# Date 2008-01-16 Time 00:39:06 PST -0800 (1200472746.19 s)
#phil __OFF__

Command line arguments: "../86.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1988
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 86

-------------------------------------------------------------------------------
  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, 47.3993, 88.1178, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8784 1.95098
Completeness in resolution range: 0.912389
Completeness with d_max=infinity: 0.909678

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8784
                             d_min =   1.9510

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, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8784 1.95098
Completeness in resolution range: 0.912389
Completeness with d_max=infinity: 0.909678

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8788 -  4.1752 [2247/2275]  2016   231  10.3%
  bin  2:  4.1752 -  3.3262 [2168/2191]  1955   213   9.8%
  bin  3:  3.3262 -  2.9093 [2142/2167]  1931   211   9.9%
  bin  4:  2.9093 -  2.6449 [2115/2131]  1901   214  10.1%
  bin  5:  2.6449 -  2.4562 [2089/2133]  1872   217  10.4%
  bin  6:  2.4562 -  2.3120 [2110/2138]  1907   203   9.6%
  bin  7:  2.3120 -  2.1966 [2072/2108]  1868   204   9.8%
  bin  8:  2.1966 -  2.1012 [2077/2119]  1874   203   9.8%
  bin  9:  2.1012 -  2.0205 [1972/2091]  1777   195   9.9%
  bin 10:  2.0205 -  1.9510 [ 597/2117]   529    68  11.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_86/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:
        1.07 -     1.84: 14
        1.84 -     2.60: 77
        2.60 -     3.37: 4173
        3.37 -     4.13: 9392
        4.13 -     4.90: 14731
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.072 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.133 3.040 -x+1,y-1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.248 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.349 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.383 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28382 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_86/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_86/model_refine_001.geo

CPU time processing inputs: 9.04


============================ 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 47.3993 88.1178 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 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5036   r_free= 0.4947   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.300064                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8788 -  4.6571 0.99   1463  161 0.4021 0.3997      6.6242      6.6556|
|  2:  4.6571 -  3.7154 0.99   1419  155 0.4223 0.4754      6.8066      6.9117|
|  3:  3.7154 -  3.2513 0.99   1370  159 0.4858 0.4565      6.7014      6.7013|
|  4:  3.2513 -  2.9566 0.99   1380  144 0.5054 0.4723      6.5247      6.4958|
|  5:  2.9566 -  2.7461 0.98   1359  152 0.5337 0.5029      6.3743      6.4244|
|  6:  2.7461 -  2.5851 0.99   1356  155 0.5326 0.5639      6.2872      6.2087|
|  7:  2.5851 -  2.4562 0.98   1328  160 0.5360 0.4609       6.226      6.1535|
|  8:  2.4562 -  2.3497 0.99   1353  142 0.5509 0.5213      6.1875      6.1518|
|  9:  2.3497 -  2.2596 0.99   1356  147 0.5511 0.5125      6.1255      6.1772|
| 10:  2.2596 -  2.1819 0.98   1347  147 0.5503 0.5970      6.0888      6.1166|
| 11:  2.1819 -  2.1139 0.97   1315  152 0.5453 0.5523       6.009      6.0312|
| 12:  2.1139 -  2.0536 0.99   1323  149 0.5502 0.5382      5.9509       5.924|
| 13:  2.0536 -  1.9997 0.75   1030  107 0.5484 0.5285       5.877      5.8308|
| 14:  1.9997 -  1.9510 0.17    231   29 0.5490 0.5472      5.9365      5.7438|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8788 -  4.6571  1463   161  0.67  37.37   0.79     0.67      81559.97|
|  2:  4.6571 -  3.7154  1419   155  0.64  40.31   0.87     0.70     130717.77|
|  3:  3.7154 -  3.2513  1370   159  0.52  50.43   0.80     0.64     137379.49|
|  4:  3.2513 -  2.9566  1380   144  0.40  59.72   0.77     0.50     121067.13|
|  5:  2.9566 -  2.7461  1359   152  0.30  67.44   0.71     0.37      96263.16|
|  6:  2.7461 -  2.5851  1356   155  0.25  71.57   0.71     0.30      86203.23|
|  7:  2.5851 -  2.4562  1328   160  0.27  69.56   0.72     0.32      72581.01|
|  8:  2.4562 -  2.3497  1353   142  0.33  65.66   0.71     0.40      61357.07|
|  9:  2.3497 -  2.2596  1356   147  0.34  64.35   0.70     0.43      56054.61|
| 10:  2.2596 -  2.1819  1347   147  0.30  67.61   0.73     0.37      50587.92|
| 11:  2.1819 -  2.1139  1315   152  0.20  75.13   0.71     0.26      53452.32|
| 12:  2.1139 -  2.0536  1323   149  0.16  77.84   0.73     0.22      49751.95|
| 13:  2.0536 -  1.9997  1030   107  0.17  77.14   0.72     0.24      43674.39|
| 14:  1.9997 -  1.9510   231    29  0.31  66.97   0.78     0.32      30181.00|
|alpha:            min =        0.22 max =            0.70 mean =         0.42|
|beta:             min =    30181.00 max =       137379.49 mean =     80512.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           89.99 mean =        62.86|
|phase err.(test): min =        0.00 max =           89.98 mean =        63.29|
|-----------------------------------------------------------------------------|

