# Date 2008-01-16 Time 00:27:24 PST -0800 (1200472044.38 s)
#phil __OFF__

Command line arguments: "../26.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 = 25284
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 26

-------------------------------------------------------------------------------
  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: (68.4938, 46.2261, 85.9581, 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: 3.30, per 1000 atoms: 1.17


================================== 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: (68.4938, 46.2261, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6986 1.95068
Completeness in resolution range: 0.95757
Completeness with d_max=infinity: 0.954583

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6986
                             d_min =   1.9507

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: (68.4938, 46.2261, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6986 1.95068
Completeness in resolution range: 0.95757
Completeness with d_max=infinity: 0.954583

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6990 -  4.1735 [2157/2184]  1939   218  10.1%
  bin  2:  4.1735 -  3.3253 [2055/2071]  1853   202   9.8%
  bin  3:  3.3253 -  2.9086 [2043/2062]  1838   205  10.0%
  bin  4:  2.9086 -  2.6444 [2012/2042]  1810   202  10.0%
  bin  5:  2.6444 -  2.4558 [2005/2024]  1801   204  10.2%
  bin  6:  2.4558 -  2.3116 [1991/2016]  1794   197   9.9%
  bin  7:  2.3116 -  2.1962 [1992/2026]  1798   194   9.7%
  bin  8:  2.1962 -  2.1009 [1975/2006]  1775   200  10.1%
  bin  9:  2.1009 -  2.0202 [1972/2013]  1775   197  10.0%
  bin 10:  2.0202 -  1.9507 [1387/2013]  1247   140  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_26/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:
        1.12 -     1.88: 15
        1.88 -     2.63: 123
        2.63 -     3.39: 4409
        3.39 -     4.14: 9640
        4.14 -     4.90: 14890
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.119 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.310 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.467 3.040 -x+1,y+1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.516 3.120 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.736 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 29072 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_26/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_26/model_refine_001.geo

