# Date 2008-01-16 Time 01:40:37 PST -0800 (1200476437.00 s)
#phil __OFF__

Command line arguments: "../522.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31041
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 522

-------------------------------------------------------------------------------
  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: (69.8988, 46.4607, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.98193
Completeness in resolution range: 0.974189
Completeness with d_max=infinity: 0.971147

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9392
                             d_min =   1.9819

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: (69.8988, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.98193
Completeness in resolution range: 0.974189
Completeness with d_max=infinity: 0.971147

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9396 -  4.2404 [2114/2138]  1901   213  10.1%
  bin  2:  4.2404 -  3.3786 [2029/2049]  1827   202  10.0%
  bin  3:  3.3786 -  2.9553 [2000/2019]  1802   198   9.9%
  bin  4:  2.9553 -  2.6868 [1982/2012]  1781   201  10.1%
  bin  5:  2.6868 -  2.4951 [1977/1996]  1779   198  10.0%
  bin  6:  2.4951 -  2.3486 [1966/1991]  1767   199  10.1%
  bin  7:  2.3486 -  2.2314 [1936/1964]  1747   189   9.8%
  bin  8:  2.2314 -  2.1346 [1954/1990]  1758   196  10.0%
  bin  9:  2.1346 -  2.0526 [1936/1978]  1742   194  10.0%
  bin 10:  2.0526 -  1.9819 [1695/1971]  1526   169  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_522/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: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 16
        2.42 -     3.04: 2220
        3.04 -     3.66: 4717
        3.66 -     4.28: 9125
        4.28 -     4.90: 12404
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.184 3.040 -x+1/2,-y+1,z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.190 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.224 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28477 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_522/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_522/model_refine_001.geo

CPU time processing inputs: 9.41


============================ 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 = 69.89875 46.4607 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4321   r_free= 0.4200   ksol= 0.00   Bsol= 0.00   scale= 0.828    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.227006                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7294 0.99   1376  152 0.3631 0.3553      6.5171      6.4889|
|  2:  4.7294 -  3.7738 0.99   1316  148 0.3303 0.3157      6.6486      6.6205|
|  3:  3.7738 -  3.3026 0.99   1293  144 0.3629 0.3437      6.5473      6.5609|
|  4:  3.3026 -  3.0033 0.99   1285  142 0.4083 0.3827      6.4569      6.3827|
|  5:  3.0033 -  2.7896 0.99   1271  141 0.4578 0.4489      6.3188      6.3485|
|  6:  2.7896 -  2.6260 0.99   1285  141 0.4537 0.5321      6.2411      6.1989|
|  7:  2.6260 -  2.4951 0.99   1264  144 0.4703 0.4401      6.2029      6.1662|
|  8:  2.4951 -  2.3870 0.98   1265  136 0.4895 0.4487      6.1596      6.1778|
|  9:  2.3870 -  2.2954 0.98   1256  141 0.4661 0.5025      6.0806      6.0928|
| 10:  2.2954 -  2.2165 1.00   1257  143 0.4999 0.4596      6.1163      6.0387|
| 11:  2.2165 -  2.1474 0.97   1252  136 0.4961 0.4191      6.0372      5.9791|
| 12:  2.1474 -  2.0862 0.98   1247  139 0.4889 0.4624      5.9818      5.9791|
| 13:  2.0862 -  2.0314 0.99   1250  138 0.4971 0.4927      5.8823      5.8697|
| 14:  2.0314 -  1.9819 0.80   1013  114 0.5186 0.5139      5.8468      5.7642|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7294  1376   152  0.73  31.97   0.81     0.76      62336.20|
|  2:  4.7294 -  3.7738  1316   148  0.78  28.42   0.92     0.84      73902.52|
|  3:  3.7738 -  3.3026  1293   144  0.71  34.44   0.89     0.81      76340.76|
|  4:  3.3026 -  3.0033  1285   142  0.65  40.08   0.84     0.71      70080.20|
|  5:  3.0033 -  2.7896  1271   141  0.54  48.68   0.78     0.62      63554.45|
|  6:  2.7896 -  2.6260  1285   141  0.51  51.21   0.76     0.57      58911.94|
|  7:  2.6260 -  2.4951  1264   144  0.48  53.57   0.77     0.55      55317.41|
|  8:  2.4951 -  2.3870  1265   136  0.48  53.96   0.76     0.55      49766.24|
|  9:  2.3870 -  2.2954  1256   141  0.52  50.64   0.76     0.58      41790.95|
| 10:  2.2954 -  2.2165  1257   143  0.53  49.72   0.78     0.60      35503.45|
| 11:  2.2165 -  2.1474  1252   136  0.54  49.40   0.77     0.62      32883.80|
| 12:  2.1474 -  2.0862  1247   139  0.49  53.40   0.81     0.58      33640.37|
| 13:  2.0862 -  2.0314  1250   138  0.44  57.37   0.76     0.52      31369.16|
| 14:  2.0314 -  1.9819  1013   114  0.43  58.17   0.74     0.46      26281.85|
|alpha:            min =        0.46 max =            0.84 mean =         0.63|
|beta:             min =    26281.85 max =        76340.76 mean =     51458.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.99 mean =        46.87|
|phase err.(test): min =        0.00 max =           89.90 mean =        47.01|
|-----------------------------------------------------------------------------|

