      final r-factor (free) = 0.1698          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2545 = 0.23 * 1.00 * 5.3830 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2245 = 0.23 * 1.00 * 5.2592 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.482)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.50   13.08    None  None   None       |
|    all(noH): 2823   0      0.00    86.50   13.08    None  None   None       |
|    Sol.    : 438    0      2.78    76.68   35.54    None  None   None       |
|    Mac.    : 2385   0      0.00    86.50   8.96     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.650: 1590   |   5:    43.248 -  51.897:   85        |
|      1:     8.650 -  17.299:  654   |   6:    51.897 -  60.547:   49        |
|      2:    17.299 -  25.949:  159   |   7:    60.547 -  69.196:   20        |
|      3:    25.949 -  34.598:  135   |   8:    69.196 -  77.846:    6        |
|      4:    34.598 -  43.248:  122   |   9:    77.846 -  86.495:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1261 r_free = 0.1698             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1259 r_free = 0.1695             target_work(ml) = 5.232         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1695   ksol= 0.32   Bsol= 31.17   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,1.98,2.67,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.231539                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1262   r_free= 0.1692   ksol= 0.32   Bsol= 33.46   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.24,1.81,2.20,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.231778                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.819400              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.372  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.493527              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.189  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1262      final r-factor (work) = 0.1149          |
| start r-factor (free) = 0.1692      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4789 = 2.82 * 0.50 * 5.2600 + 1.00 * 0.0639                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3875 = 2.82 * 0.50 * 5.1930 + 1.00 * 0.0669                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1149      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1604      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5740 = 0.49 * 1.00 * 5.1930 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5531 = 0.49 * 1.00 * 5.1522 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.482)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.57   13.19    None  None   None       |
|    all(noH): 2823   0      0.00    90.57   13.19    None  None   None       |
|    Sol.    : 438    0      2.41    81.20   36.33    None  None   None       |
|    Mac.    : 2385   0      0.00    90.57   8.94     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.057: 1649   |   5:    45.284 -  54.341:   89        |
|      1:     9.057 -  18.114:  628   |   6:    54.341 -  63.397:   50        |
|      2:    18.114 -  27.170:  150   |   7:    63.397 -  72.454:   18        |
|      3:    27.170 -  36.227:  124   |   8:    72.454 -  81.511:    6        |
|      4:    36.227 -  45.284:  106   |   9:    81.511 -  90.568:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1601             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1601             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1601   ksol= 0.32   Bsol= 33.46   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.24,1.81,2.20,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151882                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6569 0.99   1404  154 0.0993 0.1267      5.3802      5.5242|
|  2:  4.6569 -  3.7157 0.99   1362  150 0.0864 0.1163      5.4311      5.6581|
|  3:  3.7157 -  3.2517 0.99   1322  154 0.1068 0.1535      5.4755      5.8042|
|  4:  3.2517 -  2.9570 0.99   1324  142 0.1232 0.1626      5.4567      5.6324|
|  5:  2.9570 -  2.7465 0.99   1304  147 0.1282 0.1616       5.314      5.4653|
|  6:  2.7465 -  2.5854 0.98   1297  146 0.1239 0.2036      5.2158      5.5034|
|  7:  2.5854 -  2.4566 0.99   1312  145 0.1239 0.1642      5.1688      5.4108|
|  8:  2.4566 -  2.3501 0.99   1285  143 0.1151 0.1673      5.0721      5.2879|
|  9:  2.3501 -  2.2599 0.98   1295  141 0.1165 0.1872      5.0306      5.3012|
| 10:  2.2599 -  2.1822 0.98   1275  141 0.1146 0.1809      4.9813      5.2398|
| 11:  2.1822 -  2.1142 0.98   1284  145 0.1126 0.1784      4.9374      5.2937|
| 12:  2.1142 -  2.0539 0.99   1281  139 0.1089 0.1693      4.8617        5.11|
| 13:  2.0539 -  2.0000 0.97   1263  142 0.1150 0.1858       4.795      5.0721|
| 14:  2.0000 -  1.9513 0.48    622   70 0.1089 0.1657      4.7111      4.8845|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6569  1404   154  0.94   8.56   0.99     0.97       6772.18|
|  2:  4.6569 -  3.7157  1362   150  0.95   7.75   1.03     1.01       8695.91|
|  3:  3.7157 -  3.2517  1322   154  0.93  11.52   1.04     1.04      10541.66|
|  4:  3.2517 -  2.9570  1324   142  0.92  13.89   1.02     1.00      10353.18|
|  5:  2.9570 -  2.7465  1304   147  0.90  15.97   1.00     0.96       8151.68|
|  6:  2.7465 -  2.5854  1297   146  0.90  16.22   0.99     0.96       7260.66|
|  7:  2.5854 -  2.4566  1312   145  0.91  15.61   1.00     0.96       6234.39|
|  8:  2.4566 -  2.3501  1285   143  0.90  15.93   1.00     0.97       5628.42|
|  9:  2.3501 -  2.2599  1295   141  0.91  15.54   1.02     1.00       5087.80|
| 10:  2.2599 -  2.1822  1275   141  0.90  16.22   1.01     0.98       4694.55|
| 11:  2.1822 -  2.1142  1284   145  0.90  16.41   1.01     0.97       4391.48|
| 12:  2.1142 -  2.0539  1281   139  0.91  15.11   1.01     0.99       3896.60|
| 13:  2.0539 -  2.0000  1263   142  0.90  16.72   1.02     1.02       3445.22|
| 14:  2.0000 -  1.9513   622    70  0.90  15.84   1.01     0.97       2844.88|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2844.88 max =        10541.66 mean =      6453.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.72 mean =        13.85|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1601   ksol= 0.32   Bsol= 36.28   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,0.06,0.45,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151870                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1601   ksol= 0.32   Bsol= 36.28   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,0.06,0.45,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151870                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6569 0.99   1404  154 0.0993 0.1267      5.3812      5.5254|