CPU time processing inputs: 11.19


============================ 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 = 68.49375 46.22605 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4935   r_free= 0.4881   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.291226                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6990 -  4.6547 0.99   1398  154 0.4085 0.4054      6.6048      6.6317|
|  2:  4.6547 -  3.7142 0.99   1336  153 0.4142 0.4134      6.8044      6.8095|
|  3:  3.7142 -  3.2505 0.99   1321  145 0.4588 0.4474       6.693      6.7218|
|  4:  3.2505 -  2.9560 0.99   1306  138 0.4834 0.4481      6.5525        6.51|
|  5:  2.9560 -  2.7456 0.99   1305  148 0.5249 0.5074       6.378      6.4049|
|  6:  2.7456 -  2.5846 0.99   1286  148 0.5254 0.5440      6.2918      6.2322|
|  7:  2.5846 -  2.4558 0.99   1289  145 0.5297 0.5226      6.2612      6.1797|
|  8:  2.4558 -  2.3493 0.98   1295  135 0.5370 0.5375      6.2016      6.2108|
|  9:  2.3493 -  2.2592 0.98   1274  148 0.5165 0.5349      6.1078      6.1867|
| 10:  2.2592 -  2.1815 0.98   1271  139 0.5421 0.5457      6.1236      6.0995|
| 11:  2.1815 -  2.1135 0.99   1281  142 0.5438 0.5266      6.0443      6.0771|
| 12:  2.1135 -  2.0533 0.97   1262  140 0.5372 0.5377      5.9771      6.0404|
| 13:  2.0533 -  1.9993 0.99   1256  140 0.5451 0.4704       5.899      5.8273|
| 14:  1.9993 -  1.9507 0.58    750   84 0.5528 0.5522      5.8872      5.7763|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6990 -  4.6547  1398   154  0.65  38.82   0.79     0.69      87283.27|
|  2:  4.6547 -  3.7142  1336   153  0.67  37.87   0.88     0.75     120084.18|
|  3:  3.7142 -  3.2505  1321   145  0.56  47.17   0.86     0.70     125920.26|
|  4:  3.2505 -  2.9560  1306   138  0.48  53.52   0.80     0.59     109750.51|
|  5:  2.9560 -  2.7456  1305   148  0.36  62.66   0.73     0.45      90467.01|
|  6:  2.7456 -  2.5846  1286   148  0.31  66.89   0.71     0.36      80345.99|
|  7:  2.5846 -  2.4558  1289   145  0.22  73.55   0.76     0.26      76618.43|
|  8:  2.4558 -  2.3493  1295   135  0.20  75.20   0.73     0.24      70666.09|
|  9:  2.3493 -  2.2592  1274   148  0.20  75.42   0.74     0.25      65493.54|
| 10:  2.2592 -  2.1815  1271   139  0.25  71.19   0.76     0.31      55824.35|
| 11:  2.1815 -  2.1135  1281   142  0.25  71.62   0.76     0.32      52304.24|
| 12:  2.1135 -  2.0533  1262   140  0.25  71.53   0.76     0.32      46910.75|
| 13:  2.0533 -  1.9993  1256   140  0.22  73.40   0.74     0.29      40920.84|
| 14:  1.9993 -  1.9507   750    84  0.26  70.77   0.74     0.28      30988.43|
|alpha:            min =        0.24 max =            0.75 mean =         0.42|
|beta:             min =    30988.43 max =       125920.26 mean =     77085.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.01|
|phase err.(test): min =        0.00 max =           90.00 mean =        63.16|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.532903             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.468   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.884828              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.119   (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:        9 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       42 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      194 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      733 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1555 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2718 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4062 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5173 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6729 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7857 |
|-----------------------------------------------------------------------------|
|-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 |       52.730 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.084    4.900  1.196 |       3.430 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    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 = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4984   r_free= 0.4920   ksol= 0.00   Bsol= 0.00   scale= 0.767    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.292091                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4846   r_free= 0.4785   ksol= 0.41   Bsol= 20.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.76,9.22,7.19,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.283044                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.989698             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.778   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.730237              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.812   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4846      final r-factor (work) = 0.4106          |
| start r-factor (free) = 0.4785      final r-factor (free) = 0.4344          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 103.0088 = 15.99 * 0.50 * 6.2889 + 1.00 * 52.7296                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.8757 = 15.99 * 0.50 * 6.2189 + 1.00 * 0.1567                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4106      final r-factor (work) = 0.3663          |
| start r-factor (free) = 0.4344      final r-factor (free) = 0.4165          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7745 = 1.73 * 1.00 * 6.2189 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6574 = 1.73 * 1.00 * 6.1476 + 1.00 * 0.0207                              |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    56.96   12.96    None  None   None       |
|    all(noH): 2823   0      0.00    56.96   12.96    None  None   None       |
|    Sol.    : 438    0      0.00    56.96   22.33    None  None   None       |
|    Mac.    : 2385   0      0.00    56.14   11.24    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.696:  778   |   5:    28.482 -  34.178:  120        |
|      1:     5.696 -  11.393:  701   |   6:    34.178 -  39.875:   57        |
|      2:    11.393 -  17.089:  528   |   7:    39.875 -  45.571:   50        |
|      3:    17.089 -  22.786:  334   |   8:    45.571 -  51.268:   12        |
|      4:    22.786 -  28.482:  237   |   9:    51.268 -  56.964:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3663 r_free = 0.4165             target_work(ml) = 6.130         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3656 r_free = 0.4156             target_work(ml) = 6.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3656   r_free= 0.4156   ksol= 0.41   Bsol= 20.00   scale= 1.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.76,9.22,7.19,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.128425                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3636   r_free= 0.4113   ksol= 0.35   Bsol= 27.51   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.83,5.22,4.68,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.127934                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.277595              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.400   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.779276              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.075  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3636      final r-factor (work) = 0.2917          |
| start r-factor (free) = 0.4113      final r-factor (free) = 0.3517          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.4399 = 6.28 * 0.50 * 6.1435 + 1.00 * 0.1567                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0262 = 6.28 * 0.50 * 6.0344 + 1.00 * 0.0854                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2917      final r-factor (work) = 0.2682          |
| start r-factor (free) = 0.3517      final r-factor (free) = 0.3315          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7238 = 0.78 * 1.00 * 6.0344 + 1.00 * 0.0213                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6372 = 0.78 * 1.00 * 5.9202 + 1.00 * 0.0237                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.30   13.74    None  None   None       |
|    all(noH): 2823   0      0.00    80.30   13.74    None  None   None       |
|    Sol.    : 438    0      0.00    77.44   30.94    None  None   None       |
|    Mac.    : 2385   0      0.00    80.30   10.58    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 -   8.030: 1218   |   5:    40.149 -  48.178:   72        |
|      1:     8.030 -  16.059:  758   |   6:    48.178 -  56.208:   57        |
|      2:    16.059 -  24.089:  356   |   7:    56.208 -  64.238:   10        |
|      3:    24.089 -  32.119:  209   |   8:    64.238 -  72.267:   11        |
|      4:    32.119 -  40.149:  129   |   9:    72.267 -  80.297:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2682 r_free = 0.3315             target_work(ml) = 5.898         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2678 r_free = 0.3314             target_work(ml) = 5.898         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2678   r_free= 0.3314   ksol= 0.35   Bsol= 27.51   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.83,5.22,4.68,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.898017                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2665   r_free= 0.3304   ksol= 0.33   Bsol= 27.51   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.75,3.33,3.68,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.895689                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.198753              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.399  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.419974              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.761  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2665      final r-factor (work) = 0.2047          |
| start r-factor (free) = 0.3304      final r-factor (free) = 0.2603          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5522 = 3.20 * 0.50 * 5.9190 + 1.00 * 0.0854                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3279 = 3.20 * 0.50 * 5.7907 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2047      final r-factor (work) = 0.1876          |
| start r-factor (free) = 0.2603      final r-factor (free) = 0.2436          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5073 = 0.42 * 1.00 * 5.7907 + 1.00 * 0.0753                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3704 = 0.42 * 1.00 * 5.6170 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.67   13.80    None  None   None       |
|    all(noH): 2823   0      0.00    84.67   13.80    None  None   None       |
|    Sol.    : 438    0      1.23    76.19   35.35    None  None   None       |
|    Mac.    : 2385   0      0.00    84.67   9.84     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.467: 1391   |   5:    42.337 -  50.804:  102        |
|      1:     8.467 -  16.935:  740   |   6:    50.804 -  59.271:   55        |
|      2:    16.935 -  25.402:  219   |   7:    59.271 -  67.739:   19        |
|      3:    25.402 -  33.869:  166   |   8:    67.739 -  76.206:    8        |