============================== 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 = 7.505232              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.296   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.667630              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.599   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      691 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1511 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2668 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3951 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5106 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6612 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7759 |
|-----------------------------------------------------------------------------|
|-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 |       53.462 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.780 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.727)------------------------------------------|
|    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 = 11.727)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4412   r_free= 0.4266   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.232704                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4244   r_free= 0.4085   ksol= 0.36   Bsol= 16.87   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.20,9.44,8.00,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.220416                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.912727              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.070   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.627974              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.713   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4244      final r-factor (work) = 0.3173          |
| start r-factor (free) = 0.4085      final r-factor (free) = 0.3372          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.0292 = 6.91 * 0.50 * 6.2398 + 1.00 * 53.4622                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0946 = 6.91 * 0.50 * 6.0695 + 1.00 * 0.1161                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3173      final r-factor (work) = 0.2527          |
| start r-factor (free) = 0.3372      final r-factor (free) = 0.2899          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8262 = 0.63 * 1.00 * 6.0695 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7089 = 0.63 * 1.00 * 5.8864 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.727)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.36   10.86    None  None   None       |
|    all(noH): 2823   0      0.00    68.36   10.86    None  None   None       |
|    Sol.    : 438    0      0.00    64.70   27.36    None  None   None       |
|    Mac.    : 2385   0      0.00    68.36   7.83     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.836: 1379   |   5:    34.178 -  41.014:   98        |
|      1:     6.836 -  13.671:  737   |   6:    41.014 -  47.849:   40        |
|      2:    13.671 -  20.507:  248   |   7:    47.849 -  54.685:   17        |
|      3:    20.507 -  27.343:  181   |   8:    54.685 -  61.521:    7        |
|      4:    27.343 -  34.178:  113   |   9:    61.521 -  68.356:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2527 r_free = 0.2899             target_work(ml) = 5.821         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2521 r_free = 0.2895             target_work(ml) = 5.819         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2521   r_free= 0.2895   ksol= 0.36   Bsol= 16.87   scale= 1.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.20,9.44,8.00,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.819352                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2467   r_free= 0.2816   ksol= 0.34   Bsol= 35.07   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.83,5.06,4.95,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.816060                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.272456              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.488   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.356328              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.095  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2467      final r-factor (work) = 0.1651          |
| start r-factor (free) = 0.2816      final r-factor (free) = 0.2075          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7624 = 3.27 * 0.50 * 5.8958 + 1.00 * 0.1156                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2634 = 3.27 * 0.50 * 5.6233 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1651      final r-factor (work) = 0.1487          |
| start r-factor (free) = 0.2075      final r-factor (free) = 0.1925          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0159 = 0.36 * 1.00 * 5.6233 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9400 = 0.36 * 1.00 * 5.4079 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.727)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.18   11.14    None  None   None       |
|    all(noH): 2823   0      0.00    70.18   11.14    None  None   None       |
|    Sol.    : 438    0      1.16    67.11   31.50    None  None   None       |
|    Mac.    : 2385   0      0.00    70.18   7.40     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.018: 1539   |   5:    35.091 -  42.109:  136        |
|      1:     7.018 -  14.036:  619   |   6:    42.109 -  49.127:   67        |
|      2:    14.036 -  21.054:  199   |   7:    49.127 -  56.145:   25        |
|      3:    21.054 -  28.073:  116   |   8:    56.145 -  63.163:    6        |
|      4:    28.073 -  35.091:  113   |   9:    63.163 -  70.181:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1487 r_free = 0.1925             target_work(ml) = 5.373         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1485 r_free = 0.1921             target_work(ml) = 5.372         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1485   r_free= 0.1921   ksol= 0.34   Bsol= 35.07   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.83,5.06,4.95,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.371787                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1483   r_free= 0.1913   ksol= 0.32   Bsol= 35.07   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.48,4.45,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.370660                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.769978              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.663  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.166670              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.483   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1483      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1913      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5598 = 2.77 * 0.50 * 5.4132 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3770 = 2.77 * 0.50 * 5.2822 + 1.00 * 0.0612                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1222      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1654      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4566 = 2.17 * 1.00 * 5.2822 + 1.00 * 0.0118                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2471 = 2.17 * 1.00 * 5.1842 + 1.00 * 0.0146                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.727)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.17   11.87    None  None   None       |
|    all(noH): 2823   0      0.00    84.17   11.87    None  None   None       |
|    Sol.    : 438    0      0.66    76.61   35.59    None  None   None       |
|    Mac.    : 2385   0      0.00    84.17   7.51     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 -   8.417: 1746   |   5:    42.086 -  50.503:   91        |
|      1:     8.417 -  16.834:  507   |   6:    50.503 -  58.920:   62        |
|      2:    16.834 -  25.251:  158   |   7:    58.920 -  67.337:   34        |
|      3:    25.251 -  33.669:  110   |   8:    67.337 -  75.754:    8        |
|      4:    33.669 -  42.086:  104   |   9:    75.754 -  84.171:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1613             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1166 r_free = 0.1612             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1612   ksol= 0.32   Bsol= 35.07   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.48,4.45,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170877                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1610   ksol= 0.31   Bsol= 35.07   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.48,4.45,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170611                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.583979              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.129  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.281564              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.604  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1610      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7587 = 2.58 * 0.50 * 5.1840 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7144 = 2.58 * 0.50 * 5.1478 + 1.00 * 0.0635                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4647 = 0.28 * 1.00 * 5.1478 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4670 = 0.28 * 1.00 * 5.1368 + 1.00 * 0.0206                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.727)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.05   11.27    None  None   None       |