|  2:  4.6569 -  3.7157 0.99   1362  150 0.0865 0.1164      5.4318      5.6588|
|  3:  3.7157 -  3.2517 0.99   1322  154 0.1069 0.1536       5.476      5.8045|
|  4:  3.2517 -  2.9570 0.99   1324  142 0.1232 0.1625      5.4568      5.6323|
|  5:  2.9570 -  2.7465 0.99   1304  147 0.1282 0.1616      5.3138      5.4649|
|  6:  2.7465 -  2.5854 0.98   1297  146 0.1238 0.2036      5.2155      5.5032|
|  7:  2.5854 -  2.4566 0.99   1312  145 0.1239 0.1642      5.1684      5.4107|
|  8:  2.4566 -  2.3501 0.99   1285  143 0.1151 0.1671      5.0718      5.2873|
|  9:  2.3501 -  2.2599 0.98   1295  141 0.1165 0.1872      5.0303      5.3012|
| 10:  2.2599 -  2.1822 0.98   1275  141 0.1146 0.1809      4.9811      5.2395|
| 11:  2.1822 -  2.1142 0.98   1284  145 0.1125 0.1784      4.9373      5.2938|
| 12:  2.1142 -  2.0539 0.99   1281  139 0.1088 0.1693      4.8616      5.1099|
| 13:  2.0539 -  2.0000 0.97   1263  142 0.1150 0.1857      4.7948      5.0718|
| 14:  2.0000 -  1.9513 0.48    622   70 0.1089 0.1657      4.7107       4.884|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6569  1404   154  0.94   8.57   0.99     0.97       6792.64|
|  2:  4.6569 -  3.7157  1362   150  0.95   7.76   1.03     1.01       8710.97|
|  3:  3.7157 -  3.2517  1322   154  0.93  11.52   1.04     1.04      10550.24|
|  4:  3.2517 -  2.9570  1324   142  0.92  13.89   1.02     1.00      10354.24|
|  5:  2.9570 -  2.7465  1304   147  0.90  15.97   1.00     0.96       8148.50|
|  6:  2.7465 -  2.5854  1297   146  0.90  16.22   0.99     0.96       7257.12|
|  7:  2.5854 -  2.4566  1312   145  0.91  15.60   1.00     0.96       6230.17|
|  8:  2.4566 -  2.3501  1285   143  0.90  15.92   1.00     0.97       5623.69|
|  9:  2.3501 -  2.2599  1295   141  0.91  15.54   1.02     1.00       5084.63|
| 10:  2.2599 -  2.1822  1275   141  0.90  16.22   1.01     0.98       4692.93|
| 11:  2.1822 -  2.1142  1284   145  0.90  16.41   1.01     0.97       4390.94|
| 12:  2.1142 -  2.0539  1281   139  0.91  15.11   1.01     0.99       3896.11|
| 13:  2.0539 -  2.0000  1263   142  0.90  16.71   1.02     1.02       3443.10|
| 14:  2.0000 -  1.9513   622    70  0.90  15.83   1.01     0.97       2841.39|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2841.39 max =        10550.24 mean =      6455.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.90 mean =        13.85|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.482)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.75    92.32   14.94    None  None   None       |
|    all(noH): 2823   0      1.75    92.32   14.94    None  None   None       |
|    Sol.    : 438    0      4.16    82.94   38.08    None  None   None       |
|    Mac.    : 2385   0      1.75    92.32   10.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.748 -  10.804: 1649   |   5:    47.032 -  56.088:   89        |
|      1:    10.804 -  19.861:  628   |   6:    56.088 -  65.145:   50        |
|      2:    19.861 -  28.918:  150   |   7:    65.145 -  74.202:   18        |
|      3:    28.918 -  37.975:  124   |   8:    74.202 -  83.259:    6        |
|      4:    37.975 -  47.032:  106   |   9:    83.259 -  92.315:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.765 - 5.775
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 320
   mapped sites are within: 0.765 - 5.775

peak=   10.731 closest distance to " CB  VAL A 230 " =    1.439
peak=    8.995 closest distance to " CG2 VAL A 296 " =    1.311
peak=    6.075 closest distance to " O   HOH Z 278 " =    1.557
peak=    6.019 closest distance to " CG  LEU A   5 " =    1.248
peak=    5.594 closest distance to " NE2 GLN A  11 " =    1.149
peak=    5.528 closest distance to " O   HOH Z 199 " =    1.084
peak=    5.473 closest distance to " NH2 ARG A  56 " =    2.110
peak=    5.454 closest distance to " O   HOH Z 142 " =    1.821
peak=    5.411 closest distance to " O   HOH Z 279 " =    1.158
peak=    5.352 closest distance to " O   HOH Z 124 " =    1.510
peak=    5.229 closest distance to " O   HOH Z 193 " =    1.687
peak=    5.184 closest distance to " O   HOH Z 132 " =    1.504
peak=    5.082 closest distance to " CD2 LEU A   5 " =    1.178
peak=    5.038 closest distance to " O   HOH Z 126 " =    1.992
peak=    4.930 closest distance to " O   HOH Z 202 " =    1.285
peak=    4.894 closest distance to " CB  SER A  63 " =    1.238
peak=    4.794 closest distance to " CD1AILE A 234 " =    0.989
peak=    4.785 closest distance to " CG  PRO A  54 " =    1.206
peak=    4.721 closest distance to " CB  ARG A 275 " =    0.915
peak=    4.671 closest distance to " O   HOH Z 411 " =    3.816
peak=    4.668 closest distance to " O   HOH Z 427 " =    2.774
peak=    4.662 closest distance to " CG  LEU A 228 " =    1.201
peak=    4.657 closest distance to " O   HOH Z 232 " =    2.234
peak=    4.599 closest distance to " CB  GLN A 183 " =    1.341
peak=    4.595 closest distance to " CD2 LEU A 228 " =    1.190
peak=    4.591 closest distance to " O   HOH Z  59 " =    1.943
peak=    4.570 closest distance to " CB  GLN A 223 " =    1.467
peak=    4.515 closest distance to " CB  VAL A 230 " =    1.150
peak=    4.486 closest distance to " O   HOH Z  78 " =    1.778
peak=    4.387 closest distance to " O   HOH Z 108 " =    1.387
peak=    4.384 closest distance to " O   HOH Z 234 " =    3.747
peak=    4.377 closest distance to " O   HOH Z 263 " =    1.424
peak=    4.377 closest distance to " O   HOH Z 326 " =    1.459
peak=    4.376 closest distance to " O   HOH Z   3 " =    1.762
peak=    4.370 closest distance to " O   HOH Z 272 " =    1.884
peak=    4.364 closest distance to " O   HOH Z  93 " =    2.436
peak=    4.364 closest distance to " O   HOH Z 368 " =    2.090
peak=    4.357 closest distance to " CB  SER A   3 " =    1.330
peak=    4.332 closest distance to " CG  PRO A 213 " =    1.210
peak=    4.330 closest distance to " O   HOH Z 260 " =    1.279
peak=    4.325 closest distance to " O   SER A  87 " =    2.275
peak=    4.325 closest distance to " O   HOH Z 203 " =    1.574
peak=    4.321 closest distance to " O   PRO A 198 " =    1.504
peak=    4.316 closest distance to " O   HOH Z 346 " =    1.521
peak=    4.288 closest distance to " CB  GLU A 152 " =    1.142
peak=    4.266 closest distance to " CB  PRO A  54 " =    0.915
peak=    4.266 closest distance to " CB  ASN A 148 " =    1.401
peak=    4.247 closest distance to " CB  VAL A 296 " =    0.993
peak=    4.236 closest distance to " CA  ALA A  21 " =    1.111
peak=    4.226 closest distance to " CB  TYR A 169 " =    1.060
peak=    4.210 closest distance to " O   HOH Z 316 " =    2.784
peak=    4.167 closest distance to " O   HOH Z 128 " =    2.029
peak=    4.163 closest distance to " O   HOH Z  97 " =    1.888