|      4:    33.869 -  42.337:  122   |   9:    76.206 -  84.673:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1876 r_free = 0.2436             target_work(ml) = 5.591         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1871 r_free = 0.2435             target_work(ml) = 5.590         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1871   r_free= 0.2435   ksol= 0.33   Bsol= 27.51   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.75,3.33,3.68,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.589545                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1862   r_free= 0.2432   ksol= 0.32   Bsol= 32.72   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,2.05,2.85,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.587547                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.975576              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.306   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.902687              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.658  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1862      final r-factor (work) = 0.1447          |
| start r-factor (free) = 0.2432      final r-factor (free) = 0.1923          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4292 = 2.98 * 0.50 * 5.6210 + 1.00 * 0.0664                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2167 = 2.98 * 0.50 * 5.4815 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1447      final r-factor (work) = 0.1347          |
| start r-factor (free) = 0.1923      final r-factor (free) = 0.1836          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9594 = 0.90 * 1.00 * 5.4815 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8177 = 0.90 * 1.00 * 5.3229 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.08   14.15    None  None   None       |
|    all(noH): 2823   0      0.00    91.08   14.15    None  None   None       |
|    Sol.    : 438    0      0.00    85.38   39.49    None  None   None       |
|    Mac.    : 2385   0      0.00    91.08   9.50     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.108: 1580   |   5:    45.539 -  54.647:   92        |
|      1:     9.108 -  18.216:  629   |   6:    54.647 -  63.755:   67        |
|      2:    18.216 -  27.324:  186   |   7:    63.755 -  72.863:   35        |
|      3:    27.324 -  36.431:  104   |   8:    72.863 -  81.971:    8        |
|      4:    36.431 -  45.539:  119   |   9:    81.971 -  91.079:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1347 r_free = 0.1836             target_work(ml) = 5.299         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1346 r_free = 0.1834             target_work(ml) = 5.298         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1346   r_free= 0.1834   ksol= 0.32   Bsol= 32.72   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,2.05,2.85,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.297671                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1347   r_free= 0.1837   ksol= 0.31   Bsol= 34.57   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.97,1.56,2.67,0.00,0.00,0.00); trace/3= 1.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.296619                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.566305              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.004  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.175844              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.742  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1347      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1837      final r-factor (free) = 0.1723          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2308 = 1.57 * 0.50 * 5.3240 + 1.00 * 0.0613                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1768 = 1.57 * 0.50 * 5.2675 + 1.00 * 0.0516                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1256          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9389 = 0.18 * 1.00 * 5.2675 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9306 = 0.18 * 1.00 * 5.2385 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.57   13.35    None  None   None       |
|    all(noH): 2823   0      0.00    88.57   13.35    None  None   None       |
|    Sol.    : 438    0      1.85    81.67   36.25    None  None   None       |
|    Mac.    : 2385   0      0.00    88.57   9.14     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 -   8.857: 1592   |   5:    44.285 -  53.142:   75        |
|      1:     8.857 -  17.714:  656   |   6:    53.142 -  62.000:   61        |
|      2:    17.714 -  26.571:  165   |   7:    62.000 -  70.857:   17        |
|      3:    26.571 -  35.428:  139   |   8:    70.857 -  79.714:    7        |
|      4:    35.428 -  44.285:  107   |   9:    79.714 -  88.571:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1256 r_free = 0.1666             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1255 r_free = 0.1664             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1255   r_free= 0.1664   ksol= 0.31   Bsol= 34.57   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.97,1.56,2.67,0.00,0.00,0.00); trace/3= 1.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.219278                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6990 -  4.6547 0.99   1398  154 0.1076 0.1325      5.4408      5.5761|
|  2:  4.6547 -  3.7142 0.99   1336  153 0.0991 0.1263      5.5441      5.7523|
|  3:  3.7142 -  3.2505 0.99   1321  145 0.1203 0.1470      5.5822      5.8454|
|  4:  3.2505 -  2.9560 0.99   1306  138 0.1353 0.1855      5.5298      5.7141|
|  5:  2.9560 -  2.7456 0.99   1305  148 0.1435 0.1727      5.3902      5.5682|
|  6:  2.7456 -  2.5846 0.99   1286  148 0.1338 0.2026      5.2653      5.4944|
|  7:  2.5846 -  2.4558 0.99   1289  145 0.1354 0.1777      5.2225      5.3914|
|  8:  2.4558 -  2.3493 0.98   1295  135 0.1338 0.1787      5.1705      5.3743|
|  9:  2.3493 -  2.2592 0.98   1274  148 0.1353 0.1868      5.1047      5.3767|
| 10:  2.2592 -  2.1815 0.98   1271  139 0.1293 0.1663       5.029      5.1528|
| 11:  2.1815 -  2.1135 0.99   1281  142 0.1270 0.1867      4.9846      5.3222|
| 12:  2.1135 -  2.0533 0.97   1262  140 0.1290 0.1662      4.9665      5.1946|
| 13:  2.0533 -  1.9993 0.99   1256  140 0.1263 0.1917      4.8528      5.0846|
| 14:  1.9993 -  1.9507 0.58    750   84 0.1137 0.1720      4.7071      4.9727|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6990 -  4.6547  1398   154  0.94   9.66   0.99     0.97       7857.02|
|  2:  4.6547 -  3.7142  1336   153  0.95   8.93   1.03     1.02      10375.33|
|  3:  3.7142 -  3.2505  1321   145  0.92  12.87   1.05     1.04      12523.93|
|  4:  3.2505 -  2.9560  1306   138  0.91  14.54   1.02     1.01      11518.29|
|  5:  2.9560 -  2.7456  1305   148  0.89  16.59   1.01     0.97       8947.88|
|  6:  2.7456 -  2.5846  1286   148  0.89  16.66   0.99     0.96       7436.70|
|  7:  2.5846 -  2.4558  1289   145  0.90  16.55   1.01     0.96       6557.91|
|  8:  2.4558 -  2.3493  1295   135  0.90  16.19   1.01     1.00       6112.39|
|  9:  2.3493 -  2.2592  1274   148  0.90  16.37   1.02     0.99       5476.15|
| 10:  2.2592 -  2.1815  1271   139  0.89  16.47   1.02     0.98       4704.70|
| 11:  2.1815 -  2.1135  1281   142  0.90  16.42   1.02     0.99       4488.32|
| 12:  2.1135 -  2.0533  1262   140  0.90  16.44   1.03     1.03       4427.92|
| 13:  2.0533 -  1.9993  1256   140  0.90  16.46   1.02     1.02       3565.55|
| 14:  1.9993 -  1.9507   750    84  0.92  14.28   1.01     0.98       2522.18|
|alpha:            min =        0.96 max =            1.04 mean =         1.00|
|beta:             min =     2522.18 max =        12523.93 mean =      7073.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.85|
|phase err.(test): min =        0.00 max =           89.71 mean =        14.28|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1255   r_free= 0.1664   ksol= 0.31   Bsol= 36.17   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,-0.21,1.02,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.219159                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1255   r_free= 0.1664   ksol= 0.31   Bsol= 36.17   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,-0.21,1.02,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.219159                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6990 -  4.6547 0.99   1398  154 0.1075 0.1324      5.4401      5.5751|
|  2:  4.6547 -  3.7142 0.99   1336  153 0.0991 0.1263      5.5437       5.752|
|  3:  3.7142 -  3.2505 0.99   1321  145 0.1203 0.1469       5.582      5.8449|
|  4:  3.2505 -  2.9560 0.99   1306  138 0.1353 0.1855      5.5298      5.7137|
|  5:  2.9560 -  2.7456 0.99   1305  148 0.1435 0.1727      5.3903      5.5685|
|  6:  2.7456 -  2.5846 0.99   1286  148 0.1337 0.2024      5.2652      5.4936|
|  7:  2.5846 -  2.4558 0.99   1289  145 0.1355 0.1777      5.2224      5.3915|
|  8:  2.4558 -  2.3493 0.98   1295  135 0.1338 0.1786      5.1703      5.3745|
|  9:  2.3493 -  2.2592 0.98   1274  148 0.1353 0.1870      5.1047      5.3766|
| 10:  2.2592 -  2.1815 0.98   1271  139 0.1293 0.1660      5.0288      5.1522|
| 11:  2.1815 -  2.1135 0.99   1281  142 0.1270 0.1869      4.9846      5.3227|
| 12:  2.1135 -  2.0533 0.97   1262  140 0.1290 0.1663      4.9668      5.1955|
| 13:  2.0533 -  1.9993 0.99   1256  140 0.1263 0.1914      4.8529      5.0839|
| 14:  1.9993 -  1.9507 0.58    750   84 0.1136 0.1721      4.7067      4.9733|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6990 -  4.6547  1398   154  0.94   9.64   0.98     0.96       7839.32|
|  2:  4.6547 -  3.7142  1336   153  0.95   8.92   1.03     1.02      10359.63|
|  3:  3.7142 -  3.2505  1321   145  0.92  12.86   1.05     1.04      12511.98|
|  4:  3.2505 -  2.9560  1306   138  0.91  14.54   1.02     1.01      11512.78|
|  5:  2.9560 -  2.7456  1305   148  0.89  16.59   1.01     0.97       8942.05|
|  6:  2.7456 -  2.5846  1286   148  0.89  16.66   0.98     0.96       7437.27|
|  7:  2.5846 -  2.4558  1289   145  0.90  16.54   1.00     0.95       6553.74|
|  8:  2.4558 -  2.3493  1295   135  0.90  16.19   1.01     1.00       6109.90|
|  9:  2.3493 -  2.2592  1274   148  0.90  16.35   1.01     0.99       5473.64|
| 10:  2.2592 -  2.1815  1271   139  0.89  16.48   1.01     0.97       4706.60|
| 11:  2.1815 -  2.1135  1281   142  0.90  16.43   1.01     0.98       4491.61|
| 12:  2.1135 -  2.0533  1262   140  0.90  16.44   1.03     1.03       4430.37|
| 13:  2.0533 -  1.9993  1256   140  0.90  16.47   1.02     1.01       3568.62|
| 14:  1.9993 -  1.9507   750    84  0.92  14.29   1.00     0.97       2524.29|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2524.29 max =        12511.98 mean =      7069.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.84|
|phase err.(test): min =        0.00 max =           89.72 mean =        14.28|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    90.17   14.95    None  None   None       |
|    all(noH): 2823   0      1.60    90.17   14.95    None  None   None       |
|    Sol.    : 438    0      3.45    83.28   37.86    None  None   None       |
|    Mac.    : 2385   0      1.60    90.17   10.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.602 -  10.459: 1592   |   5:    45.888 -  54.745:   75        |
|      1:    10.459 -  19.317:  656   |   6:    54.745 -  63.602:   61        |
|      2:    19.317 -  28.174:  165   |   7:    63.602 -  72.459:   17        |
|      3:    28.174 -  37.031:  139   |   8:    72.459 -  81.316:    7        |
|      4:    37.031 -  45.888:  107   |   9:    81.316 -  90.173:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 337         
Filter by distance & map next to the model:
   mapped sites are within: 0.605 - 5.702
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 335 from: 337
   mapped sites are within: 0.716 - 5.702