|    all(noH): 2823   0      0.00    84.05   11.27    None  None   None       |
|    Sol.    : 438    0      1.11    72.84   33.09    None  None   None       |
|    Mac.    : 2385   0      0.00    84.05   7.27     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 -   8.405: 1798   |   5:    42.024 -  50.429:   77        |
|      1:     8.405 -  16.810:  490   |   6:    50.429 -  58.834:   53        |
|      2:    16.810 -  25.215:  130   |   7:    58.834 -  67.239:   17        |
|      3:    25.215 -  33.619:  146   |   8:    67.239 -  75.643:    5        |
|      4:    33.619 -  42.024:  105   |   9:    75.643 -  84.048:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1105 r_free = 0.1553             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1103 r_free = 0.1552             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1552   ksol= 0.31   Bsol= 35.07   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.48,4.45,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.128947                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1551   ksol= 0.32   Bsol= 35.07   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,3.24,4.49,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.128671                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.648141              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.439  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.506363              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.427   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8636 = 2.65 * 0.50 * 5.1358 + 1.00 * 0.0635                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8456 = 2.65 * 0.50 * 5.1205 + 1.00 * 0.0657                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1085      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6113 = 0.51 * 1.00 * 5.1205 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6023 = 0.51 * 1.00 * 5.1163 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.727)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.80   11.21    None  None   None       |
|    all(noH): 2823   0      0.00    85.80   11.21    None  None   None       |
|    Sol.    : 438    0      1.06    73.54   33.01    None  None   None       |
|    Mac.    : 2385   0      0.00    85.80   7.21     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 -   8.580: 1811   |   5:    42.899 -  51.479:   85        |
|      1:     8.580 -  17.160:  484   |   6:    51.479 -  60.058:   38        |
|      2:    17.160 -  25.739:  144   |   7:    60.058 -  68.638:   17        |
|      3:    25.739 -  34.319:  133   |   8:    68.638 -  77.218:    4        |
|      4:    34.319 -  42.899:  104   |   9:    77.218 -  85.798:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1079 r_free = 0.1547             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1079 r_free = 0.1547             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1547   ksol= 0.32   Bsol= 35.07   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,3.24,4.49,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118017                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7294 0.99   1376  152 0.0974 0.1251      5.3602      5.4954|
|  2:  4.7294 -  3.7738 0.99   1316  148 0.0826 0.1127      5.4147      5.6318|
|  3:  3.7738 -  3.3026 0.99   1293  144 0.1028 0.1450      5.4544      5.8159|
|  4:  3.3026 -  3.0033 0.99   1285  142 0.1165 0.1602      5.4253      5.5758|
|  5:  3.0033 -  2.7896 0.99   1271  141 0.1269 0.1666       5.316      5.5488|
|  6:  2.7896 -  2.6260 0.99   1285  141 0.1154 0.1919      5.1901      5.4656|
|  7:  2.6260 -  2.4951 0.99   1264  144 0.1233 0.1574      5.1542      5.3352|
|  8:  2.4951 -  2.3870 0.98   1265  136 0.1126 0.1712      5.0538      5.3633|
|  9:  2.3870 -  2.2954 0.98   1256  141 0.1122 0.1746      5.0151      5.2517|
| 10:  2.2954 -  2.2165 1.00   1257  143 0.1072 0.1683      4.9342      5.2162|
| 11:  2.2165 -  2.1474 0.97   1252  136 0.1076 0.1668      4.9167      5.2125|
| 12:  2.1474 -  2.0862 0.98   1247  139 0.1090 0.1697       4.852      5.2243|
| 13:  2.0862 -  2.0314 0.99   1250  138 0.1072 0.1562      4.7659      4.9945|
| 14:  2.0314 -  1.9819 0.80   1013  114 0.0989 0.1765      4.6461      4.9491|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7294  1376   152  0.94   8.76   0.98     0.96       6782.34|
|  2:  4.7294 -  3.7738  1316   148  0.96   7.56   1.02     1.01       8677.12|
|  3:  3.7738 -  3.3026  1293   144  0.94  10.75   1.03     1.02       9919.37|
|  4:  3.3026 -  3.0033  1285   142  0.92  13.02   1.01     0.99       9845.45|
|  5:  3.0033 -  2.7896  1271   141  0.91  15.38   1.00     0.97       8247.32|
|  6:  2.7896 -  2.6260  1285   141  0.90  15.75   0.98     0.95       6964.11|
|  7:  2.6260 -  2.4951  1264   144  0.91  15.55   0.99     0.96       6111.27|
|  8:  2.4951 -  2.3870  1265   136  0.91  14.52   0.99     0.97       5086.18|
|  9:  2.3870 -  2.2954  1256   141  0.91  15.07   1.01     0.98       4914.01|
| 10:  2.2954 -  2.2165  1257   143  0.91  15.04   1.00     0.97       4185.22|
| 11:  2.2165 -  2.1474  1252   136  0.90  15.90   1.00     0.97       4291.01|
| 12:  2.1474 -  2.0862  1247   139  0.91  14.80   1.02     1.01       3730.49|
| 13:  2.0862 -  2.0314  1250   138  0.91  15.30   1.01     0.99       3198.68|
| 14:  2.0314 -  1.9819  1013   114  0.92  13.85   0.99     0.96       2486.16|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2486.16 max =         9919.37 mean =      6114.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.74 mean =        13.60|
|phase err.(test): min =        0.00 max =           89.87 mean =        13.22|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1546   ksol= 0.32   Bsol= 43.59   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.58,-0.37,0.95,-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: 5.117559                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1546   ksol= 0.32   Bsol= 43.59   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.58,-0.37,0.95,-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: 5.117559                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7294 0.99   1376  152 0.0977 0.1255      5.3626       5.498|
|  2:  4.7294 -  3.7738 0.99   1316  148 0.0830 0.1133      5.4182      5.6354|
|  3:  3.7738 -  3.3026 0.99   1293  144 0.1031 0.1450       5.456      5.8173|
|  4:  3.3026 -  3.0033 0.99   1285  142 0.1163 0.1597      5.4244      5.5735|
|  5:  3.0033 -  2.7896 0.99   1271  141 0.1267 0.1664       5.314      5.5468|
|  6:  2.7896 -  2.6260 0.99   1285  141 0.1150 0.1914      5.1876      5.4634|
|  7:  2.6260 -  2.4951 0.99   1264  144 0.1231 0.1572      5.1521      5.3335|
|  8:  2.4951 -  2.3870 0.98   1265  136 0.1124 0.1710      5.0523      5.3612|
|  9:  2.3870 -  2.2954 0.98   1256  141 0.1120 0.1746      5.0141      5.2519|
| 10:  2.2954 -  2.2165 1.00   1257  143 0.1071 0.1681      4.9336      5.2156|
| 11:  2.2165 -  2.1474 0.97   1252  136 0.1075 0.1667      4.9158      5.2116|
| 12:  2.1474 -  2.0862 0.98   1247  139 0.1090 0.1696      4.8515      5.2241|
| 13:  2.0862 -  2.0314 0.99   1250  138 0.1071 0.1562       4.765      4.9938|
| 14:  2.0314 -  1.9819 0.80   1013  114 0.0989 0.1760      4.6442      4.9467|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7294  1376   152  0.94   8.82   0.98     0.96       6828.08|
|  2:  4.7294 -  3.7738  1316   148  0.96   7.58   1.02     1.01       8723.78|
|  3:  3.7738 -  3.3026  1293   144  0.94  10.77   1.03     1.02       9948.12|
|  4:  3.3026 -  3.0033  1285   142  0.92  13.00   1.01     0.99       9826.18|
|  5:  3.0033 -  2.7896  1271   141  0.91  15.35   1.00     0.97       8213.73|
|  6:  2.7896 -  2.6260  1285   141  0.90  15.71   0.99     0.96       6933.14|
|  7:  2.6260 -  2.4951  1264   144  0.91  15.51   0.99     0.96       6080.21|
|  8:  2.4951 -  2.3870  1265   136  0.91  14.49   1.00     0.97       5069.87|
|  9:  2.3870 -  2.2954  1256   141  0.91  15.05   1.01     0.99       4904.71|
| 10:  2.2954 -  2.2165  1257   143  0.91  15.03   1.01     0.97       4180.40|
| 11:  2.2165 -  2.1474  1252   136  0.90  15.89   1.00     0.97       4284.57|
| 12:  2.1474 -  2.0862  1247   139  0.91  14.78   1.02     1.01       3724.03|
| 13:  2.0862 -  2.0314  1250   138  0.91  15.28   1.01     1.00       3189.77|
| 14:  2.0314 -  1.9819  1013   114  0.92  13.81   0.99     0.96       2473.94|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2473.94 max =         9948.12 mean =      6110.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.59|
|phase err.(test): min =        0.00 max =           89.96 mean =        13.20|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.727)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.60    89.40   14.81    None  None   None       |
|    all(noH): 2823   0      3.60    89.40   14.81    None  None   None       |
|    Sol.    : 438    0      4.67    77.14   36.61    None  None   None       |
|    Mac.    : 2385   0      3.60    89.40   10.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.601 -  12.181: 1811   |   5:    46.500 -  55.079:   85        |
|      1:    12.181 -  20.760:  484   |   6:    55.079 -  63.659:   38        |
|      2:    20.760 -  29.340:  144   |   7:    63.659 -  72.239:   17        |
|      3:    29.340 -  37.920:  133   |   8:    72.239 -  80.819:    4        |
|      4:    37.920 -  46.500:  104   |   9:    80.819 -  89.398:    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)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.338 - 4.171
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 307
   mapped sites are within: 0.708 - 4.171