peak=    4.159 closest distance to " OE1 GLU A   2 " =    2.086
peak=    4.134 closest distance to " CG1BVAL A  72 " =    1.447
peak=    4.130 closest distance to " O   HOH Z 118 " =    1.625
peak=    4.117 closest distance to " O   HOH Z 392 " =    2.625
peak=    4.116 closest distance to " O   HOH Z 403 " =    1.746
peak=    4.100 closest distance to " O   HOH Z 236 " =    1.491
peak=    4.100 closest distance to " O   HOH Z  85 " =    1.346
peak=    4.095 closest distance to " CB  TRP A 179 " =    1.240
peak=    4.080 closest distance to " O   HOH Z 143 " =    1.107
peak=    4.061 closest distance to " O   HOH Z  48 " =    1.572
peak=    4.046 closest distance to " O   HOH Z 134 " =    1.532
peak=    4.046 closest distance to " O   HOH Z 423 " =    1.917
peak=    4.041 closest distance to " O   HOH Z 303 " =    2.080
peak=    4.040 closest distance to " O   HOH Z 213 " =    1.920
peak=    4.036 closest distance to " O   HOH Z 214 " =    2.236
peak=    4.010 closest distance to " O   HOH Z 298 " =    1.848
peak=    4.005 closest distance to " CA  VAL A  41 " =    0.863
peak=    3.994 closest distance to " OD1 ASN A  69 " =    2.628
peak=    3.993 closest distance to " CA  TYR A  30 " =    1.032
peak=    3.949 closest distance to " O   HOH Z 192 " =    1.583
peak=    3.947 closest distance to " O   HOH Z 371 " =    3.271
peak=    3.942 closest distance to " CB  GLN A  88 " =    1.263
peak=    3.933 closest distance to " O   HOH Z 344 " =    2.581
peak=    3.925 closest distance to " O   HOH Z 276 " =    1.322
peak=    3.918 closest distance to " NZ  LYS A 117 " =    3.156
peak=    3.910 closest distance to " O   HOH Z 334 " =    1.503
peak=    3.907 closest distance to " CB  VAL A 202 " =    1.709
peak=    3.905 closest distance to " O   HOH Z 189 " =    2.468
peak=    3.895 closest distance to " CB  GLU A 277 " =    3.473
peak=    3.892 closest distance to " CB  GLU A 128 " =    1.117
peak=    3.889 closest distance to " O   HOH Z 334 " =    2.897
peak=    3.877 closest distance to " O   HOH Z  59 " =    2.194
peak=    3.877 closest distance to " NE2 GLN A  58 " =    4.106
peak=    3.847 closest distance to " O   HOH Z 209 " =    2.386
peak=    3.836 closest distance to " O   HOH Z 209 " =    2.251
peak=    3.832 closest distance to " O   HOH Z  15 " =    2.274
peak=    3.825 closest distance to " O   HOH Z  61 " =    1.627
peak=    3.823 closest distance to " O   HOH Z  54 " =    1.554
peak=    3.823 closest distance to " O   HOH Z 344 " =    1.326
peak=    3.821 closest distance to " O   HOH Z 345 " =    3.006
peak=    3.819 closest distance to " O   HOH Z 322 " =    2.085
peak=    3.817 closest distance to " O   HOH Z 402 " =    1.372
peak=    3.813 closest distance to " O   HOH Z 128 " =    1.962
peak=    3.808 closest distance to " O   HOH Z 280 " =    1.475
peak=    3.806 closest distance to " O   HOH Z 261 " =    2.117
peak=    3.792 closest distance to " O   HOH Z 369 " =    1.934
peak=    3.785 closest distance to " O   HOH Z 227 " =    1.753
peak=    3.780 closest distance to " O   HOH Z 334 " =    1.753
peak=    3.774 closest distance to " OG BSER A 164 " =    2.172
peak=    3.771 closest distance to " CD2 TRP A 179 " =    1.407
peak=    3.761 closest distance to " CB  ASN A 148 " =    1.926
peak=    3.747 closest distance to " ND2 ASN A 187 " =    1.632
peak=    3.742 closest distance to " O   HOH Z 303 " =    1.716
peak=    3.734 closest distance to " NE2 GLN A  58 " =    5.775
peak=    3.730 closest distance to " O   HOH Z  48 " =    1.438
peak=    3.707 closest distance to " CG2 THR A 221 " =    1.120
peak=    3.706 closest distance to " O   MET A 105 " =    1.869
peak=    3.704 closest distance to " O   HOH Z 287 " =    1.803
peak=    3.701 closest distance to " O   HOH Z 366 " =    2.744
peak=    3.696 closest distance to " O   HOH Z 126 " =    2.357
peak=    3.691 closest distance to " O   HOH Z 133 " =    1.472
peak=    3.689 closest distance to " CB  VAL A 265 " =    1.197
peak=    3.688 closest distance to " O   HOH Z 425 " =    2.116
peak=    3.679 closest distance to " OD2 ASP A 286 " =    2.580
peak=    3.678 closest distance to " O   HOH Z 273 " =    2.792
peak=    3.677 closest distance to " O   HOH Z 247 " =    1.264
peak=    3.676 closest distance to " CB  ARG A  79 " =    1.368
peak=    3.676 closest distance to " CG  PRO A 198 " =    1.228
peak=    3.669 closest distance to " CB BVAL A  41 " =    1.123
peak=    3.662 closest distance to " CB  SER A  62 " =    1.257
peak=    3.659 closest distance to " O   TRP A 274 " =    1.918
peak=    3.659 closest distance to " O   HOH Z  88 " =    3.127
peak=    3.655 closest distance to " O   HOH Z 426 " =    1.410
peak=    3.654 closest distance to " O   HOH Z 380 " =    1.989
peak=    3.652 closest distance to " O   HOH Z 136 " =    1.163
peak=    3.641 closest distance to " NH1 ARG A  14 " =    1.023
peak=    3.634 closest distance to " O   HOH Z 248 " =    1.786
peak=    3.634 closest distance to " O   HOH Z 407 " =    2.400
peak=    3.632 closest distance to " O   HOH Z 392 " =    1.938
peak=    3.626 closest distance to " O   HOH Z 250 " =    1.292
peak=    3.624 closest distance to " O   HOH Z 193 " =    2.085
peak=    3.620 closest distance to " OG1 THR A 294 " =    2.342
peak=    3.612 closest distance to " CG AARG A 275 " =    1.133
peak=    3.608 closest distance to " OD1 ASP A 286 " =    1.630
peak=    3.605 closest distance to " CZ2 TRP A 274 " =    1.694
peak=    3.604 closest distance to " O   HOH Z 374 " =    2.383
peak=    3.596 closest distance to " CG  ARG A  66 " =    2.852
peak=    3.588 closest distance to " O   HOH Z 191 " =    1.421
peak=    3.584 closest distance to " CA  ASN A 176 " =    1.057
peak=    3.571 closest distance to " O   HOH Z 389 " =    1.679
peak=    3.571 closest distance to " C   ALA A 299 " =    0.945
peak=    3.567 closest distance to " O   HOH Z 422 " =    2.553
peak=    3.566 closest distance to " CA  ALA A  51 " =    0.994
peak=    3.565 closest distance to " O   HOH Z 261 " =    1.666
peak=    3.563 closest distance to " CB  SER A  26 " =    1.559
peak=    3.562 closest distance to " O   HOH Z 406 " =    1.657
peak=    3.559 closest distance to " O   HOH Z 130 " =    2.341
peak=    3.559 closest distance to " CE2 TRP A 179 " =    1.718
peak=    3.555 closest distance to " CB  ALA A   9 " =    1.598
peak=    3.548 closest distance to " O   HOH Z 327 " =    1.593
peak=    3.543 closest distance to " CA  VAL A 126 " =    1.019
peak=    3.539 closest distance to " O   HOH Z  80 " =    1.675
peak=    3.536 closest distance to " O   HOH Z 425 " =    1.352
peak=    3.536 closest distance to " O   HOH Z 419 " =    1.652
peak=    3.532 closest distance to " CA  THR A 221 " =    0.910