peak=   10.942 closest distance to " CB  VAL A 296 " =    1.532
peak=   10.531 closest distance to " CB  VAL A 230 " =    1.424
peak=    7.399 closest distance to " O   HOH Z 130 " =    1.671
peak=    7.246 closest distance to " CG  ARG A 138 " =    1.202
peak=    6.995 closest distance to " CD1AILE A 234 " =    1.081
peak=    6.670 closest distance to " CD2 LEU A   5 " =    1.327
peak=    6.444 closest distance to " O   HOH Z 178 " =    1.123
peak=    6.168 closest distance to " O   HOH Z 236 " =    1.638
peak=    5.657 closest distance to " O   HOH Z  78 " =    1.652
peak=    5.629 closest distance to " O   HOH Z 375 " =    1.376
peak=    5.628 closest distance to " CB  ARG A 275 " =    1.093
peak=    5.512 closest distance to " NH1 ARG A 138 " =    0.998
peak=    5.505 closest distance to " O   HOH Z   9 " =    1.555
peak=    5.305 closest distance to " O   HOH Z 142 " =    2.019
peak=    5.252 closest distance to " O   HOH Z 424 " =    1.374
peak=    5.077 closest distance to " O   HOH Z 124 " =    1.497
peak=    5.033 closest distance to " O   HOH Z 193 " =    1.702
peak=    5.018 closest distance to " O   HOH Z 126 " =    1.880
peak=    5.006 closest distance to " NE1 TRP A 274 " =    1.090
peak=    4.955 closest distance to " O   HOH Z  65 " =    1.215
peak=    4.952 closest distance to " O   HOH Z 403 " =    1.972
peak=    4.833 closest distance to " CG  LEU A   5 " =    1.256
peak=    4.780 closest distance to " NE2 GLN A  11 " =    1.142
peak=    4.773 closest distance to " O   HOH Z 414 " =    1.513
peak=    4.722 closest distance to " O   HOH Z  43 " =    1.443
peak=    4.665 closest distance to " CB  GLN A 278 " =    0.896
peak=    4.629 closest distance to " O   HOH Z 380 " =    1.856
peak=    4.599 closest distance to " CG  PRO A 213 " =    1.295
peak=    4.597 closest distance to " O   HOH Z 423 " =    1.600
peak=    4.570 closest distance to " CB  VAL A 230 " =    1.174
peak=    4.567 closest distance to " O   HOH Z  85 " =    1.583
peak=    4.552 closest distance to " CB  PRO A  54 " =    1.103
peak=    4.546 closest distance to " NH2 ARG A  56 " =    1.942
peak=    4.543 closest distance to " O   HOH Z  11 " =    1.780
peak=    4.533 closest distance to " CG  PRO A  54 " =    1.391
peak=    4.500 closest distance to " O   HOH Z  28 " =    1.442
peak=    4.494 closest distance to " O   HOH Z 369 " =    2.379
peak=    4.442 closest distance to " CB  GLN A 223 " =    1.661
peak=    4.441 closest distance to " O   HOH Z 427 " =    2.350
peak=    4.384 closest distance to " O   HOH Z 272 " =    1.827
peak=    4.379 closest distance to " O   HOH Z 344 " =    1.388
peak=    4.373 closest distance to " O   HOH Z  69 " =    2.234
peak=    4.361 closest distance to " O   HOH Z 232 " =    2.389
peak=    4.340 closest distance to " CB  SER A   3 " =    1.228
peak=    4.332 closest distance to " NZ  LYS A 117 " =    3.137
peak=    4.332 closest distance to " CG  LEU A 228 " =    1.178
peak=    4.320 closest distance to " O   HOH Z 123 " =    1.383
peak=    4.312 closest distance to " O   HOH Z  69 " =    1.223
peak=    4.278 closest distance to " CG2 ILE A 234 " =    0.942
peak=    4.258 closest distance to " CG  PRO A 243 " =    1.188
peak=    4.250 closest distance to " O   HOH Z 234 " =    3.487
peak=    4.220 closest distance to " CD  ARG A 138 " =    0.944
peak=    4.206 closest distance to " O   HOH Z 316 " =    2.928
peak=    4.200 closest distance to " O   SER A  87 " =    2.253
peak=    4.160 closest distance to " CB  VAL A 202 " =    1.589
peak=    4.159 closest distance to " O   HOH Z 249 " =    1.180
peak=    4.149 closest distance to " O   HOH Z 371 " =    1.848
peak=    4.139 closest distance to " O   HOH Z 406 " =    1.403
peak=    4.137 closest distance to " O   HOH Z 137 " =    1.556
peak=    4.107 closest distance to " O   HOH Z  97 " =    1.756
peak=    4.088 closest distance to " CB  SER A  26 " =    1.649
peak=    4.081 closest distance to " O   HOH Z 126 " =    1.501
peak=    4.081 closest distance to " O   HOH Z  44 " =    1.898
peak=    4.075 closest distance to " O   HOH Z 422 " =    2.179
peak=    4.059 closest distance to " O   HOH Z 423 " =    1.640
peak=    4.047 closest distance to " O   HOH Z 352 " =    1.390
peak=    4.045 closest distance to " O   HOH Z 112 " =    1.376
peak=    4.044 closest distance to " O   HOH Z 346 " =    1.680
peak=    4.024 closest distance to " O   HOH Z 146 " =    1.718
peak=    3.981 closest distance to " O   HOH Z 148 " =    1.646
peak=    3.974 closest distance to " O   HOH Z  97 " =    1.930
peak=    3.971 closest distance to " O   HOH Z  66 " =    2.067
peak=    3.965 closest distance to " O   HOH Z 419 " =    2.073
peak=    3.959 closest distance to " CB  ASN A 148 " =    1.313
peak=    3.941 closest distance to " CA  ASN A 127 " =    1.080
peak=    3.910 closest distance to " O   HOH Z 291 " =    1.478
peak=    3.889 closest distance to " O   PRO A 198 " =    1.366
peak=    3.888 closest distance to " CB  VAL A 265 " =    1.230
peak=    3.884 closest distance to " O   HOH Z 425 " =    1.508
peak=    3.882 closest distance to " O   HOH Z  59 " =    1.608
peak=    3.881 closest distance to " O   HOH Z 427 " =    1.383
peak=    3.878 closest distance to " O   HOH Z  45 " =    1.005
peak=    3.877 closest distance to " O   HOH Z 435 " =    2.079
peak=    3.862 closest distance to " O   HOH Z 366 " =    2.595
peak=    3.855 closest distance to " CB  GLN A 183 " =    1.178
peak=    3.850 closest distance to " O   HOH Z   3 " =    2.101
peak=    3.850 closest distance to " O   HOH Z 128 " =    2.002
peak=    3.840 closest distance to " CD2 LEU A 228 " =    1.229
peak=    3.837 closest distance to " OE1 GLU A   2 " =    2.008
peak=    3.817 closest distance to " CG  PRO A 198 " =    1.283
peak=    3.809 closest distance to " O   HOH Z 143 " =    1.515
peak=    3.804 closest distance to " OG BSER A 212 " =    2.888
peak=    3.801 closest distance to " O   HOH Z 276 " =    1.277
peak=    3.799 closest distance to " CB  SER A 276 " =    1.401
peak=    3.789 closest distance to " CG AARG A 275 " =    1.306
peak=    3.787 closest distance to " O   HOH Z 410 " =    1.439
peak=    3.780 closest distance to " O   HOH Z 371 " =    2.969
peak=    3.777 closest distance to " NE2 GLN A  55 " =    1.476
peak=    3.768 closest distance to " CB  ALA A 248 " =    1.360
peak=    3.765 closest distance to " O   HOH Z 347 " =    1.084
peak=    3.764 closest distance to " CB  ARG A 139 " =    0.954
peak=    3.758 closest distance to " O   HOH Z  39 " =    1.500
peak=    3.743 closest distance to " O   HOH Z 368 " =    2.064
peak=    3.736 closest distance to " O   HOH Z 128 " =    2.014
peak=    3.734 closest distance to " O   HOH Z 334 " =    1.452
peak=    3.729 closest distance to " ND1 HIS A  81 " =    1.426
peak=    3.729 closest distance to " C   ALA A 299 " =    0.929
peak=    3.727 closest distance to " O   HOH Z 425 " =    1.984
peak=    3.715 closest distance to " CE AMET A  47 " =    1.130
peak=    3.712 closest distance to " CG2 VAL A 257 " =    0.959
peak=    3.698 closest distance to " CB  ARG A  79 " =    1.462
peak=    3.686 closest distance to " NH2BARG A 190 " =    1.532
peak=    3.680 closest distance to " CG  LYS A  76 " =    1.554
peak=    3.671 closest distance to " NH1AARG A 275 " =    1.072
peak=    3.670 closest distance to " O   HOH Z 211 " =    1.118
peak=    3.670 closest distance to " O   HOH Z 345 " =    3.107
peak=    3.667 closest distance to " CA  PHE A 283 " =    1.107
peak=    3.666 closest distance to " OG BSER A 210 " =    1.490
peak=    3.664 closest distance to " O   HOH Z 176 " =    1.716
peak=    3.653 closest distance to " O   HOH Z 287 " =    1.654
peak=    3.649 closest distance to " O   HOH Z 181 " =    2.138
peak=    3.647 closest distance to " O   HOH Z 109 " =    2.091
peak=    3.642 closest distance to " CB  ALA A   9 " =    1.550
peak=    3.640 closest distance to " O   HOH Z  30 " =    1.797
peak=    3.635 closest distance to " OG  SER A  97 " =    2.877
peak=    3.634 closest distance to " O   HOH Z 213 " =    1.735
peak=    3.633 closest distance to " O   HOH Z 130 " =    1.753
peak=    3.632 closest distance to " O   HOH Z 222 " =    2.130
peak=    3.628 closest distance to " O   HOH Z 130 " =    1.765
peak=    3.626 closest distance to " CG BARG A 102 " =    1.789
peak=    3.617 closest distance to " CB  ALA A  10 " =    0.716
peak=    3.612 closest distance to " ND2 ASN A 187 " =    1.702
peak=    3.612 closest distance to " CB  THR A  31 " =    1.503
peak=    3.608 closest distance to " O   HOH Z  71 " =    1.262
peak=    3.604 closest distance to " O   HOH Z 258 " =    2.219
peak=    3.603 closest distance to " NH1 ARG A  14 " =    1.052
peak=    3.601 closest distance to " CB  GLU A 152 " =    1.239
peak=    3.601 closest distance to " O   HOH Z  47 " =    1.569
peak=    3.599 closest distance to " O   HOH Z 244 " =    1.741
peak=    3.597 closest distance to " O   HOH Z  80 " =    1.607
peak=    3.584 closest distance to " CB BVAL A  41 " =    1.211
peak=    3.581 closest distance to " O   HOH Z 298 " =    1.731
peak=    3.581 closest distance to " NH2BARG A 145 " =    1.289
peak=    3.579 closest distance to " O  BHOH Z  74 " =    1.141
peak=    3.579 closest distance to " O   HOH Z 424 " =    2.130
peak=    3.576 closest distance to " O   HOH Z  61 " =    1.486
peak=    3.574 closest distance to " N   ARG A 156 " =    1.315
peak=    3.573 closest distance to " CB  SER A  63 " =    1.238
peak=    3.568 closest distance to " NH2AARG A 145 " =    1.071
peak=    3.554 closest distance to " O   HOH Z 250 " =    1.425
peak=    3.553 closest distance to " O   HOH Z 222 " =    1.298
peak=    3.551 closest distance to " O   HOH Z 145 " =    1.797
peak=    3.548 closest distance to " O   HOH Z   4 " =    1.423
peak=    3.547 closest distance to " O   HOH Z  51 " =    1.443
peak=    3.546 closest distance to " N   ASN A 148 " =    1.114
peak=    3.545 closest distance to " CD  ARG A 269 " =    1.101
peak=    3.545 closest distance to " CB  ASN A 142 " =    1.057
peak=    3.541 closest distance to " O   HOH Z 234 " =    2.006
peak=    3.538 closest distance to " CB  ASN A 187 " =    1.067
peak=    3.537 closest distance to " O   HOH Z 295 " =    1.271
peak=    3.535 closest distance to " CB  TYR A  30 " =    1.746
peak=    3.530 closest distance to " CG2 THR A 221 " =    1.250
peak=    3.527 closest distance to " O   HOH Z 153 " =    3.528
peak=    3.521 closest distance to " CG  LEU A 281 " =    1.069
peak=    3.515 closest distance to " CB  ARG A 138 " =    1.155
peak=    3.514 closest distance to " CG2 ILE A  20 " =    1.656
peak=    3.511 closest distance to " CD1 LEU A   5 " =    1.782
peak=    3.511 closest distance to " O   HOH Z 261 " =    2.282