peak=   11.463 closest distance to " CB  VAL A 230 " =    1.457
peak=    8.340 closest distance to " CG2 VAL A 296 " =    1.213
peak=    6.434 closest distance to " CG  LEU A   5 " =    1.179
peak=    5.984 closest distance to " NE2 GLN A  11 " =    1.216
peak=    5.678 closest distance to " CG  PRO A  54 " =    1.273
peak=    5.624 closest distance to " CD2 LEU A   5 " =    1.198
peak=    5.615 closest distance to " O   HOH Z 142 " =    1.911
peak=    5.522 closest distance to " CG  LEU A 228 " =    1.140
peak=    5.414 closest distance to " NH2 ARG A  56 " =    2.118
peak=    5.014 closest distance to " CB  GLN A 183 " =    1.231
peak=    4.868 closest distance to " CB  GLN A 223 " =    1.500
peak=    4.852 closest distance to " CB  ARG A 275 " =    0.923
peak=    4.832 closest distance to " CB  VAL A 296 " =    1.058
peak=    4.762 closest distance to " O   HOH Z 209 " =    2.268
peak=    4.731 closest distance to " CB  SER A  63 " =    1.241
peak=    4.713 closest distance to " O   HOH Z 232 " =    2.375
peak=    4.713 closest distance to " CB  PRO A  54 " =    0.950
peak=    4.678 closest distance to " O   HOH Z 427 " =    2.831
peak=    4.669 closest distance to " CB  VAL A 230 " =    1.162
peak=    4.665 closest distance to " O   HOH Z 126 " =    1.899
peak=    4.623 closest distance to " O   HOH Z   9 " =    1.283
peak=    4.623 closest distance to " O   HOH Z 346 " =    1.596
peak=    4.560 closest distance to " C   PRO A 198 " =    1.446
peak=    4.535 closest distance to " CB  ARG A  79 " =    1.421
peak=    4.477 closest distance to " O   SER A  87 " =    2.331
peak=    4.438 closest distance to " CG  PRO A 213 " =    1.216
peak=    4.437 closest distance to " O   HOH Z 193 " =    1.741
peak=    4.379 closest distance to " ND2 ASN A 187 " =    1.509
peak=    4.360 closest distance to " O   HOH Z 272 " =    1.826
peak=    4.320 closest distance to " CB  GLU A 152 " =    1.224
peak=    4.304 closest distance to " O   HOH Z  61 " =    1.659
peak=    4.303 closest distance to " O   HOH Z 236 " =    1.974
peak=    4.236 closest distance to " OG ASER A 258 " =    3.054
peak=    4.231 closest distance to " O   HOH Z 203 " =    1.679
peak=    4.215 closest distance to " CB  VAL A 265 " =    1.334
peak=    4.196 closest distance to " O   HOH Z 369 " =    2.118
peak=    4.184 closest distance to " O   HOH Z 265 " =    2.403
peak=    4.125 closest distance to " O   HOH Z 158 " =    3.190
peak=    4.122 closest distance to " CB  SER A   3 " =    1.293
peak=    4.099 closest distance to " CB  ASN A 148 " =    1.362
peak=    4.085 closest distance to " O   HOH Z 303 " =    2.087
peak=    4.064 closest distance to " O   HOH Z 368 " =    2.049
peak=    4.057 closest distance to " CG  PRO A 243 " =    1.101
peak=    4.054 closest distance to " OD1 ASN A  69 " =    2.619
peak=    4.042 closest distance to " CB  TRP A 266 " =    1.029
peak=    4.035 closest distance to " O   HOH Z 298 " =    1.725
peak=    4.023 closest distance to " CD2 LEU A 228 " =    1.151
peak=    3.999 closest distance to " O   HOH Z 189 " =    2.845
peak=    3.992 closest distance to " O   HOH Z  78 " =    1.668
peak=    3.970 closest distance to " CG1BVAL A  72 " =    1.548
peak=    3.962 closest distance to " O   HOH Z 234 " =    3.545
peak=    3.949 closest distance to " O   HOH Z 126 " =    1.569
peak=    3.949 closest distance to " O   HOH Z 423 " =    1.784
peak=    3.922 closest distance to " OG BSER A 164 " =    2.122
peak=    3.917 closest distance to " CB  ASN A  39 " =    0.891
peak=    3.905 closest distance to " CB  TRP A 179 " =    1.318
peak=    3.902 closest distance to " O   HOH Z   9 " =    2.012
peak=    3.901 closest distance to " O   HOH Z 261 " =    2.112
peak=    3.889 closest distance to " CZ  PHE A 218 " =    1.124
peak=    3.886 closest distance to " O   HOH Z 147 " =    1.774
peak=    3.885 closest distance to " O   HOH Z 403 " =    1.655
peak=    3.883 closest distance to " CG  ARG A  66 " =    2.696
peak=    3.878 closest distance to " O   HOH Z  43 " =    1.929
peak=    3.871 closest distance to " CA  TYR A  30 " =    0.989
peak=    3.866 closest distance to " O   HOH Z 389 " =    1.858
peak=    3.853 closest distance to " O   HOH Z 130 " =    2.178
peak=    3.840 closest distance to " CG2 VAL A 257 " =    0.825
peak=    3.838 closest distance to " N   PHE A 130 " =    1.261
peak=    3.837 closest distance to " CB  GLU A 277 " =    3.540
peak=    3.828 closest distance to " CB  VAL A 202 " =    1.565
peak=    3.821 closest distance to " O   HOH Z 193 " =    1.740
peak=    3.814 closest distance to " O   HOH Z 371 " =    2.942
peak=    3.802 closest distance to " O   HOH Z 126 " =    1.506
peak=    3.801 closest distance to " O   HOH Z 411 " =    3.805
peak=    3.784 closest distance to " O   HOH Z 145 " =    2.020
peak=    3.763 closest distance to " O   HOH Z 193 " =    1.906
peak=    3.763 closest distance to " CA  ASN A 215 " =    1.081
peak=    3.753 closest distance to " CB  GLU A 128 " =    0.986
peak=    3.747 closest distance to " O   HOH Z 313 " =    1.859
peak=    3.727 closest distance to " O   HOH Z  10 " =    1.790
peak=    3.715 closest distance to " O   HOH Z 423 " =    2.755
peak=    3.713 closest distance to " O   HOH Z  66 " =    2.271
peak=    3.709 closest distance to " CA  ASP A 162 " =    1.034
peak=    3.707 closest distance to " CB  ASN A 142 " =    1.000
peak=    3.704 closest distance to " CB  ALA A   9 " =    1.575
peak=    3.697 closest distance to " O   HOH Z  97 " =    2.453
peak=    3.692 closest distance to " CD2 TRP A 179 " =    1.356
peak=    3.686 closest distance to " O   HOH Z 402 " =    1.414
peak=    3.683 closest distance to " O   HOH Z 128 " =    2.084
peak=    3.677 closest distance to " CA  PHE A 283 " =    1.249
peak=    3.676 closest distance to " CB  ASP A 140 " =    0.892
peak=    3.666 closest distance to " CG  LEU A 167 " =    1.210
peak=    3.666 closest distance to " CB  ARG A 190 " =    1.566
peak=    3.663 closest distance to " CB  SER A  26 " =    1.668
peak=    3.652 closest distance to " O   HOH Z  97 " =    1.971
peak=    3.648 closest distance to " O   HOH Z 214 " =    2.112
peak=    3.646 closest distance to " CB AVAL A  41 " =    1.198
peak=    3.644 closest distance to " O   HOH Z 425 " =    1.355
peak=    3.644 closest distance to " O   HOH Z 180 " =    2.119
peak=    3.643 closest distance to " O   HOH Z 392 " =    3.121
peak=    3.637 closest distance to " CB  SER A 216 " =    0.794
peak=    3.636 closest distance to " O   HOH Z   3 " =    1.953
peak=    3.630 closest distance to " NZ  LYS A 117 " =    3.267
peak=    3.630 closest distance to " O   HOH Z 250 " =    1.374
peak=    3.627 closest distance to " CB  ARG A 139 " =    0.982
peak=    3.624 closest distance to " O   HOH Z 425 " =    2.080
peak=    3.622 closest distance to " O   HOH Z 273 " =    2.754
peak=    3.621 closest distance to " CG  PRO A 198 " =    1.205
peak=    3.616 closest distance to " N   ASN A  39 " =    1.185
peak=    3.616 closest distance to " O   HOH Z  30 " =    1.427
peak=    3.611 closest distance to " O   HOH Z   1 " =    1.840
peak=    3.606 closest distance to " CB  ASN A 187 " =    1.150
peak=    3.602 closest distance to " CB  LEU A 143 " =    1.150
peak=    3.593 closest distance to " O   HOH Z 419 " =    1.930
peak=    3.591 closest distance to " O   HOH Z 422 " =    2.581
peak=    3.589 closest distance to " O   HOH Z  59 " =    1.840
peak=    3.588 closest distance to " O   HOH Z 145 " =    3.475
peak=    3.571 closest distance to " O   HOH Z  44 " =    1.670
peak=    3.566 closest distance to " CA  ALA A  51 " =    0.974
peak=    3.565 closest distance to " O   HOH Z 280 " =    2.990
peak=    3.560 closest distance to " CA  ALA A 158 " =    1.294
peak=    3.553 closest distance to " CA  LYS A 117 " =    1.189
peak=    3.552 closest distance to " CA  ALA A  21 " =    1.172
peak=    3.547 closest distance to " O   HOH Z  40 " =    1.953
peak=    3.545 closest distance to " CB  THR A 157 " =    1.153
peak=    3.545 closest distance to " O   HOH Z 353 " =    2.532
peak=    3.545 closest distance to " CG1 ILE A  49 " =    1.418
peak=    3.544 closest distance to " O   HOH Z  88 " =    2.959
peak=    3.543 closest distance to " O   GLN A 278 " =    1.280
peak=    3.539 closest distance to " O   HOH Z 248 " =    1.542
peak=    3.538 closest distance to " O   HOH Z 124 " =    1.309
peak=    3.522 closest distance to " CB  SER A 212 " =    1.129
peak=    3.521 closest distance to " O   HOH Z   1 " =    1.746
peak=    3.517 closest distance to " O   HOH Z  61 " =    1.510
peak=    3.504 closest distance to " OD2 ASP A 286 " =    2.730
peak=    3.502 closest distance to " CB  ASN A 148 " =    1.912
peak=    3.495 closest distance to " O   HOH Z 132 " =    2.544
peak=    3.494 closest distance to " CD1 LEU A 228 " =    2.044
peak=    3.493 closest distance to " O   HOH Z 234 " =    1.841
peak=    3.492 closest distance to " CD BLYS A 290 " =    1.207
peak=    3.488 closest distance to " CD1 ILE A 106 " =    1.045
peak=    3.481 closest distance to " O   HOH Z 322 " =    2.006
peak=    3.479 closest distance to " NH2 ARG A 156 " =    1.103
peak=    3.474 closest distance to " O   HOH Z 263 " =    1.636
peak=    3.473 closest distance to " CD  LYS A 166 " =    1.315
peak=    3.471 closest distance to " CG1 VAL A 153 " =    0.932
peak=    3.470 closest distance to " CE  LYS A  76 " =    0.901
peak=    3.469 closest distance to " CD1 ILE A  33 " =    1.659
peak=    3.467 closest distance to " O   HOH Z 407 " =    2.338
peak=    3.464 closest distance to " CA  ALA A 291 " =    0.906
peak=    3.463 closest distance to " O   HOH Z  78 " =    2.113
peak=    3.463 closest distance to " O   HOH Z 175 " =    2.043