peak=    3.528 closest distance to " O   HOH Z  49 " =    2.248
peak=    3.526 closest distance to " CB  SER A 216 " =    0.804
peak=    3.517 closest distance to " O   HOH Z 283 " =    1.840
peak=    3.516 closest distance to " CG2 VAL A 257 " =    0.813
peak=    3.511 closest distance to " CB  LEU A 228 " =    1.437
peak=    3.505 closest distance to " O   HOH Z 148 " =    3.084
peak=    3.496 closest distance to " CZ AARG A 102 " =    1.644
peak=    3.492 closest distance to " CD  LYS A 166 " =    1.403
peak=    3.483 closest distance to " CB  ARG A 102 " =    0.766
peak=    3.482 closest distance to " CG  ARG A  66 " =    0.968
peak=    3.470 closest distance to " O   HOH Z 108 " =    1.854
peak=    3.467 closest distance to " CD BLYS A 290 " =    1.186
peak=    3.465 closest distance to " CE BMET A  47 " =    0.871
peak=    3.465 closest distance to " CB  ALA A 248 " =    1.382
peak=    3.458 closest distance to " O   HOH Z 116 " =    1.653
peak=    3.456 closest distance to " O   HOH Z 357 " =    1.878
peak=    3.455 closest distance to " O   HOH Z  44 " =    1.882
peak=    3.453 closest distance to " CE1 TYR A 186 " =    1.215
peak=    3.453 closest distance to " NZ  LYS A  76 " =    1.324
peak=    3.453 closest distance to " NH2BARG A 145 " =    2.173
peak=    3.452 closest distance to " CD2 LEU A 255 " =    1.250
peak=    3.451 closest distance to " O   HOH Z 180 " =    2.215
peak=    3.448 closest distance to " OG  SER A  22 " =    2.736
peak=    3.447 closest distance to " CD  LYS A 119 " =    1.667
peak=    3.444 closest distance to " CD  GLN A 194 " =    1.407
peak=    3.444 closest distance to " CD1 ILE A  33 " =    1.650
peak=    3.443 closest distance to " CG  MET A 185 " =    1.110
peak=    3.441 closest distance to " O   HOH Z 352 " =    1.251
peak=    3.429 closest distance to " CD2 HIS A  81 " =    1.249
peak=    3.428 closest distance to " CG  GLN A  58 " =    2.629
peak=    3.426 closest distance to " O   HOH Z  43 " =    2.758
peak=    3.424 closest distance to " CB  ARG A 190 " =    1.782
peak=    3.415 closest distance to " OG  SER A  97 " =    2.527
peak=    3.412 closest distance to " O   HOH Z 173 " =    2.169
peak=    3.410 closest distance to " CG2 ILE A  20 " =    1.554
peak=    3.409 closest distance to " CG1 ILE A  33 " =    1.355
peak=    3.405 closest distance to " CG  MET A 185 " =    1.243
peak=    3.404 closest distance to " O   SER A  26 " =    1.598
peak=    3.403 closest distance to " O   HOH Z  61 " =    1.608
peak=    3.400 closest distance to " C   LYS A 290 " =    1.230
peak=    3.396 closest distance to " O   HOH Z 214 " =    1.116
peak=    3.394 closest distance to " CB  ARG A 139 " =    1.025
peak=    3.391 closest distance to " C   ALA A   1 " =    1.699
peak=    3.391 closest distance to " CA  ASN A 215 " =    1.182
peak=    3.389 closest distance to " O   HOH Z  50 " =    1.533
peak=    3.386 closest distance to " O   HOH Z 329 " =    3.287
peak=    3.385 closest distance to " O   HOH Z  68 " =    1.605
peak=    3.384 closest distance to " O   HOH Z  30 " =    2.110
peak=    3.377 closest distance to " O   HOH Z 292 " =    1.652
peak=    3.377 closest distance to " CD  ARG A 269 " =    1.023
peak=    3.375 closest distance to " O   HOH Z 193 " =    1.709
peak=    3.374 closest distance to " CG  LEU A 167 " =    1.159
peak=    3.371 closest distance to " CA  PHE A 283 " =    1.329
peak=    3.371 closest distance to " O   HOH Z  19 " =    1.985
peak=    3.365 closest distance to " CD1 ILE A 106 " =    1.268
peak=    3.364 closest distance to " O   HOH Z  15 " =    1.460
peak=    3.361 closest distance to " O   HOH Z  10 " =    1.766
peak=    3.356 closest distance to " OE1 GLN A  11 " =    1.700
peak=    3.355 closest distance to " O   HOH Z 150 " =    1.754
peak=    3.355 closest distance to " O   HOH Z 172 " =    3.890
peak=    3.355 closest distance to " O   HOH Z 155 " =    1.624
peak=    3.349 closest distance to " CG  PRO A 243 " =    1.279
peak=    3.348 closest distance to " O   ALA A 165 " =    1.293
peak=    3.347 closest distance to " CG  MET A 188 " =    1.405
peak=    3.344 closest distance to " O   HOH Z 123 " =    1.060
peak=    3.339 closest distance to " CA  ASP A 140 " =    1.159
peak=    3.339 closest distance to " O   HOH Z  20 " =    2.338
peak=    3.337 closest distance to " CB  ALA A   1 " =    1.213
peak=    3.336 closest distance to " NH2BARG A 190 " =    1.954
peak=    3.334 closest distance to " CA  ARG A  36 " =    1.022
peak=    3.333 closest distance to " CA  LYS A 117 " =    1.253
peak=    3.329 closest distance to " O   HOH Z  85 " =    1.085
peak=    3.327 closest distance to " CG  GLN A  77 " =    2.244
peak=    3.324 closest distance to " CB  LEU A 255 " =    0.765
peak=    3.324 closest distance to " CG1 VAL A 153 " =    0.957
peak=    3.322 closest distance to " CA  GLN A 194 " =    1.224
peak=    3.313 closest distance to " CA  ALA A 295 " =    1.083
peak=    3.313 closest distance to " O   HOH Z 164 " =    1.968
peak=    3.304 closest distance to " O   HOH Z 435 " =    2.120
peak=    3.304 closest distance to " O   HOH Z 217 " =    1.243
peak=    3.303 closest distance to " O   GLY A  91 " =    1.699
peak=    3.294 closest distance to " O   HOH Z 302 " =    1.620
peak=    3.293 closest distance to " CG  MET A  93 " =    1.020
peak=    3.287 closest distance to " O   HOH Z 277 " =    2.369
peak=    3.285 closest distance to " CA  ASP A 191 " =    0.952
peak=    3.284 closest distance to " O   HOH Z 102 " =    1.142
peak=    3.282 closest distance to " O   THR A  31 " =    1.517
peak=    3.282 closest distance to " O   ALA A 158 " =    1.299
peak=    3.278 closest distance to " CB  SER A 141 " =    1.094
peak=    3.277 closest distance to " O   ASN A 217 " =    1.280
peak=    3.277 closest distance to " O   HOH Z 112 " =    1.674
peak=    3.276 closest distance to " CB  TYR A  30 " =    1.550
peak=    3.274 closest distance to " O   HOH Z 280 " =    2.263
peak=    3.273 closest distance to " O   HOH Z  21 " =    1.832
peak=    3.272 closest distance to " O   HOH Z 271 " =    1.855
peak=    3.271 closest distance to " O   HOH Z 244 " =    1.572
peak=    3.270 closest distance to " N   ARG A 156 " =    1.266
peak=    3.267 closest distance to " O   HOH Z 265 " =    2.213
peak=    3.266 closest distance to " CB  GLN A 205 " =    1.264
peak=    3.265 closest distance to " CB  ASN A  39 " =    0.796
peak=    3.264 closest distance to " N   ASN A  39 " =    1.151
peak=    3.263 closest distance to " O   HOH Z 355 " =    1.837
peak=    3.257 closest distance to " CB  ALA A 295 " =    1.343
peak=    3.253 closest distance to " CD2 TYR A  30 " =    0.939
peak=    3.252 closest distance to " O   HOH Z 420 " =    1.890