peak=    3.506 closest distance to " ND2 ASN A 249 " =    0.992
peak=    3.504 closest distance to " O   HOH Z 353 " =    2.505
peak=    3.501 closest distance to " N   PHE A 130 " =    1.341
peak=    3.501 closest distance to " O   ARG A 275 " =    1.051
peak=    3.496 closest distance to " O   HOH Z 437 " =    2.217
peak=    3.493 closest distance to " O   HOH Z 203 " =    1.547
peak=    3.492 closest distance to " O   HOH Z 344 " =    2.530
peak=    3.486 closest distance to " O   HOH Z 238 " =    0.957
peak=    3.485 closest distance to " O   HOH Z 365 " =    1.917
peak=    3.482 closest distance to " CA  ILE A 234 " =    0.995
peak=    3.479 closest distance to " CB  ALA A 114 " =    1.155
peak=    3.454 closest distance to " CB  ASN A 215 " =    1.108
peak=    3.454 closest distance to " CA  ASN A 215 " =    0.914
peak=    3.452 closest distance to " CZ  PHE A  38 " =    1.196
peak=    3.445 closest distance to " O   HOH Z  95 " =    1.251
peak=    3.436 closest distance to " CB  HIS A 108 " =    0.890
peak=    3.436 closest distance to " CD  GLN A 194 " =    1.435
peak=    3.432 closest distance to " O   HOH Z 233 " =    1.652
peak=    3.430 closest distance to " O   HOH Z 245 " =    1.455
peak=    3.426 closest distance to " NH2AARG A 190 " =    1.783
peak=    3.424 closest distance to " O   HOH Z  59 " =    2.153
peak=    3.423 closest distance to " OG  SER A  62 " =    2.889
peak=    3.422 closest distance to " OD1 ASN A  45 " =    1.350
peak=    3.418 closest distance to " CB  ASN A 148 " =    1.882
peak=    3.415 closest distance to " O   HOH Z 337 " =    1.669
peak=    3.409 closest distance to " CB  SER A 216 " =    0.839
peak=    3.404 closest distance to " CA  ALA A  51 " =    1.048
peak=    3.401 closest distance to " CG2 ILE A 120 " =    1.378
peak=    3.401 closest distance to " O   HOH Z   9 " =    1.850
peak=    3.397 closest distance to " CB  GLU A 128 " =    1.023
peak=    3.395 closest distance to " O   HOH Z 147 " =    1.532
peak=    3.393 closest distance to " O   HOH Z 130 " =    1.712
peak=    3.392 closest distance to " CG2 ILE A  20 " =    1.245
peak=    3.386 closest distance to " OD2 ASP A 286 " =    2.291
peak=    3.386 closest distance to " CG  LEU A 167 " =    1.232
peak=    3.385 closest distance to " O   HOH Z 411 " =    3.638
peak=    3.383 closest distance to " CA  LEU A 282 " =    1.206
peak=    3.377 closest distance to " O   HOH Z 227 " =    1.963
peak=    3.372 closest distance to " O   HOH Z 106 " =    2.664
peak=    3.372 closest distance to " CB  GLN A  88 " =    1.373
peak=    3.368 closest distance to " CB  ALA A 114 " =    1.475
peak=    3.368 closest distance to " O   HOH Z 389 " =    1.385
peak=    3.366 closest distance to " O   HOH Z 261 " =    1.664
peak=    3.361 closest distance to " O   HOH Z 261 " =    2.158
peak=    3.356 closest distance to " O   HOH Z 254 " =    1.522
peak=    3.354 closest distance to " O   HOH Z 303 " =    2.200
peak=    3.353 closest distance to " CB  TRP A 266 " =    1.147
peak=    3.349 closest distance to " N   SER A 271 " =    1.007
peak=    3.347 closest distance to " NH1BARG A 145 " =    1.539
peak=    3.346 closest distance to " O   HOH Z 156 " =    2.901
peak=    3.340 closest distance to " NE2 GLN A  73 " =    1.638
peak=    3.340 closest distance to " O   HOH Z 248 " =    1.709
peak=    3.339 closest distance to " O   HOH Z 402 " =    1.341
peak=    3.339 closest distance to " CE  MET A  93 " =    1.570
peak=    3.338 closest distance to " O   HOH Z 132 " =    1.100
peak=    3.336 closest distance to " O   HOH Z 193 " =    2.058
peak=    3.334 closest distance to " OG ASER A  99 " =    1.521
peak=    3.334 closest distance to " CA  ASN A 284 " =    0.929
peak=    3.331 closest distance to " O   HOH Z 162 " =    1.620
peak=    3.331 closest distance to " O   HOH Z 118 " =    1.661
peak=    3.328 closest distance to " O   HOH Z 422 " =    0.976
peak=    3.317 closest distance to " OG BSER A 164 " =    2.240
peak=    3.316 closest distance to " O   HOH Z 222 " =    1.896
peak=    3.315 closest distance to " O   HOH Z 392 " =    2.929
peak=    3.310 closest distance to " NE  ARG A  56 " =    3.326
peak=    3.310 closest distance to " O   HOH Z   6 " =    1.435
peak=    3.308 closest distance to " CB  GLU A 277 " =    1.083
peak=    3.307 closest distance to " O   HOH Z  89 " =    1.760
peak=    3.304 closest distance to " CA  ASN A 217 " =    1.147
peak=    3.302 closest distance to " CB  TYR A 169 " =    0.812
peak=    3.297 closest distance to " C   LYS A 290 " =    1.227
peak=    3.296 closest distance to " CB  GLU A 277 " =    3.468
peak=    3.289 closest distance to " O  BHOH Z  74 " =    1.410
peak=    3.289 closest distance to " O   HOH Z  40 " =    1.329
peak=    3.282 closest distance to " CB  TRP A 179 " =    1.118
peak=    3.282 closest distance to " O   HOH Z 290 " =    1.197
peak=    3.280 closest distance to " NH1AARG A 145 " =    1.016
peak=    3.265 closest distance to " O   HOH Z 404 " =    1.763
peak=    3.264 closest distance to " O   HOH Z  61 " =    1.627
peak=    3.261 closest distance to " O   HOH Z 375 " =    2.166
peak=    3.256 closest distance to " CD2 TRP A 179 " =    1.404
peak=    3.255 closest distance to " CG1 VAL A 153 " =    0.868
peak=    3.250 closest distance to " O   HOH Z  59 " =    1.880
peak=    3.249 closest distance to " CA  ALA A 129 " =    1.482
peak=    3.244 closest distance to " O   GLY A 147 " =    1.539
peak=    3.244 closest distance to " CG1BVAL A  72 " =    1.356
peak=    3.244 closest distance to " CG  MET A 185 " =    1.326
peak=    3.243 closest distance to " O   HOH Z 169 " =    1.019
peak=    3.240 closest distance to " O   HOH Z  58 " =    1.772
peak=    3.240 closest distance to " N   ASN A  39 " =    1.161
peak=    3.239 closest distance to " CB  PRO A 198 " =    0.840
peak=    3.237 closest distance to " CA  ASN A 176 " =    1.339
peak=    3.235 closest distance to " O   HOH Z 119 " =    1.461
peak=    3.228 closest distance to " O   HOH Z 188 " =    1.374
peak=    3.226 closest distance to " O   HOH Z 392 " =    1.175
peak=    3.226 closest distance to " CG  LYS A 119 " =    1.032
peak=    3.226 closest distance to " O   HOH Z 227 " =    2.139
peak=    3.222 closest distance to " CD2 LEU A 297 " =    1.047
peak=    3.221 closest distance to " CB  GLN A 205 " =    1.114
peak=    3.221 closest distance to " O   HOH Z   1 " =    4.446
peak=    3.220 closest distance to " O   HOH Z 192 " =    2.003
peak=    3.220 closest distance to " O   HOH Z 194 " =    2.002
peak=    3.218 closest distance to " N   THR A  18 " =    1.062
peak=    3.217 closest distance to " CD1 ILE A  33 " =    1.726
peak=    3.213 closest distance to " CG  LYS A 166 " =    1.437
peak=    3.209 closest distance to " O   HOH Z 305 " =    3.354
peak=    3.207 closest distance to " N   SER A  12 " =    1.412
peak=    3.206 closest distance to " NZ BLYS A 290 " =    1.023
peak=    3.198 closest distance to " CE  MET A  40 " =    1.041
peak=    3.192 closest distance to " CG  ARG A  66 " =    1.071
peak=    3.191 closest distance to " O   HOH Z 263 " =    1.485
peak=    3.190 closest distance to " O   HOH Z 215 " =    1.426
peak=    3.186 closest distance to " CB  SER A  62 " =    1.126
peak=    3.183 closest distance to " NZ  LYS A 117 " =    1.219
peak=    3.182 closest distance to " CA  PRO A 163 " =    0.958
peak=    3.181 closest distance to " O   HOH Z 410 " =    1.190
peak=    3.180 closest distance to " CD1 ILE A 263 " =    1.434
peak=    3.178 closest distance to " O   HOH Z  33 " =    1.988
peak=    3.175 closest distance to " O   HOH Z 426 " =    1.644
peak=    3.171 closest distance to " CB  LEU A 255 " =    0.891
peak=    3.171 closest distance to " O   HOH Z 388 " =    1.921
peak=    3.170 closest distance to " CE1 HIS A 108 " =    1.221
peak=    3.169 closest distance to " O   HOH Z 389 " =    1.486
peak=    3.167 closest distance to " N   GLU A   2 " =    1.244
peak=    3.165 closest distance to " O   HOH Z 324 " =    1.477
peak=    3.165 closest distance to " OE2 GLU A   2 " =    1.981
peak=    3.164 closest distance to " CA  TYR A  30 " =    1.073
peak=    3.164 closest distance to " N   ALA A   1 " =    3.243
peak=    3.162 closest distance to " OD1 ASP A 286 " =    1.156
peak=    3.152 closest distance to " O   HOH Z 257 " =    1.316
peak=    3.149 closest distance to " CD  GLN A  58 " =    5.702
peak=    3.147 closest distance to " OG BSER A  99 " =    2.251
peak=    3.146 closest distance to " O   HOH Z   6 " =    2.144
peak=    3.145 closest distance to " CA  PRO A  90 " =    1.100
peak=    3.144 closest distance to " CB  THR A  52 " =    1.084
peak=    3.140 closest distance to " CA  ASP A 124 " =    0.766
peak=    3.140 closest distance to " O   HOH Z 143 " =    1.091
peak=    3.138 closest distance to " CZ2 TRP A 150 " =    1.123
peak=    3.138 closest distance to " O   HOH Z  41 " =    2.497
peak=    3.135 closest distance to " O   HOH Z 408 " =    1.738
peak=    3.133 closest distance to " O   SER A 164 " =    1.299
peak=    3.129 closest distance to " O   HOH Z 418 " =    2.209
peak=    3.129 closest distance to " O   HOH Z 267 " =    2.006
peak=    3.126 closest distance to " CB  PRO A  90 " =    1.149
peak=    3.125 closest distance to " OG1 THR A 246 " =    1.247
peak=    3.122 closest distance to " CA  SER A 210 " =    1.489
peak=    3.120 closest distance to " O   HOH Z 303 " =    1.606
peak=    3.117 closest distance to " CE ALYS A 290 " =    1.031
peak=    3.115 closest distance to " O   GLN A  58 " =    1.416
peak=    3.112 closest distance to " O   HOH Z 183 " =    1.725
peak=    3.110 closest distance to " CB  ASN A  39 " =    0.943
peak=    3.106 closest distance to " N   ASP A 162 " =    1.204
peak=    3.102 closest distance to " O   HOH Z 113 " =    1.958
peak=    3.100 closest distance to " O   ASN A  74 " =    1.656
peak=    3.098 closest distance to " CA  LYS A 117 " =    1.142
peak=    3.096 closest distance to " ND1 HIS A  81 " =    1.177
peak=    3.093 closest distance to " CB  LEU A  83 " =    0.720
peak=    3.087 closest distance to " O   HOH Z 172 " =    3.274
peak=    3.086 closest distance to " CB  GLU A 277 " =    3.650
peak=    3.084 closest distance to " O   HOH Z 356 " =    1.356
peak=    3.083 closest distance to " CA  CYS A 168 " =    0.867
peak=    3.082 closest distance to " OG1 THR A 221 " =    1.342
peak=    3.075 closest distance to " O   HOH Z 412 " =    1.468
peak=    3.075 closest distance to " O   HOH Z 355 " =    1.787
peak=    3.070 closest distance to " CG1 ILE A  33 " =    1.377
peak=    3.068 closest distance to " CA  GLY A  91 " =    1.488
peak=    3.011 closest distance to " N   VAL A 257 " =    1.578