peak=    3.461 closest distance to " CB  ILE A  20 " =    1.516
peak=    3.460 closest distance to " CB  ASN A 110 " =    1.086
peak=    3.460 closest distance to " O   HOH Z 128 " =    2.117
peak=    3.459 closest distance to " O   HOH Z 286 " =    2.327
peak=    3.455 closest distance to " O   HOH Z  40 " =    2.138
peak=    3.455 closest distance to " O   HOH Z 371 " =    1.651
peak=    3.450 closest distance to " O   HOH Z  89 " =    2.154
peak=    3.447 closest distance to " ND1 HIS A  86 " =    1.718
peak=    3.447 closest distance to " CB  HIS A 108 " =    0.818
peak=    3.444 closest distance to " CG1 ILE A  33 " =    1.294
peak=    3.434 closest distance to " O  BHOH Z 338 " =    2.403
peak=    3.431 closest distance to " O   HOH Z 148 " =    3.380
peak=    3.430 closest distance to " CE1 TYR A 186 " =    1.369
peak=    3.425 closest distance to " CB  ASN A 224 " =    1.049
peak=    3.416 closest distance to " CG  GLN A  88 " =    1.076
peak=    3.415 closest distance to " O   HOH Z 213 " =    1.998
peak=    3.415 closest distance to " N   ARG A 156 " =    1.320
peak=    3.414 closest distance to " CA  THR A 264 " =    0.777
peak=    3.412 closest distance to " O   HOH Z 344 " =    3.029
peak=    3.412 closest distance to " CG  MET A 185 " =    1.230
peak=    3.411 closest distance to " CA  VAL A  41 " =    0.795
peak=    3.399 closest distance to " O   HOH Z 435 " =    1.997
peak=    3.398 closest distance to " O   HOH Z 112 " =    1.656
peak=    3.393 closest distance to " O   HOH Z 368 " =    3.630
peak=    3.392 closest distance to " CB  THR A  31 " =    1.608
peak=    3.389 closest distance to " O   HOH Z   2 " =    1.491
peak=    3.384 closest distance to " NH1AARG A 145 " =    1.076
peak=    3.384 closest distance to " CA  SER A 146 " =    1.727
peak=    3.382 closest distance to " O   HOH Z  21 " =    1.707
peak=    3.380 closest distance to " O   HOH Z 380 " =    1.701
peak=    3.371 closest distance to " O   HOH Z 305 " =    3.576
peak=    3.371 closest distance to " CB  ALA A 248 " =    1.359
peak=    3.369 closest distance to " O   HOH Z 291 " =    1.513
peak=    3.367 closest distance to " O   LYS A 290 " =    2.384
peak=    3.365 closest distance to " O   HOH Z 366 " =    2.860
peak=    3.362 closest distance to " CB  ALA A 291 " =    1.427
peak=    3.356 closest distance to " CG BARG A 102 " =    1.827
peak=    3.356 closest distance to " CB  LYS A 117 " =    1.214
peak=    3.352 closest distance to " O   HOH Z 245 " =    1.383
peak=    3.352 closest distance to " O   HOH Z 299 " =    4.171
peak=    3.348 closest distance to " CA  ARG A  36 " =    1.016
peak=    3.347 closest distance to " CG2 ILE A 120 " =    1.219
peak=    3.345 closest distance to " CB  ALA A 233 " =    1.313
peak=    3.345 closest distance to " O   HOH Z 417 " =    3.419
peak=    3.344 closest distance to " CG2 THR A 221 " =    1.259
peak=    3.336 closest distance to " O   HOH Z 359 " =    3.670
peak=    3.330 closest distance to " O   HOH Z  88 " =    2.535
peak=    3.326 closest distance to " CB  LYS A 290 " =    0.988
peak=    3.326 closest distance to " CB  ALA A  34 " =    1.038
peak=    3.322 closest distance to " OE1 GLU A   2 " =    2.041
peak=    3.317 closest distance to " O   HOH Z 222 " =    2.472
peak=    3.317 closest distance to " CD1 LEU A 300 " =    1.271
peak=    3.307 closest distance to " CG  GLN A  77 " =    2.294
peak=    3.300 closest distance to " CB  GLU A  46 " =    1.048
peak=    3.299 closest distance to " CB  GLN A 278 " =    0.908
peak=    3.299 closest distance to " O   HOH Z 426 " =    1.866
peak=    3.299 closest distance to " NH2BARG A 145 " =    2.023
peak=    3.298 closest distance to " CB  TRP A 150 " =    1.441
peak=    3.297 closest distance to " O   HOH Z 437 " =    1.903
peak=    3.297 closest distance to " O   HOH Z 227 " =    1.747
peak=    3.296 closest distance to " O   ASP A 124 " =    1.095
peak=    3.295 closest distance to " CB  GLN A  88 " =    1.201
peak=    3.294 closest distance to " O   HOH Z 329 " =    3.935
peak=    3.286 closest distance to " O   HOH Z 303 " =    3.021
peak=    3.280 closest distance to " CA  ALA A 233 " =    1.118
peak=    3.279 closest distance to " CA  ALA A 299 " =    0.968
peak=    3.278 closest distance to " CB  MET A  40 " =    0.834
peak=    3.278 closest distance to " O   HOH Z 337 " =    3.590
peak=    3.274 closest distance to " CG  MET A 185 " =    1.031
peak=    3.273 closest distance to " N   VAL A 126 " =    1.286
peak=    3.269 closest distance to " CB  GLN A 205 " =    1.198
peak=    3.265 closest distance to " CG  MET A 113 " =    1.051
peak=    3.263 closest distance to " O   HOH Z 109 " =    2.509
peak=    3.262 closest distance to " O   HOH Z 345 " =    3.274
peak=    3.258 closest distance to " N   SER A 135 " =    1.273
peak=    3.252 closest distance to " CA  TYR A  30 " =    1.056
peak=    3.252 closest distance to " O   HOH Z 251 " =    1.652
peak=    3.249 closest distance to " CA  ARG A 195 " =    1.180
peak=    3.247 closest distance to " O   HOH Z  85 " =    1.308
peak=    3.246 closest distance to " CG2 THR A 294 " =    1.664
peak=    3.241 closest distance to " O   HOH Z 421 " =    1.891
peak=    3.238 closest distance to " O   HOH Z 128 " =    1.915
peak=    3.236 closest distance to " O   HOH Z 424 " =    1.459
peak=    3.236 closest distance to " CD  LYS A 119 " =    1.463
peak=    3.231 closest distance to " O   HOH Z 261 " =    1.498
peak=    3.230 closest distance to " O   PRO A  90 " =    1.407
peak=    3.228 closest distance to " CB  SER A 273 " =    0.832
peak=    3.223 closest distance to " CG2 ILE A  20 " =    1.497
peak=    3.221 closest distance to " NH1 ARG A 138 " =    1.142
peak=    3.220 closest distance to " O   HOH Z 133 " =    2.481
peak=    3.217 closest distance to " CB  LEU A 228 " =    1.254
peak=    3.216 closest distance to " CG  LYS A 119 " =    1.100
peak=    3.215 closest distance to " O   HOH Z 303 " =    1.768
peak=    3.214 closest distance to " OG  SER A  22 " =    2.771
peak=    3.214 closest distance to " CD1 ILE A 263 " =    1.341
peak=    3.212 closest distance to " O   HOH Z 409 " =    3.050
peak=    3.212 closest distance to " CG1 ILE A 151 " =    1.037
peak=    3.211 closest distance to " O   MET A 105 " =    1.825
peak=    3.209 closest distance to " O   TRP A 274 " =    1.842
peak=    3.207 closest distance to " CB  ALA A 248 " =    0.977
peak=    3.206 closest distance to " O   HOH Z 154 " =    2.125
peak=    3.204 closest distance to " CA  TYR A 116 " =    1.397
peak=    3.195 closest distance to " CA  LYS A 290 " =    1.210
peak=    3.194 closest distance to " OE2 GLU A  53 " =    1.957
peak=    3.189 closest distance to " CD  GLN A 194 " =    1.329
peak=    3.184 closest distance to " O   HOH Z  54 " =    1.569
peak=    3.181 closest distance to " O   HOH Z 172 " =    3.364
peak=    3.181 closest distance to " CB  LEU A 255 " =    0.758
peak=    3.179 closest distance to " N   ASP A 162 " =    1.253
peak=    3.179 closest distance to " O   HOH Z  85 " =    2.135
peak=    3.174 closest distance to " CD1 LEU A 261 " =    1.174
peak=    3.172 closest distance to " O   HOH Z  89 " =    2.318
peak=    3.170 closest distance to " ND1 HIS A  81 " =    1.712
peak=    3.170 closest distance to " O   HOH Z 189 " =    2.648
peak=    3.165 closest distance to " CA  GLY A 267 " =    0.809
peak=    3.164 closest distance to " O   HOH Z 282 " =    1.992
peak=    3.160 closest distance to " O   HOH Z 290 " =    1.040
peak=    3.160 closest distance to " CB  ALA A 242 " =    0.847
peak=    3.155 closest distance to " N   GLN A 278 " =    1.157
peak=    3.153 closest distance to " CA  ASN A 127 " =    1.074
peak=    3.152 closest distance to " O   HOH Z 251 " =    1.514
peak=    3.151 closest distance to " CG1 ILE A 120 " =    1.133
peak=    3.151 closest distance to " CB  SER A  62 " =    1.317
peak=    3.149 closest distance to " O   HOH Z 433 " =    1.789
peak=    3.143 closest distance to " O   HOH Z  53 " =    2.528
peak=    3.140 closest distance to " NZ  LYS A  76 " =    1.483
peak=    3.139 closest distance to " O   HOH Z 116 " =    1.647
peak=    3.137 closest distance to " O   HOH Z 285 " =    2.823
peak=    3.134 closest distance to " O   HOH Z 218 " =    2.281
peak=    3.134 closest distance to " CB  PRO A  90 " =    1.219
peak=    3.132 closest distance to " CD2 LEU A   5 " =    0.708
peak=    3.131 closest distance to " CB  VAL A 268 " =    0.837
peak=    3.129 closest distance to " O   HOH Z 357 " =    1.873
peak=    3.127 closest distance to " O   GLN A  58 " =    1.479
peak=    3.119 closest distance to " CD1 LEU A  96 " =    0.764
peak=    3.117 closest distance to " O   ALA A   1 " =    1.697
peak=    3.116 closest distance to " CD2 TYR A 186 " =    1.029
peak=    3.096 closest distance to " CB  ALA A 114 " =    1.315
peak=    3.096 closest distance to " O   HOH Z 406 " =    1.595
peak=    3.092 closest distance to " CA  MET A 105 " =    0.924
peak=    3.084 closest distance to " O   HOH Z 383 " =    1.785
peak=    3.083 closest distance to " O   HOH Z 374 " =    2.564
peak=    3.081 closest distance to " CG  LEU A 281 " =    1.033
peak=    3.079 closest distance to " CA  SER A  87 " =    0.990
peak=    3.078 closest distance to " O   HOH Z  89 " =    2.161
peak=    3.078 closest distance to " CA  ILE A 106 " =    0.718
peak=    3.076 closest distance to " CA  GLN A 194 " =    1.274
peak=    3.060 closest distance to " CG  LYS A  76 " =    0.928
peak=    3.054 closest distance to " CB  ALA A 114 " =    1.517
peak=    3.054 closest distance to " CB  ASN A 215 " =    1.136
peak=    3.029 closest distance to " OE2 GLU A   2 " =    1.729