peak=    3.247 closest distance to " O   HOH Z  43 " =    2.246
peak=    3.241 closest distance to " O   HOH Z 132 " =    3.106
peak=    3.232 closest distance to " O   HOH Z  89 " =    1.606
peak=    3.232 closest distance to " O   HOH Z 408 " =    1.466
peak=    3.227 closest distance to " OD1 ASP A 231 " =    1.840
peak=    3.226 closest distance to " O   GLN A  58 " =    1.499
peak=    3.225 closest distance to " O   HOH Z  40 " =    1.906
peak=    3.223 closest distance to " O   HOH Z 158 " =    2.960
peak=    3.223 closest distance to " NH2 ARG A 219 " =    1.754
peak=    3.206 closest distance to " O   HOH Z 245 " =    1.377
peak=    3.205 closest distance to " O   HOH Z 143 " =    1.163
peak=    3.204 closest distance to " CG  GLN A  88 " =    1.022
peak=    3.201 closest distance to " O   HOH Z 151 " =    1.709
peak=    3.199 closest distance to " O   HOH Z 411 " =    1.660
peak=    3.192 closest distance to " O   PHE A  38 " =    1.871
peak=    3.187 closest distance to " O   HOH Z 251 " =    1.560
peak=    3.185 closest distance to " CG2 ILE A 120 " =    1.229
peak=    3.184 closest distance to " O   HOH Z 281 " =    4.466
peak=    3.181 closest distance to " O   HOH Z  66 " =    2.153
peak=    3.181 closest distance to " O   SER A 164 " =    1.325
peak=    3.178 closest distance to " SG ACYS A 201 " =    0.766
peak=    3.174 closest distance to " CE BLYS A 290 " =    1.106
peak=    3.170 closest distance to " CH2 TRP A 274 " =    2.264
peak=    3.167 closest distance to " O   HOH Z 380 " =    2.002
peak=    3.165 closest distance to " O   HOH Z 438 " =    2.087
peak=    3.162 closest distance to " CB  ASN A 110 " =    1.256
peak=    3.157 closest distance to " CA  THR A 264 " =    0.783
peak=    3.156 closest distance to " O   HOH Z 152 " =    1.694
peak=    3.151 closest distance to " O   HOH Z 394 " =    1.718
peak=    3.150 closest distance to " CA  ALA A 158 " =    1.117
peak=    3.149 closest distance to " CB  TRP A 266 " =    1.030
peak=    3.146 closest distance to " O   HOH Z 222 " =    2.329
peak=    3.139 closest distance to " O   HOH Z 367 " =    3.555
peak=    3.133 closest distance to " CB  ALA A 100 " =    1.176
peak=    3.133 closest distance to " O   HOH Z  33 " =    1.816
peak=    3.121 closest distance to " O   HOH Z 285 " =    1.551
peak=    3.120 closest distance to " O   HOH Z  59 " =    1.889
peak=    3.118 closest distance to " CB  ALA A  71 " =    1.308
peak=    3.111 closest distance to " O   HOH Z 426 " =    2.930
peak=    3.110 closest distance to " CB  ALA A 291 " =    1.323
peak=    3.108 closest distance to " O   HOH Z 328 " =    2.116
peak=    3.107 closest distance to " O   HOH Z 278 " =    1.190
peak=    3.099 closest distance to " O   HOH Z   9 " =    2.249
peak=    3.099 closest distance to " O   HOH Z 407 " =    3.714
peak=    3.098 closest distance to " CB  THR A  31 " =    1.721
peak=    3.093 closest distance to " OE2 GLU A  53 " =    2.025
peak=    3.088 closest distance to " O   HOH Z 141 " =    1.583
peak=    3.088 closest distance to " CB  GLN A 278 " =    0.809
peak=    3.087 closest distance to " O   HOH Z 155 " =    2.676
peak=    3.082 closest distance to " N   SER A 135 " =    1.240
peak=    3.082 closest distance to " CG2 VAL A 126 " =    1.779
peak=    3.080 closest distance to " O   HOH Z 342 " =    0.826
peak=    3.067 closest distance to " O   HOH Z 106 " =    2.215
peak=    3.051 closest distance to " CB  PRO A 198 " =    1.013
peak=    3.037 closest distance to " CB  GLU A  46 " =    1.098
peak=    3.010 closest distance to " O   HOH Z  40 " =    2.289

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.423 - 5.129
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 198
   mapped sites are within: 0.763 - 5.129

peak=   -5.107 closest distance to " CG2 VAL A 230 " =    0.802
peak=   -4.579 closest distance to " CD  ARG A 156 " =    2.051
peak=   -4.507 closest distance to " SG  CYS A 254 " =    3.179
peak=   -4.471 closest distance to " O   PRO A 163 " =    2.024
peak=   -4.364 closest distance to " O   HOH Z 266 " =    4.305
peak=   -4.346 closest distance to " CB  ALA A 161 " =    2.548
peak=   -4.270 closest distance to " OXT GLY A 302 " =    2.735
peak=   -4.236 closest distance to " CD1 LEU A 101 " =    2.434
peak=   -4.187 closest distance to " O   VAL A  67 " =    2.682
peak=   -4.167 closest distance to " O   HOH Z  11 " =    1.761
peak=   -4.048 closest distance to " CE2 TYR A  30 " =    2.866
peak=   -4.042 closest distance to " O   HOH Z 166 " =    1.416
peak=   -4.035 closest distance to " N   GLN A  58 " =    1.639
peak=   -4.021 closest distance to " N   HIS A 115 " =    1.948
peak=   -3.996 closest distance to " CG  LYS A 193 " =    2.189
peak=   -3.989 closest distance to " N   ALA A 248 " =    1.676
peak=   -3.948 closest distance to " O   HOH Z 231 " =    1.607
peak=   -3.942 closest distance to " O   ALA A 161 " =    1.527
peak=   -3.926 closest distance to " O   HOH Z  43 " =    1.845
peak=   -3.925 closest distance to " O   HOH Z  98 " =    1.589
peak=   -3.901 closest distance to " CB  TYR A  15 " =    2.148
peak=   -3.883 closest distance to " O   VAL A  67 " =    2.781
peak=   -3.882 closest distance to " CD  ARG A 139 " =    1.736
peak=   -3.875 closest distance to " OG ASER A 134 " =    1.283
peak=   -3.868 closest distance to " O   HOH Z 166 " =    2.017
peak=   -3.861 closest distance to " C   HIS A 108 " =    1.158
peak=   -3.858 closest distance to " O   HOH Z 290 " =    0.934
peak=   -3.848 closest distance to " CB  ALA A 248 " =    1.904
peak=   -3.845 closest distance to " OD1 ASN A 249 " =    1.237
peak=   -3.831 closest distance to " ND2 ASN A  45 " =    1.047
peak=   -3.820 closest distance to " CG  ASP A  50 " =    2.390
peak=   -3.807 closest distance to " O   HOH Z 165 " =    2.087
peak=   -3.795 closest distance to " CD1 LEU A 255 " =    2.695
peak=   -3.776 closest distance to " CG  LEU A 228 " =    1.040
peak=   -3.766 closest distance to " OG BSER A 134 " =    1.567
peak=   -3.754 closest distance to " O   HOH Z 103 " =    1.807
peak=   -3.746 closest distance to " NH2 ARG A  79 " =    1.887
peak=   -3.743 closest distance to " O   HOH Z  92 " =    1.723
peak=   -3.723 closest distance to " N   THR A 157 " =    1.464
peak=   -3.716 closest distance to " O   HOH Z 198 " =    2.282
peak=   -3.705 closest distance to " CZ  TYR A 169 " =    1.788
peak=   -3.703 closest distance to " CD2 LEU A 300 " =    2.848
peak=   -3.702 closest distance to " O   ALA A   8 " =    1.739
peak=   -3.695 closest distance to " N   SER A 276 " =    1.214
peak=   -3.689 closest distance to " O   HOH Z  13 " =    1.442
peak=   -3.687 closest distance to " O   ASN A 187 " =    1.453
peak=   -3.686 closest distance to " O   HOH Z  56 " =    2.108