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.560 - 5.595
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 211
   mapped sites are within: 0.714 - 5.595

peak=   -4.751 closest distance to " CD  ARG A 138 " =    1.166
peak=   -4.720 closest distance to " O   PRO A 198 " =    1.084
peak=   -4.670 closest distance to " O   HOH Z  69 " =    1.396
peak=   -4.523 closest distance to " O   HOH Z 290 " =    0.823
peak=   -4.458 closest distance to " CG2 VAL A 230 " =    0.759
peak=   -4.434 closest distance to " O   HOH Z 429 " =    1.952
peak=   -4.411 closest distance to " O   HOH Z 178 " =    0.756
peak=   -4.346 closest distance to " OG BSER A 134 " =    1.189
peak=   -4.307 closest distance to " O   HOH Z 100 " =    0.889
peak=   -4.213 closest distance to " CD  ARG A 156 " =    1.945
peak=   -4.139 closest distance to " CG  ARG A 138 " =    0.873
peak=   -4.066 closest distance to " C   HIS A 108 " =    1.275
peak=   -4.051 closest distance to " CG  GLN A  58 " =    0.914
peak=   -3.997 closest distance to " CD1 LEU A 255 " =    2.729
peak=   -3.945 closest distance to " NH2 ARG A  79 " =    2.019
peak=   -3.934 closest distance to " O   HOH Z 423 " =    2.578
peak=   -3.926 closest distance to " OG  SER A   3 " =    1.152
peak=   -3.923 closest distance to " O   HOH Z 377 " =    0.801
peak=   -3.861 closest distance to " CZ  PHE A 130 " =    0.812
peak=   -3.851 closest distance to " O   HOH Z 164 " =    5.595
peak=   -3.845 closest distance to " NE2 GLN A  88 " =    1.131
peak=   -3.845 closest distance to " CG2 ILE A  20 " =    2.751
peak=   -3.839 closest distance to " O   ILE A  49 " =    1.702
peak=   -3.816 closest distance to " O   HOH Z 185 " =    1.837
peak=   -3.811 closest distance to " O   HOH Z  24 " =    1.002
peak=   -3.794 closest distance to " O   HOH Z 134 " =    3.081
peak=   -3.783 closest distance to " O   HOH Z 130 " =    1.796
peak=   -3.778 closest distance to " CG BARG A 275 " =    0.855
peak=   -3.772 closest distance to " O   HOH Z 427 " =    1.607
peak=   -3.772 closest distance to " O   HOH Z 313 " =    1.428
peak=   -3.772 closest distance to " O   SER A 135 " =    1.487
peak=   -3.769 closest distance to " O   HOH Z 192 " =    0.714
peak=   -3.755 closest distance to " N   GLN A  58 " =    2.242
peak=   -3.750 closest distance to " CG  PHE A 283 " =    2.541
peak=   -3.745 closest distance to " CE2 TYR A  30 " =    2.810
peak=   -3.740 closest distance to " CB  SER A 210 " =    1.170
peak=   -3.698 closest distance to " CD2 LEU A   5 " =    0.978
peak=   -3.691 closest distance to " CD  ARG A  14 " =    3.101
peak=   -3.685 closest distance to " CA  GLY A  23 " =    1.734
peak=   -3.676 closest distance to " O   ALA A 161 " =    1.740
peak=   -3.669 closest distance to " OD2 ASP A 191 " =    1.322
peak=   -3.660 closest distance to " O   SER A  95 " =    1.423
peak=   -3.638 closest distance to " C   ASN A 285 " =    1.952
peak=   -3.626 closest distance to " O   ALA A  51 " =    1.217
peak=   -3.625 closest distance to " O   HOH Z 235 " =    1.048
peak=   -3.593 closest distance to " O   SER A  22 " =    2.276
peak=   -3.590 closest distance to " CD  GLU A 277 " =    0.809
peak=   -3.590 closest distance to " OD2 ASP A  50 " =    1.370
peak=   -3.585 closest distance to " O   HOH Z 368 " =    2.495
peak=   -3.576 closest distance to " O   HOH Z 234 " =    3.888
peak=   -3.576 closest distance to " CD  PRO A 243 " =    1.951
peak=   -3.575 closest distance to " N   THR A 157 " =    1.451
peak=   -3.575 closest distance to " CD1 LEU A 101 " =    2.190
peak=   -3.566 closest distance to " N   GLN A  58 " =    1.061
peak=   -3.559 closest distance to " CE3 TRP A 274 " =    2.123
peak=   -3.538 closest distance to " OD1 ASN A  39 " =    2.060
peak=   -3.537 closest distance to " O   ALA A 292 " =    2.191
peak=   -3.535 closest distance to " O   HOH Z 314 " =    1.603
peak=   -3.535 closest distance to " O   HOH Z 421 " =    2.885
peak=   -3.522 closest distance to " O   HOH Z 140 " =    1.202
peak=   -3.514 closest distance to " O   HOH Z 437 " =    1.938
peak=   -3.511 closest distance to " O   HOH Z 238 " =    0.821
peak=   -3.510 closest distance to " OG  SER A  97 " =    2.235
peak=   -3.508 closest distance to " O   HOH Z 359 " =    1.720
peak=   -3.506 closest distance to " O   HOH Z  88 " =    1.636
peak=   -3.506 closest distance to " CB  TYR A 172 " =    2.482
peak=   -3.493 closest distance to " C   GLN A 205 " =    1.918
peak=   -3.486 closest distance to " N   PRO A 163 " =    1.602
peak=   -3.483 closest distance to " CG  ARG A 219 " =    2.330
peak=   -3.483 closest distance to " O   HOH Z 193 " =    1.675
peak=   -3.480 closest distance to " C   LYS A  76 " =    1.492
peak=   -3.478 closest distance to " O   HOH Z 137 " =    1.467
peak=   -3.468 closest distance to " CB  ALA A 244 " =    2.126
peak=   -3.465 closest distance to " CB  ALA A  43 " =    2.180
peak=   -3.453 closest distance to " O   HOH Z  65 " =    1.044
peak=   -3.448 closest distance to " N   HIS A 115 " =    2.126
peak=   -3.441 closest distance to " C   MET A 188 " =    1.656
peak=   -3.440 closest distance to " N   ALA A 248 " =    1.604
peak=   -3.436 closest distance to " O   HOH Z 203 " =    1.737
peak=   -3.433 closest distance to " O   HOH Z  79 " =    1.648
peak=   -3.431 closest distance to " O   HOH Z 165 " =    2.279
peak=   -3.431 closest distance to " CG  ARG A 219 " =    2.096
peak=   -3.410 closest distance to " O   HOH Z  11 " =    1.901
peak=   -3.405 closest distance to " CB  TRP A 266 " =    1.878
peak=   -3.401 closest distance to " O   HOH Z 344 " =    2.432
peak=   -3.394 closest distance to " CB  GLN A  55 " =    1.269
peak=   -3.386 closest distance to " O   HOH Z 131 " =    4.084
peak=   -3.386 closest distance to " O   HOH Z 359 " =    3.425
peak=   -3.379 closest distance to " CE1 TYR A 247 " =    2.488
peak=   -3.379 closest distance to " C   LEU A 222 " =    1.443
peak=   -3.376 closest distance to " O   HOH Z 147 " =    0.943
peak=   -3.375 closest distance to " OG  SER A 206 " =    1.357
peak=   -3.371 closest distance to " O   HOH Z 125 " =    3.301
peak=   -3.370 closest distance to " CG2 THR A  52 " =    2.987
peak=   -3.364 closest distance to " CE2 PHE A 218 " =    2.347
peak=   -3.354 closest distance to " CD  LYS A 289 " =    2.470
peak=   -3.350 closest distance to " CG  TYR A 169 " =    2.194
peak=   -3.345 closest distance to " OE1 GLN A 183 " =    1.486
peak=   -3.343 closest distance to " O   HOH Z 414 " =    2.505
peak=   -3.341 closest distance to " O   HOH Z  97 " =    1.163
peak=   -3.338 closest distance to " O   HOH Z 211 " =    1.724
peak=   -3.332 closest distance to " O   HOH Z 347 " =    0.933