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.563 - 5.450
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 200
   mapped sites are within: 0.760 - 5.450

peak=   -5.362 closest distance to " CG2 VAL A 230 " =    0.762
peak=   -4.701 closest distance to " CB  PRO A 243 " =    2.674
peak=   -4.539 closest distance to " OG BSER A 134 " =    1.256
peak=   -4.464 closest distance to " CD  ARG A 156 " =    2.049
peak=   -4.442 closest distance to " SG  CYS A 254 " =    3.285
peak=   -4.329 closest distance to " O   HOH Z 266 " =    4.995
peak=   -4.282 closest distance to " CG  GLN A 223 " =    2.022
peak=   -4.212 closest distance to " C   HIS A 108 " =    1.198
peak=   -4.211 closest distance to " O   HOH Z 435 " =    2.825
peak=   -4.161 closest distance to " CG2 VAL A 296 " =    1.360
peak=   -4.131 closest distance to " O   HOH Z 290 " =    1.151
peak=   -4.097 closest distance to " CB  ALA A 248 " =    2.044
peak=   -4.070 closest distance to " CA  VAL A  67 " =    2.783
peak=   -4.058 closest distance to " CB  PHE A 192 " =    1.897
peak=   -3.999 closest distance to " CD  GLN A  58 " =    1.104
peak=   -3.974 closest distance to " CA  ASN A 110 " =    2.561
peak=   -3.934 closest distance to " CE  MET A 105 " =    2.323
peak=   -3.915 closest distance to " O   VAL A  67 " =    2.585
peak=   -3.913 closest distance to " O   HOH Z 351 " =    1.527
peak=   -3.909 closest distance to " O   HOH Z 114 " =    3.015
peak=   -3.874 closest distance to " O   PRO A 198 " =    1.226
peak=   -3.856 closest distance to " ND2 ASN A  45 " =    1.536
peak=   -3.838 closest distance to " CE2 PHE A 218 " =    2.542
peak=   -3.824 closest distance to " O   HOH Z 389 " =    1.929
peak=   -3.816 closest distance to " O   HOH Z 185 " =    2.292
peak=   -3.805 closest distance to " O   HOH Z  11 " =    1.911
peak=   -3.796 closest distance to " CB  PRO A 280 " =    2.152
peak=   -3.772 closest distance to " CB  ALA A 291 " =    2.319
peak=   -3.772 closest distance to " O   PRO A 163 " =    2.031
peak=   -3.746 closest distance to " N   THR A 157 " =    1.438
peak=   -3.720 closest distance to " CG1 VAL A 112 " =    2.741
peak=   -3.719 closest distance to " O   HOH Z 211 " =    1.586
peak=   -3.707 closest distance to " CB  PRO A 163 " =    2.478
peak=   -3.692 closest distance to " CE2 TYR A  30 " =    2.780
peak=   -3.690 closest distance to " ND2 ASN A 187 " =    1.438
peak=   -3.687 closest distance to " CZ  TYR A 169 " =    1.649
peak=   -3.684 closest distance to " O   HOH Z 231 " =    2.126
peak=   -3.682 closest distance to " N   GLN A  58 " =    1.745
peak=   -3.665 closest distance to " N   HIS A 115 " =    2.108
peak=   -3.659 closest distance to " OD1 ASN A 187 " =    1.682
peak=   -3.658 closest distance to " CB  ASP A 132 " =    2.350
peak=   -3.656 closest distance to " OXT GLY A 302 " =    2.890
peak=   -3.647 closest distance to " O   HOH Z 166 " =    2.258
peak=   -3.645 closest distance to " CG  ASP A 231 " =    0.779
peak=   -3.644 closest distance to " O   ALA A 161 " =    1.684
peak=   -3.643 closest distance to " O   HOH Z 394 " =    1.456
peak=   -3.639 closest distance to " O   SER A  22 " =    2.270
peak=   -3.628 closest distance to " CB  ALA A 248 " =    2.337
peak=   -3.616 closest distance to " O   HOH Z 166 " =    2.059
peak=   -3.612 closest distance to " NH2 ARG A  79 " =    1.942
peak=   -3.591 closest distance to " O   PRO A 198 " =    1.322
peak=   -3.581 closest distance to " CZ  PHE A  59 " =    1.446
peak=   -3.574 closest distance to " O   HOH Z 313 " =    1.611
peak=   -3.571 closest distance to " CB  ASP A 171 " =    2.110
peak=   -3.570 closest distance to " N   ALA A  43 " =    2.580
peak=   -3.564 closest distance to " O   HOH Z 103 " =    1.672
peak=   -3.555 closest distance to " N   ALA A 248 " =    1.735
peak=   -3.555 closest distance to " CZ3 TRP A 179 " =    1.219
peak=   -3.552 closest distance to " C   MET A 188 " =    1.416
peak=   -3.549 closest distance to " ND2 ASN A 249 " =    2.417
peak=   -3.546 closest distance to " CE BMET A  47 " =    1.662
peak=   -3.543 closest distance to " OG  SER A  62 " =    1.517
peak=   -3.525 closest distance to " O   HOH Z  60 " =    2.051
peak=   -3.516 closest distance to " O   VAL A 189 " =    2.543
peak=   -3.514 closest distance to " CB  ALA A  43 " =    2.364
peak=   -3.513 closest distance to " CG2 THR A 178 " =    2.211
peak=   -3.512 closest distance to " O   ARG A 145 " =    1.652
peak=   -3.509 closest distance to " N   ALA A 226 " =    2.002
peak=   -3.505 closest distance to " OG BSER A 134 " =    1.595
peak=   -3.504 closest distance to " OG  SER A  87 " =    1.376
peak=   -3.503 closest distance to " O   HOH Z 140 " =    1.788
peak=   -3.502 closest distance to " CG  TRP A 266 " =    1.855
peak=   -3.497 closest distance to " NE2 GLN A  88 " =    1.901
peak=   -3.493 closest distance to " CG  PHE A 283 " =    2.617
peak=   -3.483 closest distance to " CG2 VAL A 202 " =    2.672
peak=   -3.482 closest distance to " O   HOH Z 166 " =    1.467
peak=   -3.473 closest distance to " CA  GLY A 241 " =    2.257
peak=   -3.472 closest distance to " CD  LYS A 289 " =    2.459
peak=   -3.470 closest distance to " O   HOH Z 198 " =    2.094
peak=   -3.467 closest distance to " CD1 LEU A 228 " =    2.092
peak=   -3.464 closest distance to " NH2AARG A 275 " =    5.133
peak=   -3.447 closest distance to " CB  ASN A  39 " =    2.246
peak=   -3.443 closest distance to " CA  GLY A  98 " =    1.837
peak=   -3.436 closest distance to " CD  ARG A 139 " =    1.591
peak=   -3.434 closest distance to " CG  LEU A 228 " =    1.011
peak=   -3.433 closest distance to " O   HOH Z 102 " =    1.649
peak=   -3.426 closest distance to " O   HOH Z 191 " =    5.450
peak=   -3.425 closest distance to " O   HOH Z 407 " =    3.006
peak=   -3.423 closest distance to " OD1 ASN A 148 " =    1.455
peak=   -3.411 closest distance to " NZ  LYS A 119 " =    3.396
peak=   -3.410 closest distance to " CB  ASP A 132 " =    2.304
peak=   -3.399 closest distance to " CG1 VAL A 197 " =    2.215
peak=   -3.390 closest distance to " CG1 VAL A 230 " =    1.877
peak=   -3.388 closest distance to " O   HOH Z 198 " =    1.419
peak=   -3.382 closest distance to " CD2 LEU A 300 " =    2.780
peak=   -3.374 closest distance to " CG1 VAL A 112 " =    2.657
peak=   -3.373 closest distance to " NE2 GLN A 278 " =    1.906
peak=   -3.369 closest distance to " O   HOH Z 313 " =    1.088