peak=   -3.681 closest distance to " CG  GLN A 223 " =    2.399
peak=   -3.671 closest distance to " CB  ALA A 291 " =    2.364
peak=   -3.665 closest distance to " O   ASP A 231 " =    2.509
peak=   -3.657 closest distance to " CD  GLN A  88 " =    0.946
peak=   -3.649 closest distance to " CG2 VAL A 296 " =    1.623
peak=   -3.636 closest distance to " O   PRO A 198 " =    1.298
peak=   -3.632 closest distance to " CB  ALA A  51 " =    1.807
peak=   -3.631 closest distance to " O   PRO A 198 " =    1.308
peak=   -3.624 closest distance to " O   HOH Z 407 " =    2.913
peak=   -3.615 closest distance to " CB  PRO A 280 " =    2.105
peak=   -3.611 closest distance to " CG  ASP A 231 " =    0.763
peak=   -3.571 closest distance to " OD1 ASP A 200 " =    1.190
peak=   -3.570 closest distance to " OG BSER A 134 " =    1.265
peak=   -3.564 closest distance to " CB  ASP A 132 " =    2.217
peak=   -3.541 closest distance to " O   HOH Z 423 " =    2.238
peak=   -3.533 closest distance to " N   GLN A 122 " =    1.478
peak=   -3.532 closest distance to " O   HOH Z 389 " =    4.592
peak=   -3.528 closest distance to " CG  PHE A 283 " =    2.696
peak=   -3.527 closest distance to " O   MET A  40 " =    2.697
peak=   -3.523 closest distance to " ND2 ASN A  39 " =    1.238
peak=   -3.518 closest distance to " O   HOH Z 292 " =    4.207
peak=   -3.517 closest distance to " CD  GLU A 152 " =    2.663
peak=   -3.516 closest distance to " OXT GLY A 302 " =    3.506
peak=   -3.511 closest distance to " CA  ASP A 298 " =    1.065
peak=   -3.511 closest distance to " O   HOH Z 113 " =    2.334
peak=   -3.511 closest distance to " CB  ASN A  39 " =    2.020
peak=   -3.509 closest distance to " C   ALA A 158 " =    1.230
peak=   -3.498 closest distance to " C   ASN A 187 " =    1.829
peak=   -3.497 closest distance to " O   HOH Z  17 " =    1.428
peak=   -3.485 closest distance to " NH2AARG A 275 " =    5.129
peak=   -3.481 closest distance to " CE  MET A 105 " =    2.017
peak=   -3.473 closest distance to " CG  GLU A   2 " =    2.049
peak=   -3.472 closest distance to " O   ALA A  51 " =    1.327
peak=   -3.468 closest distance to " O   HOH Z 423 " =    1.119
peak=   -3.467 closest distance to " O   HOH Z  63 " =    0.966
peak=   -3.462 closest distance to " ND2 ASN A 187 " =    1.748
peak=   -3.453 closest distance to " CB  PRO A 243 " =    2.521
peak=   -3.449 closest distance to " OG1 THR A  82 " =    1.362
peak=   -3.447 closest distance to " O   HOH Z 427 " =    1.491
peak=   -3.439 closest distance to " CE  LYS A  76 " =    2.922
peak=   -3.430 closest distance to " CD  LYS A 289 " =    2.504
peak=   -3.424 closest distance to " OH  TYR A 214 " =    1.314
peak=   -3.420 closest distance to " O   HOH Z  97 " =    1.454
peak=   -3.415 closest distance to " O   HOH Z  11 " =    1.798
peak=   -3.405 closest distance to " C   ASN A 285 " =    2.287
peak=   -3.392 closest distance to " O   HOH Z  71 " =    1.205
peak=   -3.387 closest distance to " CE3 TRP A  70 " =    2.770
peak=   -3.387 closest distance to " O   HOH Z 191 " =    4.892
peak=   -3.383 closest distance to " N   ALA A 226 " =    1.975
peak=   -3.379 closest distance to " NH1 ARG A  56 " =    2.519
peak=   -3.379 closest distance to " N   ALA A 248 " =    2.202
peak=   -3.372 closest distance to " CB  PRO A 163 " =    2.627
peak=   -3.367 closest distance to " O   HOH Z 431 " =    1.591
peak=   -3.352 closest distance to " N   VAL A 230 " =    1.257
peak=   -3.347 closest distance to " OG  SER A  97 " =    2.087
peak=   -3.339 closest distance to " O   SER A 135 " =    1.547
peak=   -3.331 closest distance to " C   LEU A 143 " =    1.113
peak=   -3.331 closest distance to " O   VAL A 197 " =    1.224
peak=   -3.326 closest distance to " O   ALA A 160 " =    1.278
peak=   -3.323 closest distance to " CD1 PHE A  59 " =    1.819
peak=   -3.323 closest distance to " OD2 ASP A  50 " =    1.426
peak=   -3.316 closest distance to " OD1 ASP A 191 " =    1.666
peak=   -3.314 closest distance to " CB  ALA A  43 " =    2.233
peak=   -3.314 closest distance to " ND2 ASN A 209 " =    1.617
peak=   -3.312 closest distance to " CD2 LEU A 237 " =    2.695
peak=   -3.310 closest distance to " CD1 LEU A 228 " =    2.165
peak=   -3.303 closest distance to " O   HOH Z 234 " =    4.141
peak=   -3.299 closest distance to " CD2 TYR A 293 " =    2.101
peak=   -3.299 closest distance to " CA  GLY A 133 " =    1.876
peak=   -3.296 closest distance to " OG1 THR A 178 " =    1.166
peak=   -3.288 closest distance to " O   HOH Z 134 " =    2.616
peak=   -3.286 closest distance to " O   GLY A 196 " =    1.054
peak=   -3.284 closest distance to " O   ALA A 256 " =    1.525
peak=   -3.283 closest distance to " O   HOH Z 429 " =    2.149
peak=   -3.282 closest distance to " CG  PHE A  59 " =    2.164
peak=   -3.278 closest distance to " O   HOH Z 250 " =    1.490
peak=   -3.271 closest distance to " O   HOH Z  70 " =    1.347
peak=   -3.267 closest distance to " O   HOH Z 385 " =    1.913
peak=   -3.257 closest distance to " CA  GLY A  35 " =    2.037
peak=   -3.255 closest distance to " CD  GLN A  88 " =    2.252
peak=   -3.252 closest distance to " CG  MET A 105 " =    0.898
peak=   -3.251 closest distance to " CD2 LEU A 167 " =    1.753
peak=   -3.250 closest distance to " CA  GLY A  23 " =    1.678
peak=   -3.245 closest distance to " CE BMET A  47 " =    1.447
peak=   -3.243 closest distance to " O   GLU A  44 " =    1.834
peak=   -3.242 closest distance to " CD  ARG A 259 " =    2.493
peak=   -3.242 closest distance to " CE2 PHE A 218 " =    2.652
peak=   -3.240 closest distance to " OG  SER A 206 " =    1.586
peak=   -3.237 closest distance to " OG  SER A  26 " =    1.087
peak=   -3.237 closest distance to " O   MET A 113 " =    2.682
peak=   -3.228 closest distance to " O   HOH Z 313 " =    1.860
peak=   -3.228 closest distance to " CG  ASN A  45 " =    1.682
peak=   -3.228 closest distance to " CA  ALA A 291 " =    2.501
peak=   -3.224 closest distance to " CA  ASN A 127 " =    1.099
peak=   -3.223 closest distance to " O   HOH Z 339 " =    1.734
peak=   -3.221 closest distance to " O   SER A 210 " =    1.795
peak=   -3.219 closest distance to " CG  TRP A 266 " =    1.696
peak=   -3.217 closest distance to " O   VAL A 174 " =    1.878
peak=   -3.215 closest distance to " CB  ASP A 132 " =    2.121
peak=   -3.212 closest distance to " CG  PRO A 163 " =    2.787
peak=   -3.209 closest distance to " O   ILE A 120 " =    1.339
peak=   -3.207 closest distance to " O   HOH Z 175 " =    4.380
peak=   -3.206 closest distance to " CB  CYS A 254 " =    2.430
peak=   -3.202 closest distance to " O   HOH Z 281 " =    2.913
peak=   -3.198 closest distance to " CD1 TYR A 247 " =    2.543