peak=   -3.329 closest distance to " O   VAL A  67 " =    2.470
peak=   -3.326 closest distance to " CB  ASP A 200 " =    2.602
peak=   -3.326 closest distance to " OG  SER A 245 " =    1.250
peak=   -3.322 closest distance to " O   HOH Z 266 " =    4.777
peak=   -3.314 closest distance to " O   HOH Z 111 " =    4.248
peak=   -3.307 closest distance to " O   HOH Z 307 " =    2.021
peak=   -3.307 closest distance to " CB  ALA A   7 " =    2.017
peak=   -3.301 closest distance to " O   HOH Z   9 " =    1.493
peak=   -3.301 closest distance to " O   HOH Z 169 " =    0.998
peak=   -3.299 closest distance to " ND2 ASN A 173 " =    1.275
peak=   -3.297 closest distance to " CB  PRO A 163 " =    2.521
peak=   -3.294 closest distance to " CG1 VAL A 197 " =    2.294
peak=   -3.290 closest distance to " OE2 GLU A   2 " =    1.096
peak=   -3.287 closest distance to " OG  SER A  87 " =    1.352
peak=   -3.285 closest distance to " O   HOH Z 394 " =    1.421
peak=   -3.284 closest distance to " O   ALA A 100 " =    2.505
peak=   -3.282 closest distance to " OXT GLY A 302 " =    2.872
peak=   -3.281 closest distance to " ND2 ASN A 209 " =    1.992
peak=   -3.281 closest distance to " CG2 ILE A 151 " =    2.558
peak=   -3.281 closest distance to " N   VAL A  72 " =    1.931
peak=   -3.274 closest distance to " O   HOH Z 351 " =    1.413
peak=   -3.272 closest distance to " CZ  PHE A  16 " =    1.746
peak=   -3.271 closest distance to " OXT GLY A 302 " =    4.200
peak=   -3.268 closest distance to " CB  TRP A 274 " =    2.688
peak=   -3.267 closest distance to " O   HOH Z 385 " =    1.707
peak=   -3.266 closest distance to " OE2 GLU A  53 " =    1.270
peak=   -3.258 closest distance to " O   HOH Z 265 " =    1.883
peak=   -3.258 closest distance to " CA  GLY A  35 " =    2.072
peak=   -3.255 closest distance to " O   HOH Z  47 " =    1.685
peak=   -3.252 closest distance to " O   HOH Z  56 " =    1.967
peak=   -3.250 closest distance to " CG  GLN A 278 " =    1.912
peak=   -3.249 closest distance to " O   ILE A 106 " =    2.006
peak=   -3.247 closest distance to " O   HOH Z 175 " =    1.245
peak=   -3.247 closest distance to " OH  TYR A 169 " =    0.775
peak=   -3.243 closest distance to " O   HOH Z 286 " =    1.660
peak=   -3.242 closest distance to " C   PRO A 213 " =    1.796
peak=   -3.240 closest distance to " O   HOH Z  34 " =    1.903
peak=   -3.238 closest distance to " CD2 PHE A 225 " =    0.921
peak=   -3.238 closest distance to " O   HOH Z 150 " =    2.177
peak=   -3.237 closest distance to " CG1 VAL A 230 " =    1.746
peak=   -3.233 closest distance to " NE2 GLN A  94 " =    1.632
peak=   -3.232 closest distance to " O   HOH Z 281 " =    3.174
peak=   -3.231 closest distance to " CG  LEU A  83 " =    2.069
peak=   -3.229 closest distance to " CD2 TYR A 293 " =    2.066
peak=   -3.228 closest distance to " SG ACYS A 201 " =    0.909
peak=   -3.226 closest distance to " CA  GLY A  98 " =    1.794
peak=   -3.225 closest distance to " CB  ALA A  64 " =    2.609
peak=   -3.223 closest distance to " O   ALA A   1 " =    1.560
peak=   -3.221 closest distance to " O   GLU A 152 " =    1.479
peak=   -3.217 closest distance to " C   ASP A 231 " =    2.393
peak=   -3.210 closest distance to " C   ARG A 269 " =    1.274
peak=   -3.209 closest distance to " O   HOH Z  77 " =    2.216
peak=   -3.209 closest distance to " CA  GLY A 133 " =    1.945
peak=   -3.208 closest distance to " O   HOH Z 428 " =    1.676
peak=   -3.206 closest distance to " CA  ALA A 299 " =    2.419
peak=   -3.205 closest distance to " O   HOH Z 431 " =    1.305
peak=   -3.205 closest distance to " O   HOH Z 231 " =    1.385
peak=   -3.201 closest distance to " N   ALA A 226 " =    1.887
peak=   -3.194 closest distance to " O   HOH Z 191 " =    5.131
peak=   -3.193 closest distance to " CG1 ILE A 109 " =    2.715
peak=   -3.190 closest distance to " O   PRO A 163 " =    1.101
peak=   -3.189 closest distance to " CG  GLN A 223 " =    1.358
peak=   -3.187 closest distance to " CB  ALA A 114 " =    2.343
peak=   -3.186 closest distance to " CG  ASP A 231 " =    0.790
peak=   -3.183 closest distance to " O   VAL A 174 " =    2.132
peak=   -3.181 closest distance to " OG ASER A 134 " =    1.405
peak=   -3.179 closest distance to " O   PRO A 243 " =    2.518
peak=   -3.172 closest distance to " N   ILE A 263 " =    1.005
peak=   -3.165 closest distance to " O   HOH Z 220 " =    2.064
peak=   -3.159 closest distance to " CB  LEU A 300 " =    2.432
peak=   -3.156 closest distance to " CG1 VAL A 296 " =    2.309
peak=   -3.152 closest distance to " CB  ALA A 291 " =    2.222
peak=   -3.148 closest distance to " O   HOH Z 414 " =    2.515
peak=   -3.147 closest distance to " O   HOH Z 122 " =    2.299
peak=   -3.145 closest distance to " CD2 PHE A 192 " =    2.068
peak=   -3.138 closest distance to " O   ARG A  24 " =    1.862
peak=   -3.137 closest distance to " N   MET A 188 " =    1.984
peak=   -3.135 closest distance to " CB  ASN A  69 " =    1.284
peak=   -3.134 closest distance to " O   HOH Z 394 " =    1.207
peak=   -3.134 closest distance to " O   HOH Z  15 " =    1.423
peak=   -3.131 closest distance to " OE1 GLN A  88 " =    1.100
peak=   -3.126 closest distance to " OG BSER A  99 " =    0.872
peak=   -3.125 closest distance to " CD1 TRP A 179 " =    1.057
peak=   -3.118 closest distance to " CD1 TRP A 274 " =    1.273
peak=   -3.117 closest distance to " O   ASN A 301 " =    1.528
peak=   -3.115 closest distance to " O   SER A 273 " =    1.454
peak=   -3.110 closest distance to " CA  SER A 276 " =    0.997
peak=   -3.107 closest distance to " O   HOH Z 430 " =    1.860
peak=   -3.104 closest distance to " C   LEU A 143 " =    0.976
peak=   -3.104 closest distance to " O   HOH Z 346 " =    1.761
peak=   -3.104 closest distance to " O   HOH Z 407 " =    2.456
peak=   -3.100 closest distance to " O   HOH Z  71 " =    0.754
peak=   -3.100 closest distance to " OD1 ASN A 301 " =    1.998
peak=   -3.100 closest distance to " O   HOH Z 414 " =    2.143
peak=   -3.097 closest distance to " N   ARG A  66 " =    1.657
peak=   -3.097 closest distance to " O   HOH Z 278 " =    1.080
peak=   -3.094 closest distance to " O   HOH Z  63 " =    1.886
peak=   -3.091 closest distance to " O   HOH Z 250 " =    1.294
peak=   -3.088 closest distance to " CD1 ILE A 199 " =    2.306
peak=   -3.087 closest distance to " CA  LYS A 166 " =    2.002
peak=   -3.074 closest distance to " N   SER A 276 " =    1.116
peak=   -3.073 closest distance to " CD  GLN A  11 " =    0.851
peak=   -3.072 closest distance to " CD1 PHE A  61 " =    2.908
peak=   -3.057 closest distance to " O   HOH Z 387 " =    1.936
peak=   -3.053 closest distance to " CD  GLU A 152 " =    0.761