peak=   -3.368 closest distance to " O   HOH Z  90 " =    2.505
peak=   -3.352 closest distance to " O   HOH Z  63 " =    1.612
peak=   -3.348 closest distance to " O   HOH Z 350 " =    1.935
peak=   -3.346 closest distance to " N   ALA A 248 " =    2.218
peak=   -3.342 closest distance to " O   HOH Z  56 " =    2.479
peak=   -3.341 closest distance to " O   HOH Z  43 " =    1.811
peak=   -3.341 closest distance to " O   HOH Z 359 " =    3.309
peak=   -3.341 closest distance to " O   ALA A  51 " =    1.319
peak=   -3.340 closest distance to " O   HOH Z 281 " =    2.763
peak=   -3.336 closest distance to " CD1 LEU A 101 " =    2.314
peak=   -3.335 closest distance to " O   HOH Z   9 " =    1.441
peak=   -3.334 closest distance to " CA  GLY A 203 " =    2.337
peak=   -3.330 closest distance to " CD1 PHE A  59 " =    1.950
peak=   -3.329 closest distance to " N   SER A 276 " =    1.305
peak=   -3.327 closest distance to " CA  GLY A 241 " =    3.087
peak=   -3.327 closest distance to " CD2 LEU A 237 " =    2.702
peak=   -3.327 closest distance to " C   LEU A 222 " =    0.760
peak=   -3.324 closest distance to " N   GLN A  77 " =    1.740
peak=   -3.324 closest distance to " CA  GLY A 133 " =    1.959
peak=   -3.323 closest distance to " O   PHE A 218 " =    1.683
peak=   -3.321 closest distance to " O   HOH Z 345 " =    1.975
peak=   -3.321 closest distance to " O   LEU A 101 " =    2.805
peak=   -3.307 closest distance to " N   ASN A  60 " =    1.384
peak=   -3.297 closest distance to " CB  ALA A 291 " =    2.180
peak=   -3.296 closest distance to " CB  ASN A  69 " =    1.150
peak=   -3.292 closest distance to " CB  TYR A  15 " =    2.172
peak=   -3.289 closest distance to " CG1 VAL A 296 " =    1.362
peak=   -3.287 closest distance to " CG2 ILE A 263 " =    2.287
peak=   -3.283 closest distance to " C   LEU A 143 " =    1.022
peak=   -3.279 closest distance to " O   HOH Z 309 " =    2.530
peak=   -3.272 closest distance to " O   HOH Z 134 " =    3.046
peak=   -3.270 closest distance to " CA  ASP A 298 " =    1.076
peak=   -3.270 closest distance to " O   HOH Z 243 " =    1.917
peak=   -3.269 closest distance to " OD2 ASP A 191 " =    1.317
peak=   -3.263 closest distance to " CG1 VAL A 250 " =    2.737
peak=   -3.261 closest distance to " OH  TYR A 214 " =    1.195
peak=   -3.260 closest distance to " O   HOH Z 423 " =    2.148
peak=   -3.257 closest distance to " CE3 TRP A 150 " =    1.987
peak=   -3.256 closest distance to " CB  VAL A 296 " =    1.087
peak=   -3.252 closest distance to " O   HOH Z 423 " =    1.091
peak=   -3.251 closest distance to " O   HOH Z 165 " =    2.013
peak=   -3.250 closest distance to " OG1 THR A 178 " =    1.235
peak=   -3.247 closest distance to " C   ASP A 231 " =    2.490
peak=   -3.242 closest distance to " ND2 ASN A 252 " =    1.837
peak=   -3.237 closest distance to " SG BCYS A 201 " =    1.977
peak=   -3.236 closest distance to " CD1 ILE A 239 " =    2.351
peak=   -3.233 closest distance to " O   TYR A  30 " =    2.875
peak=   -3.229 closest distance to " O   HOH Z  13 " =    1.687
peak=   -3.228 closest distance to " CE BMET A  47 " =    1.275
peak=   -3.226 closest distance to " CG2 THR A  18 " =    2.732
peak=   -3.224 closest distance to " OD1 ASP A 191 " =    1.501
peak=   -3.224 closest distance to " C   ALA A 158 " =    1.349
peak=   -3.223 closest distance to " O   HOH Z 131 " =    4.028
peak=   -3.215 closest distance to " O   SER A 210 " =    1.926
peak=   -3.208 closest distance to " CG2 THR A 157 " =    2.137
peak=   -3.205 closest distance to " O   HOH Z 139 " =    3.022
peak=   -3.205 closest distance to " CD2 LEU A 300 " =    2.778
peak=   -3.203 closest distance to " NH2 ARG A 159 " =    2.338
peak=   -3.189 closest distance to " N   MET A 188 " =    1.811
peak=   -3.189 closest distance to " O   TRP A  70 " =    1.444
peak=   -3.186 closest distance to " O   HOH Z 210 " =    1.105
peak=   -3.183 closest distance to " O   SER A 135 " =    1.431
peak=   -3.183 closest distance to " O   ALA A   8 " =    1.934
peak=   -3.183 closest distance to " OE2 GLU A 152 " =    1.183
peak=   -3.179 closest distance to " O   GLY A  80 " =    2.494
peak=   -3.176 closest distance to " O   HOH Z  38 " =    1.767
peak=   -3.173 closest distance to " O   HOH Z 295 " =    1.580
peak=   -3.170 closest distance to " OG  SER A  97 " =    2.194
peak=   -3.167 closest distance to " C   GLY A  17 " =    1.230
peak=   -3.157 closest distance to " ND2 ASN A  69 " =    1.765
peak=   -3.156 closest distance to " O   ALA A 248 " =    1.808
peak=   -3.155 closest distance to " O   LYS A 117 " =    1.717
peak=   -3.152 closest distance to " O   ARG A  24 " =    1.967
peak=   -3.151 closest distance to " OD1 ASN A 301 " =    1.985
peak=   -3.146 closest distance to " O   GLN A 240 " =    2.000
peak=   -3.145 closest distance to " O   HOH Z 427 " =    1.575
peak=   -3.143 closest distance to " O   ALA A   1 " =    1.733
peak=   -3.138 closest distance to " CD2 TYR A 293 " =    2.046
peak=   -3.137 closest distance to " O   SER A  95 " =    1.542
peak=   -3.124 closest distance to " O   HOH Z 353 " =    2.059
peak=   -3.123 closest distance to " CG  GLN A 278 " =    2.093
peak=   -3.120 closest distance to " CD  PRO A 213 " =    2.126
peak=   -3.118 closest distance to " OG ASER A 216 " =    1.043
peak=   -3.116 closest distance to " CG  ASP A  50 " =    2.263
peak=   -3.115 closest distance to " O   HOH Z 200 " =    4.357
peak=   -3.105 closest distance to " CG  PRO A 163 " =    2.612
peak=   -3.105 closest distance to " CA  PRO A 243 " =    2.228
peak=   -3.101 closest distance to " O   HOH Z 189 " =    1.886
peak=   -3.100 closest distance to " CD2 PHE A 225 " =    1.048
peak=   -3.086 closest distance to " O   GLU A  44 " =    1.667
peak=   -3.085 closest distance to " N   ASP A 171 " =    2.255
peak=   -3.076 closest distance to " O   HOH Z 111 " =    2.345
peak=   -3.071 closest distance to " O   HOH Z 175 " =    4.288
peak=   -3.065 closest distance to " CD2 PHE A  61 " =    1.989
peak=   -3.065 closest distance to " O   HOH Z 193 " =    2.009
peak=   -3.064 closest distance to " O   GLY A  75 " =    1.887
peak=   -3.061 closest distance to " CG  GLU A 152 " =    1.443
peak=   -3.058 closest distance to " NH1 ARG A  36 " =    2.037
peak=   -3.053 closest distance to " CG  GLU A 277 " =    1.229
peak=   -3.035 closest distance to " O   HOH Z 359 " =    1.621