============================== 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 = 20.383969             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.563   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.846582              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.356   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.835 -  1.241:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.241 -  1.648:       14 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.648 -  2.054:       54 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.054 -  2.461:      374 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.461 -  2.867:     1133 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.867 -  3.274:     2326 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.274 -  3.680:     3853 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.680 -  4.087:     5253 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.087 -  4.493:     7003 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.493 -  4.900:     8418 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.654 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  0.835 |       3.128 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    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 = 11.775)------------------------------------------|
|    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 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5090   r_free= 0.4970   ksol= 0.00   Bsol= 0.00   scale= 0.747    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.300516                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4957   r_free= 0.4908   ksol= 0.32   Bsol= 1.31   scale= 0.988    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.97,8.77,10.94,0.00,0.00,0.00); trace/3= 9.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.293785                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.188637             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.918   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.783141              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.697   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4957      final r-factor (work) = 0.4257          |
| start r-factor (free) = 0.4908      final r-factor (free) = 0.4498          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 110.9346 = 18.19 * 0.50 * 6.2985 + 1.00 * 53.6540                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 56.8942 = 18.19 * 0.50 * 6.2385 + 1.00 * 0.1591                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4257      final r-factor (work) = 0.3831          |
| start r-factor (free) = 0.4498      final r-factor (free) = 0.4442          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1386 = 1.78 * 1.00 * 6.2385 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0255 = 1.78 * 1.00 * 6.1708 + 1.00 * 0.0221                              |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.94   15.50    None  None   None       |
|    all(noH): 2823   0      0.00    78.94   15.50    None  None   None       |
|    Sol.    : 438    0      0.00    78.85   26.67    None  None   None       |
|    Mac.    : 2385   0      0.00    78.94   13.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.894:  955   |   5:    39.469 -  47.362:   78        |
|      1:     7.894 -  15.788:  740   |   6:    47.362 -  55.256:   45        |
|      2:    15.788 -  23.681:  493   |   7:    55.256 -  63.150:   25        |
|      3:    23.681 -  31.575:  330   |   8:    63.150 -  71.044:    8        |
|      4:    31.575 -  39.469:  140   |   9:    71.044 -  78.937:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3831 r_free = 0.4442             target_work(ml) = 6.158         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3828 r_free = 0.4443             target_work(ml) = 6.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3828   r_free= 0.4443   ksol= 0.32   Bsol= 1.31   scale= 1.125    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.97,8.77,10.94,0.00,0.00,0.00); trace/3= 9.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.157608                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3794   r_free= 0.4401   ksol= 0.33   Bsol= 37.63   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.69,4.61,6.60,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.158572                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.117756             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.216  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.666758              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.228  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3794      final r-factor (work) = 0.2941          |
| start r-factor (free) = 0.4401      final r-factor (free) = 0.3525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.4408 = 11.12 * 0.50 * 6.1670 + 1.00 * 0.1591                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.8234 = 11.12 * 0.50 * 6.0671 + 1.00 * 0.0973                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2941      final r-factor (work) = 0.2681          |
| start r-factor (free) = 0.3525      final r-factor (free) = 0.3274          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0691 = 0.67 * 1.00 * 6.0671 + 1.00 * 0.0239                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9571 = 0.67 * 1.00 * 5.9147 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.05   15.04    None  None   None       |
|    all(noH): 2823   0      0.00    81.05   15.04    None  None   None       |
|    Sol.    : 438    0      0.00    79.65   33.28    None  None   None       |
|    Mac.    : 2385   0      0.00    81.05   11.69    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 -   8.105: 1101   |   5:    40.524 -  48.629:  111        |
|      1:     8.105 -  16.210:  783   |   6:    48.629 -  56.734:   43        |
|      2:    16.210 -  24.314:  407   |   7:    56.734 -  64.838:   24        |
|      3:    24.314 -  32.419:  208   |   8:    64.838 -  72.943:   18        |
|      4:    32.419 -  40.524:  124   |   9:    72.943 -  81.048:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2681 r_free = 0.3274             target_work(ml) = 5.883         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2679 r_free = 0.3272             target_work(ml) = 5.882         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2679   r_free= 0.3272   ksol= 0.33   Bsol= 37.63   scale= 1.072   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.69,4.61,6.60,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.882085                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2653   r_free= 0.3245   ksol= 0.34   Bsol= 57.34   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.25,2.59,3.91,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.881061                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.857476              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.671  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.251558              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.620  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2653      final r-factor (work) = 0.1935          |