peak=   -3.193 closest distance to " O   HOH Z 297 " =    2.742
peak=   -3.193 closest distance to " N   SER A 206 " =    1.916
peak=   -3.190 closest distance to " CB  ALA A 131 " =    1.984
peak=   -3.187 closest distance to " O   SER A 146 " =    0.894
peak=   -3.180 closest distance to " N   ASP A 270 " =    1.464
peak=   -3.179 closest distance to " NH2 ARG A  66 " =    1.845
peak=   -3.176 closest distance to " CG1 VAL A 112 " =    2.720
peak=   -3.174 closest distance to " O   HOH Z 222 " =    1.571
peak=   -3.173 closest distance to " O   HOH Z 404 " =    1.532
peak=   -3.171 closest distance to " OD1 ASP A 191 " =    1.420
peak=   -3.168 closest distance to " CG2 VAL A 189 " =    1.990
peak=   -3.165 closest distance to " CG  GLU A 277 " =    1.208
peak=   -3.163 closest distance to " O   HOH Z 210 " =    1.037
peak=   -3.159 closest distance to " CG  GLU A  53 " =    1.419
peak=   -3.158 closest distance to " O   HOH Z 118 " =    2.380
peak=   -3.155 closest distance to " O   TRP A  92 " =    1.717
peak=   -3.149 closest distance to " O   HOH Z 189 " =    1.741
peak=   -3.148 closest distance to " CE2 TRP A 179 " =    1.308
peak=   -3.143 closest distance to " CD2 LEU A 237 " =    2.787
peak=   -3.139 closest distance to " OG  SER A  62 " =    1.579
peak=   -3.137 closest distance to " O   HOH Z 407 " =    3.474
peak=   -3.130 closest distance to " O   GLY A  80 " =    2.526
peak=   -3.122 closest distance to " CE3 TRP A 274 " =    2.387
peak=   -3.120 closest distance to " SD BMET A  47 " =    2.565
peak=   -3.115 closest distance to " CB  ASP A 132 " =    2.129
peak=   -3.111 closest distance to " O   HOH Z 193 " =    1.975
peak=   -3.110 closest distance to " O   HOH Z 198 " =    1.631
peak=   -3.108 closest distance to " O   HOH Z 256 " =    1.142
peak=   -3.108 closest distance to " OD1 ASP A 171 " =    1.542
peak=   -3.105 closest distance to " O   SER A  95 " =    1.412
peak=   -3.097 closest distance to " O   HOH Z  44 " =    2.063
peak=   -3.095 closest distance to " O   SER A  22 " =    2.271
peak=   -3.090 closest distance to " OG  SER A   3 " =    1.407
peak=   -3.072 closest distance to " O   HOH Z 310 " =    1.527
peak=   -3.071 closest distance to " ND2 ASN A  60 " =    1.350
peak=   -3.070 closest distance to " O   HOH Z 131 " =    3.883
peak=   -3.067 closest distance to " N   ALA A  43 " =    2.592
peak=   -3.065 closest distance to " O   HOH Z  12 " =    3.564
peak=   -3.057 closest distance to " O   ILE A  49 " =    1.773
peak=   -3.052 closest distance to " O   HOH Z 341 " =    1.221
peak=   -3.050 closest distance to " CE  LYS A 166 " =    3.045
peak=   -3.050 closest distance to " O   SER A 258 " =    1.914
peak=   -3.004 closest distance to " O   HOH Z 389 " =    4.091

================= 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    :  0.4700 0.4739   6.271818e+00   6.265245e+00
   1_bss:  0.4617 0.4619   6.267725e+00   6.251124e+00
   1_xyz:  0.3853 0.4060   6.158488e+00   6.189646e+00
   1_adp:  0.3356 0.3839   6.073858e+00   6.159312e+00
   1_occ:  0.3354 0.3837   6.073908e+00   6.160312e+00
   2_bss:  0.3311 0.3814   6.073096e+00   6.157609e+00
   2_xyz:  0.2508 0.3077   5.838060e+00   5.985732e+00
   2_adp:  0.2299 0.2891   5.770234e+00   5.936419e+00
   2_occ:  0.2297 0.2896   5.770078e+00   5.937059e+00
   3_bss:  0.2280 0.2877   5.767609e+00   5.933807e+00
   3_xyz:  0.1766 0.2343   5.551744e+00   5.760415e+00
   3_adp:  0.1620 0.2172   5.471034e+00   5.688815e+00
   3_occ:  0.1618 0.2168   5.470508e+00   5.688328e+00
   4_bss:  0.1614 0.2159   5.468089e+00   5.684868e+00
   4_xyz:  0.1309 0.1780   5.273143e+00   5.501479e+00
   4_adp:  0.1261 0.1698   5.232670e+00   5.452121e+00
   4_occ:  0.1259 0.1695   5.231539e+00   5.450861e+00
   5_bss:  0.1262 0.1692   5.231778e+00   5.449561e+00
   5_xyz:  0.1149 0.1604   5.162624e+00   5.395962e+00
   5_adp:  0.1122 0.1601   5.151921e+00   5.393988e+00
   5_occ:  0.1121 0.1601   5.151882e+00   5.394103e+00
   5_bss:  0.1121 0.1601   5.151870e+00   5.394103e+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:  0.360   8.016   7.033   7.650  10.019   0.000   0.000   0.000
   1_xyz:  0.360   8.016   7.033   7.650  10.019   0.000   0.000   0.000
   1_adp:  0.360   8.016   7.033   7.650  10.019   0.000   0.000   0.000
   1_occ:  0.360   8.016   7.033   7.650  10.019   0.000   0.000   0.000
   2_bss:  0.324  25.751   3.453   3.900   6.791   0.000   0.000   0.000
   2_xyz:  0.324  25.751   3.453   3.900   6.791   0.000   0.000   0.000
   2_adp:  0.324  25.751   3.453   3.900   6.791   0.000   0.000   0.000
   2_occ:  0.324  25.751   3.453   3.900   6.791   0.000   0.000   0.000
   3_bss:  0.314  30.649   1.924   2.549   3.945   0.000   0.000   0.000
   3_xyz:  0.314  30.649   1.924   2.549   3.945   0.000   0.000   0.000
   3_adp:  0.314  30.649   1.924   2.549   3.945   0.000   0.000   0.000
   3_occ:  0.314  30.649   1.924   2.549   3.945   0.000   0.000   0.000
   4_bss:  0.315  31.172   1.375   1.983   2.671   0.000   0.000   0.000
   4_xyz:  0.315  31.172   1.375   1.983   2.671   0.000   0.000   0.000
   4_adp:  0.315  31.172   1.375   1.983   2.671   0.000   0.000   0.000
   4_occ:  0.315  31.172   1.375   1.983   2.671   0.000   0.000   0.000
   5_bss:  0.318  33.458   1.236   1.807   2.200   0.000   0.000   0.000
   5_xyz:  0.318  33.458   1.236   1.807   2.200   0.000   0.000   0.000
   5_adp:  0.318  33.458   1.236   1.807   2.200   0.000   0.000   0.000
   5_occ:  0.318  33.458   1.236   1.807   2.200   0.000   0.000   0.000
   5_bss:  0.321  36.280  -0.512   0.060   0.452   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.032 0.4455  0.5282    69074.964
   1_bss:  55.990 0.4433  0.6621    64988.881
   1_xyz:  47.037 0.5559  0.8188    48868.083
   1_adp:  43.682 0.5977  0.9118    44074.009
   1_occ:  43.786 0.5964  0.9100    44228.997
   2_bss:  43.418 0.6008  0.8104    43738.061
   2_xyz:  32.384 0.7302  0.9660    25420.090
   2_adp:  29.731 0.7603  1.0075    22209.088
   2_occ:  29.754 0.7601  1.0069    22253.683
   3_bss:  29.521 0.7625  0.9414    22006.912
   3_xyz:  23.187 0.8297  0.9895    14211.704
   3_adp:  20.923 0.8529  1.0016    12134.862
   3_occ:  20.911 0.8531  1.0012    12121.624
   4_bss:  20.779 0.8542  0.9723    11974.212
   4_xyz:  16.640 0.8922  0.9912     8054.803
   4_adp:  15.435 0.9031  0.9948     7301.571
   4_occ:  15.407 0.9033  0.9947     7283.957
   5_bss:  15.373 0.9036  0.9856     7266.691
   5_xyz:  14.273 0.9126  0.9898     6466.954
   5_adp:  14.211 0.9133  0.9876     6452.553
   5_occ:  14.209 0.9134  0.9874     6454.337
   5_bss:  14.208 0.9134  0.9875     6455.997
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3045e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3045e+01