================= 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    :  0.4321 0.4200   6.227006e+00   6.201422e+00
   1_bss:  0.4244 0.4085   6.220416e+00   6.186654e+00
   1_xyz:  0.3173 0.3372   6.011537e+00   6.049245e+00
   1_adp:  0.2527 0.2899   5.821049e+00   5.924350e+00
   1_occ:  0.2521 0.2895   5.819352e+00   5.924542e+00
   2_bss:  0.2467 0.2816   5.816060e+00   5.917140e+00
   2_xyz:  0.1651 0.2075   5.463343e+00   5.641199e+00
   2_adp:  0.1487 0.1925   5.372866e+00   5.571301e+00
   2_occ:  0.1485 0.1921   5.371787e+00   5.570052e+00
   3_bss:  0.1483 0.1913   5.370660e+00   5.567204e+00
   3_xyz:  0.1222 0.1654   5.206369e+00   5.432049e+00
   3_adp:  0.1167 0.1613   5.171283e+00   5.406799e+00
   3_occ:  0.1166 0.1612   5.170877e+00   5.406207e+00
   4_bss:  0.1167 0.1610   5.170611e+00   5.404603e+00
   4_xyz:  0.1103 0.1572   5.134852e+00   5.385239e+00
   4_adp:  0.1105 0.1553   5.130176e+00   5.374428e+00
   4_occ:  0.1103 0.1552   5.128947e+00   5.373248e+00
   5_bss:  0.1103 0.1551   5.128671e+00   5.373065e+00
   5_xyz:  0.1085 0.1544   5.118808e+00   5.370772e+00
   5_adp:  0.1079 0.1547   5.118136e+00   5.372092e+00
   5_occ:  0.1079 0.1547   5.118017e+00   5.371967e+00
   5_bss:  0.1078 0.1546   5.117559e+00   5.371516e+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:  0.358  16.872   7.203   9.435   8.005   0.000   0.000   0.000
   1_xyz:  0.358  16.872   7.203   9.435   8.005   0.000   0.000   0.000
   1_adp:  0.358  16.872   7.203   9.435   8.005   0.000   0.000   0.000
   1_occ:  0.358  16.872   7.203   9.435   8.005   0.000   0.000   0.000
   2_bss:  0.344  35.071   3.826   5.060   4.948   0.000   0.000   0.000
   2_xyz:  0.344  35.071   3.826   5.060   4.948   0.000   0.000   0.000
   2_adp:  0.344  35.071   3.826   5.060   4.948   0.000   0.000   0.000
   2_occ:  0.344  35.071   3.826   5.060   4.948   0.000   0.000   0.000
   3_bss:  0.322  35.071   3.061   3.483   4.450   0.000   0.000   0.000
   3_xyz:  0.322  35.071   3.061   3.483   4.450   0.000   0.000   0.000
   3_adp:  0.322  35.071   3.061   3.483   4.450   0.000   0.000   0.000
   3_occ:  0.322  35.071   3.061   3.483   4.450   0.000   0.000   0.000
   4_bss:  0.314  35.071   3.061   3.483   4.450   0.000   0.000   0.000
   4_xyz:  0.314  35.071   3.061   3.483   4.450   0.000   0.000   0.000
   4_adp:  0.314  35.071   3.061   3.483   4.450   0.000   0.000   0.000
   4_occ:  0.314  35.071   3.061   3.483   4.450   0.000   0.000   0.000
   5_bss:  0.317  35.071   2.993   3.245   4.491   0.000   0.000   0.000
   5_xyz:  0.317  35.071   2.993   3.245   4.491   0.000   0.000   0.000
   5_adp:  0.317  35.071   2.993   3.245   4.491   0.000   0.000   0.000
   5_occ:  0.317  35.071   2.993   3.245   4.491   0.000   0.000   0.000
   5_bss:  0.323  43.594  -0.577  -0.370   0.947  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.881 0.5610  0.6294    51458.520
   1_bss:  46.963 0.5575  0.7994    48831.934
   1_xyz:  36.017 0.6890  0.9615    30868.118
   1_adp:  28.431 0.7762  1.0619    21439.032
   1_occ:  28.439 0.7761  1.0606    21365.281
   2_bss:  28.059 0.7799  0.9342    20827.994
   2_xyz:  19.802 0.8635  1.0003    10815.627
   2_adp:  17.863 0.8822  1.0093     9318.881
   2_occ:  17.827 0.8825  1.0094     9281.772
   3_bss:  17.750 0.8831  0.9753     9197.040
   3_xyz:  14.980 0.9065  0.9883     6899.640
   3_adp:  14.414 0.9114  0.9876     6555.393
   3_occ:  14.404 0.9115  0.9875     6544.047
   4_bss:  14.379 0.9117  0.9869     6522.320
   4_xyz:  13.864 0.9162  0.9878     6261.457
   4_adp:  13.615 0.9183  0.9858     6148.733
   4_occ:  13.592 0.9185  0.9858     6133.169
   5_bss:  13.586 0.9185  0.9827     6130.474
   5_xyz:  13.539 0.9188  0.9833     6104.757
   5_adp:  13.564 0.9187  0.9805     6117.805
   5_occ:  13.563 0.9187  0.9804     6114.093
   5_bss:  13.551 0.9188  0.9816     6110.524
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3462e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3462e+01
   1_xyz:   1.512  0.011  0.100 17.808  0.006  4.119   1.1610e-01
   1_adp:   1.512  0.011  0.100 17.808  0.006  4.119   1.1610e-01
   1_occ:   1.512  0.011  0.100 17.808  0.006  4.119   1.1610e-01
   2_bss:   1.512  0.011  0.100 17.808  0.006  4.119   1.1610e-01
   2_xyz:   0.982  0.007  0.076 15.861  0.004  4.117   6.2520e-02
   2_adp:   0.982  0.007  0.076 15.861  0.004  4.117   6.2520e-02
   2_occ:   0.982  0.007  0.076 15.861  0.004  4.117   6.2520e-02
   3_bss:   0.982  0.007  0.076 15.861  0.004  4.117   6.2520e-02
   3_xyz:   1.000  0.007  0.078 15.701  0.004  4.120   6.1189e-02
   3_adp:   1.000  0.007  0.078 15.701  0.004  4.120   6.1189e-02
   3_occ:   1.000  0.007  0.078 15.701  0.004  4.120   6.1189e-02
   4_bss:   1.000  0.007  0.078 15.701  0.004  4.120   6.1189e-02
   4_xyz:   1.008  0.007  0.082 15.620  0.004  4.113   6.3469e-02
   4_adp:   1.008  0.007  0.082 15.620  0.004  4.113   6.3469e-02
   4_occ:   1.008  0.007  0.082 15.620  0.004  4.113   6.3469e-02
   5_bss:   1.008  0.007  0.082 15.620  0.004  4.113   6.3469e-02
   5_xyz:   1.042  0.008  0.084 15.572  0.004  4.113   6.5703e-02
   5_adp:   1.042  0.008  0.084 15.572  0.004  4.113   6.5703e-02
   5_occ:   1.042  0.008  0.084 15.572  0.004  4.113   6.5703e-02
   5_bss:   1.042  0.008  0.084 15.572  0.004  4.113   6.5703e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9311e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9311e+00
   1_xyz:  12.553  0.142  0.419 89.462  0.031  2.266   8.5206e-02
   1_adp:  12.553  0.142  0.419 89.462  0.031  2.266   8.5206e-02
   1_occ:  12.553  0.142  0.419 89.462  0.031  2.266   8.5206e-02
   2_bss:  12.553  0.142  0.419 89.462  0.031  2.266   8.5206e-02
   2_xyz:   6.533  0.084  0.338 83.640  0.039  2.306   6.5820e-02
   2_adp:   6.533  0.084  0.338 83.640  0.039  2.306   6.5820e-02
   2_occ:   6.533  0.084  0.338 83.640  0.039  2.306   6.5820e-02
   3_bss:   6.533  0.084  0.338 83.640  0.039  2.306   6.5820e-02
   3_xyz:   6.609  0.042  0.473 83.933  0.029  2.270   4.3037e-02
   3_adp:   6.609  0.042  0.473 83.933  0.029  2.270   4.3037e-02
   3_occ:   6.609  0.042  0.473 83.933  0.029  2.270   4.3037e-02
   4_bss:   6.609  0.042  0.473 83.933  0.029  2.270   4.3037e-02
   4_xyz:   6.355  0.045  0.517 83.813  0.038  2.317   5.8246e-02
   4_adp:   6.355  0.045  0.517 83.813  0.038  2.317   5.8246e-02
   4_occ:   6.355  0.045  0.517 83.813  0.038  2.317   5.8246e-02
   5_bss:   6.355  0.045  0.517 83.813  0.038  2.317   5.8246e-02
   5_xyz:   6.299  0.047  0.566 83.408  0.038  2.249   4.8694e-02
   5_adp:   6.299  0.047  0.566 83.408  0.038  2.249   4.8694e-02
   5_occ:   6.299  0.047  0.566 83.408  0.038  2.249   4.8694e-02
   5_bss:   6.299  0.047  0.566 83.408  0.038  2.249   4.8694e-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:  68.36   0.00  10.86  68.36   0.00   7.83  64.70   0.00  27.36
   1_occ:  68.36   0.00  10.86  68.36   0.00   7.83  64.70   0.00  27.36
   2_bss:  68.36   0.00  10.86  68.36   0.00   7.83  64.70   0.00  27.36
   2_xyz:  68.36   0.00  10.86  68.36   0.00   7.83  64.70   0.00  27.36
   2_adp:  70.18   0.00  11.14  70.18   0.00   7.40  67.11   1.16  31.50
   2_occ:  70.18   0.00  11.14  70.18   0.00   7.40  67.11   1.16  31.50
   3_bss:  70.18   0.00  11.14  70.18   0.00   7.40  67.11   1.16  31.50
   3_xyz:  70.18   0.00  11.14  70.18   0.00   7.40  67.11   1.16  31.50
   3_adp:  84.17   0.00  11.87  84.17   0.00   7.51  76.61   0.66  35.59
   3_occ:  84.17   0.00  11.87  84.17   0.00   7.51  76.61   0.66  35.59
   4_bss:  84.17   0.00  11.87  84.17   0.00   7.51  76.61   0.66  35.59
   4_xyz:  84.17   0.00  11.87  84.17   0.00   7.51  76.61   0.66  35.59
   4_adp:  84.05   0.00  11.27  84.05   0.00   7.27  72.84   1.11  33.09
   4_occ:  84.05   0.00  11.27  84.05   0.00   7.27  72.84   1.11  33.09
   5_bss:  84.05   0.00  11.27  84.05   0.00   7.27  72.84   1.11  33.09
   5_xyz:  84.05   0.00  11.27  84.05   0.00   7.27  72.84   1.11  33.09
   5_adp:  85.80   0.00  11.21  85.80   0.00   7.21  73.54   1.06  33.01
   5_occ:  85.80   0.00  11.21  85.80   0.00   7.21  73.54   1.06  33.01
   5_bss:  89.40   3.60  14.81  89.40   3.60  10.81  77.14   4.67  36.61
------------------------------------------------------------------------
 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:    1.183    0.020    0.401
   1_adp:    1.183    0.020    0.401
   1_occ:    1.183    0.020    0.401
   2_bss:    1.183    0.020    0.401
   2_xyz:    1.340    0.026    0.505
   2_adp:    1.340    0.026    0.505
   2_occ:    1.340    0.026    0.505
   3_bss:    1.340    0.026    0.505
   3_xyz:    1.426    0.032    0.541
   3_adp:    1.426    0.032    0.541
   3_occ:    1.426    0.032    0.541
   4_bss:    1.426    0.032    0.541
   4_xyz:    1.497    0.043    0.559
   4_adp:    1.497    0.043    0.559
   4_occ:    1.497    0.043    0.559
   5_bss:    1.497    0.043    0.559
   5_xyz:    1.548    0.059    0.566
   5_adp:    1.548    0.059    0.566
   5_occ:    1.548    0.059    0.566
   5_bss:    1.548    0.059    0.566
------------------------------------------------------------------------

CPU time actual refinement: 324.20


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_522/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_522/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_522/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_522/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_522/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.04 
  Macro-tasks:
    bulk solvent and scale       = 41.13  
    individual site refinement   = 127.09 
    weights calculation          = 32.59  
    collect and process          = 6.46   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 207.39 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 99.18  
    alpha_beta                      = 8.21   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 108.28 
    fmodel                         = 7.07   
    r_factors                      = 0.11   
    phase_errors                   = 10.58  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 236.64 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.634 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    635 calls, 98.74 s
gradients_fft:          580 calls, 95.55 s

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

# Date 2008-01-16 Time 01:46:13 PST -0800 (1200476773.53 s)
Start R-work = 0.4321, R-free = 0.4200 (no bulk solvent and anisotropic scale)
Final R-work = 0.1260, R-free = 0.1717 (no bulk solvent and anisotropic scale)

Start R-work = 0.4244, R-free = 0.4085
Final R-work = 0.1078, R-free = 0.1546