================= 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    :  0.4935 0.4881   6.291226e+00   6.285920e+00
   1_bss:  0.4846 0.4785   6.283044e+00   6.275676e+00
   1_xyz:  0.4106 0.4344   6.194098e+00   6.226474e+00
   1_adp:  0.3663 0.4165   6.129557e+00   6.206097e+00
   1_occ:  0.3656 0.4156   6.128425e+00   6.206461e+00
   2_bss:  0.3636 0.4113   6.127934e+00   6.203980e+00
   2_xyz:  0.2917 0.3517   5.954877e+00   6.086479e+00
   2_adp:  0.2682 0.3315   5.898231e+00   6.043096e+00
   2_occ:  0.2678 0.3314   5.898017e+00   6.043226e+00
   3_bss:  0.2665 0.3304   5.895689e+00   6.040790e+00
   3_xyz:  0.2047 0.2603   5.660066e+00   5.843408e+00
   3_adp:  0.1876 0.2436   5.590638e+00   5.787177e+00
   3_occ:  0.1871 0.2435   5.589545e+00   5.785909e+00
   4_bss:  0.1862 0.2432   5.587547e+00   5.784311e+00
   4_xyz:  0.1447 0.1923   5.357030e+00   5.573604e+00
   4_adp:  0.1347 0.1836   5.298735e+00   5.526646e+00
   4_occ:  0.1346 0.1834   5.297671e+00   5.525077e+00
   5_bss:  0.1347 0.1837   5.296619e+00   5.523885e+00
   5_xyz:  0.1257 0.1723   5.236205e+00   5.466490e+00
   5_adp:  0.1256 0.1666   5.220703e+00   5.435440e+00
   5_occ:  0.1255 0.1664   5.219278e+00   5.433408e+00
   5_bss:  0.1255 0.1664   5.219159e+00   5.433254e+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:  0.405  19.999   7.759   9.217   7.188   0.000   0.000   0.000
   1_xyz:  0.405  19.999   7.759   9.217   7.188   0.000   0.000   0.000
   1_adp:  0.405  19.999   7.759   9.217   7.188   0.000   0.000   0.000
   1_occ:  0.405  19.999   7.759   9.217   7.188   0.000   0.000   0.000
   2_bss:  0.353  27.514   4.833   5.221   4.679   0.000   0.000   0.000
   2_xyz:  0.353  27.514   4.833   5.221   4.679   0.000   0.000   0.000
   2_adp:  0.353  27.514   4.833   5.221   4.679   0.000   0.000   0.000
   2_occ:  0.353  27.514   4.833   5.221   4.679   0.000   0.000   0.000
   3_bss:  0.327  27.514   2.752   3.330   3.683   0.000   0.000   0.000
   3_xyz:  0.327  27.514   2.752   3.330   3.683   0.000   0.000   0.000
   3_adp:  0.327  27.514   2.752   3.330   3.683   0.000   0.000   0.000
   3_occ:  0.327  27.514   2.752   3.330   3.683   0.000   0.000   0.000
   4_bss:  0.323  32.720   1.374   2.046   2.846   0.000   0.000   0.000
   4_xyz:  0.323  32.720   1.374   2.046   2.846   0.000   0.000   0.000
   4_adp:  0.323  32.720   1.374   2.046   2.846   0.000   0.000   0.000
   4_occ:  0.323  32.720   1.374   2.046   2.846   0.000   0.000   0.000
   5_bss:  0.311  34.567   0.967   1.563   2.671   0.000   0.000   0.000
   5_xyz:  0.311  34.567   0.967   1.563   2.671   0.000   0.000   0.000
   5_adp:  0.311  34.567   0.967   1.563   2.671   0.000   0.000   0.000
   5_occ:  0.311  34.567   0.967   1.563   2.671   0.000   0.000   0.000
   5_bss:  0.311  36.169  -0.813  -0.206   1.019   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.026 0.3541  0.4227    77081.407
   1_bss:  62.422 0.3603  0.5389    73719.439
   1_xyz:  51.870 0.4957  0.7359    57556.038
   1_adp:  47.098 0.5567  0.8705    52398.216
   1_occ:  47.053 0.5572  0.8691    52255.905
   2_bss:  46.629 0.5623  0.7827    51457.698
   2_xyz:  37.520 0.6717  0.9213    34272.241
   2_adp:  34.812 0.7035  0.9596    30200.616
   2_occ:  34.810 0.7036  0.9590    30240.715
   3_bss:  34.576 0.7062  0.9052    29855.801
   3_xyz:  25.539 0.8057  0.9999    17198.854
   3_adp:  23.477 0.8279  1.0171    15218.069
   3_occ:  23.448 0.8282  1.0170    15162.037
   4_bss:  23.357 0.8291  0.9751    15087.076
   4_xyz:  18.074 0.8799  1.0015     9431.763
   4_adp:  16.922 0.8907  0.9999     8624.710
   4_occ:  16.889 0.8909  0.9999     8588.232
   5_bss:  16.831 0.8914  0.9870     8541.275
   5_xyz:  15.541 0.9026  0.9931     7524.707
   5_adp:  14.824 0.9087  0.9953     7112.712
   5_occ:  14.791 0.9090  0.9953     7072.452
   5_bss:  14.787 0.9090  0.9904     7068.355
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.084   5.2730e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.084   5.2730e+01
   1_xyz:   1.784  0.014  0.109 18.166  0.007  4.102   1.5671e-01
   1_adp:   1.784  0.014  0.109 18.166  0.007  4.102   1.5671e-01
   1_occ:   1.784  0.014  0.109 18.166  0.007  4.102   1.5671e-01
   2_bss:   1.784  0.014  0.109 18.166  0.007  4.102   1.5671e-01
   2_xyz:   1.187  0.009  0.080 15.917  0.005  4.114   8.5401e-02
   2_adp:   1.187  0.009  0.080 15.917  0.005  4.114   8.5401e-02
   2_occ:   1.187  0.009  0.080 15.917  0.005  4.114   8.5401e-02
   3_bss:   1.187  0.009  0.080 15.917  0.005  4.114   8.5401e-02
   3_xyz:   1.055  0.007  0.071 15.422  0.004  4.109   6.6366e-02
   3_adp:   1.055  0.007  0.071 15.422  0.004  4.109   6.6366e-02
   3_occ:   1.055  0.007  0.071 15.422  0.004  4.109   6.6366e-02
   4_bss:   1.055  0.007  0.071 15.422  0.004  4.109   6.6366e-02
   4_xyz:   1.005  0.006  0.071 15.435  0.004  4.112   6.1336e-02
   4_adp:   1.005  0.006  0.071 15.435  0.004  4.112   6.1336e-02
   4_occ:   1.005  0.006  0.071 15.435  0.004  4.112   6.1336e-02
   5_bss:   1.005  0.006  0.071 15.435  0.004  4.112   6.1336e-02
   5_xyz:   0.893  0.005  0.064 15.323  0.003  4.108   5.1556e-02
   5_adp:   0.893  0.005  0.064 15.323  0.003  4.108   5.1556e-02
   5_occ:   0.893  0.005  0.064 15.323  0.003  4.108   5.1556e-02
   5_bss:   0.893  0.005  0.064 15.323  0.003  4.108   5.1556e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8233e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8233e+00
   1_xyz:  15.563  0.167  0.505 87.991  0.036  2.139   1.0399e-01
   1_adp:  15.563  0.167  0.505 87.991  0.036  2.139   1.0399e-01
   1_occ:  15.563  0.167  0.505 87.991  0.036  2.139   1.0399e-01
   2_bss:  15.563  0.167  0.505 87.991  0.036  2.139   1.0399e-01
   2_xyz:   7.619  0.117  0.384 82.508  0.047  2.221   7.0481e-02
   2_adp:   7.619  0.117  0.384 82.508  0.047  2.221   7.0481e-02
   2_occ:   7.619  0.117  0.384 82.508  0.047  2.221   7.0481e-02
   3_bss:   7.619  0.117  0.384 82.508  0.047  2.221   7.0481e-02
   3_xyz:   7.152  0.063  0.250 78.785  0.024  2.300   7.2240e-02
   3_adp:   7.152  0.063  0.250 78.785  0.024  2.300   7.2240e-02
   3_occ:   7.152  0.063  0.250 78.785  0.024  2.300   7.2240e-02
   4_bss:   7.152  0.063  0.250 78.785  0.024  2.300   7.2240e-02
   4_xyz:   8.341  0.045  0.253 86.722  0.029  2.384   5.1488e-02
   4_adp:   8.341  0.045  0.253 86.722  0.029  2.384   5.1488e-02
   4_occ:   8.341  0.045  0.253 86.722  0.029  2.384   5.1488e-02
   5_bss:   8.341  0.045  0.253 86.722  0.029  2.384   5.1488e-02
   5_xyz:   7.303  0.037  0.207 83.372  0.027  2.399   2.9663e-02
   5_adp:   7.303  0.037  0.207 83.372  0.027  2.399   2.9663e-02
   5_occ:   7.303  0.037  0.207 83.372  0.027  2.399   2.9663e-02
   5_bss:   7.303  0.037  0.207 83.372  0.027  2.399   2.9663e-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:  56.96   0.00  12.96  56.14   0.00  11.24  56.96   0.00  22.33
   1_occ:  56.96   0.00  12.96  56.14   0.00  11.24  56.96   0.00  22.33
   2_bss:  56.96   0.00  12.96  56.14   0.00  11.24  56.96   0.00  22.33
   2_xyz:  56.96   0.00  12.96  56.14   0.00  11.24  56.96   0.00  22.33
   2_adp:  80.30   0.00  13.74  80.30   0.00  10.58  77.44   0.00  30.94
   2_occ:  80.30   0.00  13.74  80.30   0.00  10.58  77.44   0.00  30.94
   3_bss:  80.30   0.00  13.74  80.30   0.00  10.58  77.44   0.00  30.94
   3_xyz:  80.30   0.00  13.74  80.30   0.00  10.58  77.44   0.00  30.94
   3_adp:  84.67   0.00  13.80  84.67   0.00   9.84  76.19   1.23  35.35
   3_occ:  84.67   0.00  13.80  84.67   0.00   9.84  76.19   1.23  35.35
   4_bss:  84.67   0.00  13.80  84.67   0.00   9.84  76.19   1.23  35.35
   4_xyz:  84.67   0.00  13.80  84.67   0.00   9.84  76.19   1.23  35.35
   4_adp:  91.08   0.00  14.15  91.08   0.00   9.50  85.38   0.00  39.49
   4_occ:  91.08   0.00  14.15  91.08   0.00   9.50  85.38   0.00  39.49
   5_bss:  91.08   0.00  14.15  91.08   0.00   9.50  85.38   0.00  39.49
   5_xyz:  91.08   0.00  14.15  91.08   0.00   9.50  85.38   0.00  39.49
   5_adp:  88.57   0.00  13.35  88.57   0.00   9.14  81.67   1.85  36.25
   5_occ:  88.57   0.00  13.35  88.57   0.00   9.14  81.67   1.85  36.25
   5_bss:  90.17   1.60  14.95  90.17   1.60  10.75  83.28   3.45  37.86
------------------------------------------------------------------------
 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:    1.250    0.028    0.420
   1_adp:    1.250    0.028    0.420
   1_occ:    1.250    0.028    0.420
   2_bss:    1.250    0.028    0.420
   2_xyz:    1.525    0.029    0.565
   2_adp:    1.525    0.029    0.565
   2_occ:    1.525    0.029    0.565
   3_bss:    1.525    0.029    0.565
   3_xyz:    1.566    0.025    0.666
   3_adp:    1.566    0.025    0.666
   3_occ:    1.566    0.025    0.666
   4_bss:    1.566    0.025    0.666
   4_xyz:    1.665    0.031    0.745
   4_adp:    1.665    0.031    0.745
   4_occ:    1.665    0.031    0.745
   5_bss:    1.665    0.031    0.745
   5_xyz:    1.734    0.052    0.764
   5_adp:    1.734    0.052    0.764
   5_occ:    1.734    0.052    0.764
   5_bss:    1.734    0.052    0.764
------------------------------------------------------------------------

CPU time actual refinement: 340.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_26/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_26/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_26/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_26/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_26/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 340.56 
  Macro-tasks:
    bulk solvent and scale       = 41.74  
    individual site refinement   = 143.52 
    weights calculation          = 31.47  
    collect and process          = 6.36   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 223.19 
  Micro-tasks:
    mask                            = 2.35   
    f_calc                          = 106.18 
    alpha_beta                      = 8.26   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 116.94 
    fmodel                         = 6.69   
    r_factors                      = 0.26   
    phase_errors                   = 10.04  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 252.17 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.781 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    658 calls, 105.82 s
gradients_fft:          603 calls, 103.33 s

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

# Date 2008-01-16 Time 00:33:21 PST -0800 (1200472401.77 s)
Start R-work = 0.4935, R-free = 0.4881 (no bulk solvent and anisotropic scale)
Final R-work = 0.1424, R-free = 0.1818 (no bulk solvent and anisotropic scale)

Start R-work = 0.4846, R-free = 0.4785
Final R-work = 0.1255, R-free = 0.1664