   1_xyz:   1.623  0.012  0.105 18.197  0.007  4.107   1.3433e-01
   1_adp:   1.623  0.012  0.105 18.197  0.007  4.107   1.3433e-01
   1_occ:   1.623  0.012  0.105 18.197  0.007  4.107   1.3433e-01
   2_bss:   1.623  0.012  0.105 18.197  0.007  4.107   1.3433e-01
   2_xyz:   1.139  0.008  0.083 16.356  0.005  4.106   7.9732e-02
   2_adp:   1.139  0.008  0.083 16.356  0.005  4.106   7.9732e-02
   2_occ:   1.139  0.008  0.083 16.356  0.005  4.106   7.9732e-02
   3_bss:   1.139  0.008  0.083 16.356  0.005  4.106   7.9732e-02
   3_xyz:   0.995  0.007  0.071 15.615  0.004  4.115   6.1360e-02
   3_adp:   0.995  0.007  0.071 15.615  0.004  4.115   6.1360e-02
   3_occ:   0.995  0.007  0.071 15.615  0.004  4.115   6.1360e-02
   4_bss:   0.995  0.007  0.071 15.615  0.004  4.115   6.1360e-02
   4_xyz:   1.045  0.006  0.077 15.708  0.004  4.117   6.3861e-02
   4_adp:   1.045  0.006  0.077 15.708  0.004  4.117   6.3861e-02
   4_occ:   1.045  0.006  0.077 15.708  0.004  4.117   6.3861e-02
   5_bss:   1.045  0.006  0.077 15.708  0.004  4.117   6.3861e-02
   5_xyz:   1.075  0.007  0.081 15.725  0.004  4.107   6.6929e-02
   5_adp:   1.075  0.007  0.081 15.725  0.004  4.107   6.6929e-02
   5_occ:   1.075  0.007  0.081 15.725  0.004  4.107   6.6929e-02
   5_bss:   1.075  0.007  0.081 15.725  0.004  4.107   6.6929e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.864   6.8732e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.864   6.8732e+00
   1_xyz:  14.077  0.162  0.459 86.881  0.053  2.198   9.2872e-02
   1_adp:  14.077  0.162  0.459 86.881  0.053  2.198   9.2872e-02
   1_occ:  14.077  0.162  0.459 86.881  0.053  2.198   9.2872e-02
   2_bss:  14.077  0.162  0.459 86.881  0.053  2.198   9.2872e-02
   2_xyz:   7.520  0.088  0.354 84.140  0.044  2.306   5.8488e-02
   2_adp:   7.520  0.088  0.354 84.140  0.044  2.306   5.8488e-02
   2_occ:   7.520  0.088  0.354 84.140  0.044  2.306   5.8488e-02
   3_bss:   7.520  0.088  0.354 84.140  0.044  2.306   5.8488e-02
   3_xyz:   6.313  0.050  0.321 89.734  0.029  2.388   9.2101e-02
   3_adp:   6.313  0.050  0.321 89.734  0.029  2.388   9.2101e-02
   3_occ:   6.313  0.050  0.321 89.734  0.029  2.388   9.2101e-02
   4_bss:   6.313  0.050  0.321 89.734  0.029  2.388   9.2101e-02
   4_xyz:   6.829  0.038  0.477 81.602  0.034  2.337   4.4893e-02
   4_adp:   6.829  0.038  0.477 81.602  0.034  2.337   4.4893e-02
   4_occ:   6.829  0.038  0.477 81.602  0.034  2.337   4.4893e-02
   5_bss:   6.829  0.038  0.477 81.602  0.034  2.337   4.4893e-02
   5_xyz:   6.708  0.042  0.536 83.149  0.038  2.246   6.0232e-02
   5_adp:   6.708  0.042  0.536 83.149  0.038  2.246   6.0232e-02
   5_occ:   6.708  0.042  0.536 83.149  0.038  2.246   6.0232e-02
   5_bss:   6.708  0.042  0.536 83.149  0.038  2.246   6.0232e-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:  79.24   0.00  12.82  79.24   0.00  10.33  68.40   0.00  26.37
   1_occ:  79.24   0.00  12.82  79.24   0.00  10.33  68.40   0.00  26.37
   2_bss:  79.24   0.00  12.82  79.24   0.00  10.33  68.40   0.00  26.37
   2_xyz:  79.24   0.00  12.82  79.24   0.00  10.33  68.40   0.00  26.37
   2_adp:  79.92   0.00  13.11  79.92   0.00   9.84  67.90   0.00  30.90
   2_occ:  79.92   0.00  13.11  79.92   0.00   9.84  67.90   0.00  30.90
   3_bss:  79.92   0.00  13.11  79.92   0.00   9.84  67.90   0.00  30.90
   3_xyz:  79.92   0.00  13.11  79.92   0.00   9.84  67.90   0.00  30.90
   3_adp:  84.31   0.00  13.49  84.31   0.00   9.29  74.85   2.27  36.35
   3_occ:  84.31   0.00  13.49  84.31   0.00   9.29  74.85   2.27  36.35
   4_bss:  84.31   0.00  13.49  84.31   0.00   9.29  74.85   2.27  36.35
   4_xyz:  84.31   0.00  13.49  84.31   0.00   9.29  74.85   2.27  36.35
   4_adp:  86.50   0.00  13.08  86.50   0.00   8.96  76.68   2.78  35.54
   4_occ:  86.50   0.00  13.08  86.50   0.00   8.96  76.68   2.78  35.54
   5_bss:  86.50   0.00  13.08  86.50   0.00   8.96  76.68   2.78  35.54
   5_xyz:  86.50   0.00  13.08  86.50   0.00   8.96  76.68   2.78  35.54
   5_adp:  90.57   0.00  13.19  90.57   0.00   8.94  81.20   2.41  36.33
   5_occ:  90.57   0.00  13.19  90.57   0.00   8.94  81.20   2.41  36.33
   5_bss:  92.32   1.75  14.94  92.32   1.75  10.68  82.94   4.16  38.08
------------------------------------------------------------------------
 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:    1.226    0.012    0.406
   1_adp:    1.226    0.012    0.406
   1_occ:    1.226    0.012    0.406
   2_bss:    1.226    0.012    0.406
   2_xyz:    1.623    0.016    0.569
   2_adp:    1.623    0.016    0.569
   2_occ:    1.623    0.016    0.569
   3_bss:    1.623    0.016    0.569
   3_xyz:    1.485    0.054    0.623
   3_adp:    1.485    0.054    0.623
   3_occ:    1.485    0.054    0.623
   4_bss:    1.485    0.054    0.623
   4_xyz:    1.605    0.032    0.679
   4_adp:    1.605    0.032    0.679
   4_occ:    1.605    0.032    0.679
   5_bss:    1.605    0.032    0.679
   5_xyz:    1.722    0.030    0.700
   5_adp:    1.722    0.030    0.700
   5_occ:    1.722    0.030    0.700
   5_bss:    1.722    0.030    0.700
------------------------------------------------------------------------

CPU time actual refinement: 276.55


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_418/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_418/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_418/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_418/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_418/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 276.41 
  Macro-tasks:
    bulk solvent and scale       = 34.55  
    individual site refinement   = 114.72 
    weights calculation          = 26.67  
    collect and process          = 5.37   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 181.40 
  Micro-tasks:
    mask                            = 2.06   
    f_calc                          = 84.99  
    alpha_beta                      = 6.95   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 93.41  
    fmodel                         = 5.56   
    r_factors                      = 0.28   
    phase_errors                   = 8.53   
    foms                           = 0.16   
    TOTAL for micro-tasks          = 202.94 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.932 micro seconds
Total CPU time: 4.81 minutes
from_scatterers_fft:    622 calls, 84.61 s
gradients_fft:          567 calls, 82.53 s

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

# Date 2008-01-16 Time 01:32:02 PST -0800 (1200475922.52 s)
Start R-work = 0.4700, R-free = 0.4739 (no bulk solvent and anisotropic scale)
Final R-work = 0.1295, R-free = 0.1768 (no bulk solvent and anisotropic scale)

Start R-work = 0.4617, R-free = 0.4619
Final R-work = 0.1121, R-free = 0.1601