| start r-factor (free) = 0.3245      final r-factor (free) = 0.2452          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4307 = 5.86 * 0.50 * 5.9184 + 1.00 * 0.0973                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9686 = 5.86 * 0.50 * 5.7668 + 1.00 * 0.0791                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1935      final r-factor (work) = 0.1773          |
| start r-factor (free) = 0.2452      final r-factor (free) = 0.2295          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4641 = 0.25 * 1.00 * 5.7668 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4191 = 0.25 * 1.00 * 5.5674 + 1.00 * 0.0185                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.02   14.67    None  None   None       |
|    all(noH): 2823   0      0.00    80.02   14.67    None  None   None       |
|    Sol.    : 438    0      3.01    76.98   35.32    None  None   None       |
|    Mac.    : 2385   0      0.00    80.02   10.88    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 -   8.002: 1161   |   5:    40.008 -  48.010:  117        |
|      1:     8.002 -  16.003:  847   |   6:    48.010 -  56.012:   49        |
|      2:    16.003 -  24.005:  296   |   7:    56.012 -  64.013:   27        |
|      3:    24.005 -  32.007:  172   |   8:    64.013 -  72.015:   16        |
|      4:    32.007 -  40.008:  135   |   9:    72.015 -  80.016:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1773 r_free = 0.2295             target_work(ml) = 5.532         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1771 r_free = 0.2295             target_work(ml) = 5.531         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1771   r_free= 0.2295   ksol= 0.34   Bsol= 57.34   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.25,2.59,3.91,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.530503                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1754   r_free= 0.2278   ksol= 0.34   Bsol= 57.34   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,1.13,2.44,0.00,0.00,0.00); trace/3= 1.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.528666                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.214902              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.424  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.689602              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.008   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1754      final r-factor (work) = 0.1455          |
| start r-factor (free) = 0.2278      final r-factor (free) = 0.1916          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0441 = 3.21 * 0.50 * 5.5771 + 1.00 * 0.0791                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8331 = 3.21 * 0.50 * 5.4529 + 1.00 * 0.0678                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1455      final r-factor (work) = 0.1347          |
| start r-factor (free) = 0.1916      final r-factor (free) = 0.1827          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7724 = 0.69 * 1.00 * 5.4529 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7029 = 0.69 * 1.00 * 5.3276 + 1.00 * 0.0290                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.54   15.21    None  None   None       |
|    all(noH): 2823   0      0.00    86.54   15.21    None  None   None       |
|    Sol.    : 438    0      3.11    82.48   40.52    None  None   None       |
|    Mac.    : 2385   0      0.00    86.54   10.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.654: 1287   |   5:    43.272 -  51.926:  109        |
|      1:     8.654 -  17.309:  867   |   6:    51.926 -  60.581:   74        |
|      2:    17.309 -  25.963:  211   |   7:    60.581 -  69.235:   36        |
|      3:    25.963 -  34.618:  115   |   8:    69.235 -  77.889:   23        |
|      4:    34.618 -  43.272:   92   |   9:    77.889 -  86.544:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1347 r_free = 0.1827             target_work(ml) = 5.307         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1343 r_free = 0.1830             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1830   ksol= 0.34   Bsol= 57.34   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,1.13,2.44,0.00,0.00,0.00); trace/3= 1.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.305270                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1346   r_free= 0.1838   ksol= 0.33   Bsol= 57.34   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,0.74,2.12,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.306646                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.928038              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.389  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.371101              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.225   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1346      final r-factor (work) = 0.1205          |
| start r-factor (free) = 0.1838      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5315 = 3.93 * 0.50 * 5.3277 + 1.00 * 0.0678                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4164 = 3.93 * 0.50 * 5.2607 + 1.00 * 0.0842                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1205      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1709      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9878 = 0.37 * 1.00 * 5.2607 + 1.00 * 0.0356                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9472 = 0.37 * 1.00 * 5.2182 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.75   14.76    None  None   None       |
|    all(noH): 2823   0      0.00    86.75   14.76    None  None   None       |
|    Sol.    : 438    0      3.55    86.75   38.84    None  None   None       |
|    Mac.    : 2385   0      0.00    84.91   10.34    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 -   8.676: 1305   |   5:    43.377 -  52.053:  100        |
|      1:     8.676 -  17.351:  878   |   6:    52.053 -  60.728:   58        |
|      2:    17.351 -  26.026:  199   |   7:    60.728 -  69.404:   31        |
|      3:    26.026 -  34.702:  119   |   8:    69.404 -  78.079:   19        |
|      4:    34.702 -  43.377:  106   |   9:    78.079 -  86.755:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1182 r_free = 0.1675             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1181 r_free = 0.1674             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1674   ksol= 0.33   Bsol= 57.34   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,0.74,2.12,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206508                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8788 -  4.6571 0.99   1463  161 0.0991 0.1392      5.4162       5.619|
|  2:  4.6571 -  3.7154 0.99   1419  155 0.0851 0.1126      5.4548      5.6834|
|  3:  3.7154 -  3.2513 0.99   1370  159 0.1137 0.1604      5.5243      5.8432|
|  4:  3.2513 -  2.9566 0.99   1380  144 0.1287 0.1704       5.469      5.6658|
|  5:  2.9566 -  2.7461 0.98   1359  152 0.1432 0.1650      5.3974      5.5545|
|  6:  2.7461 -  2.5851 0.99   1356  155 0.1310 0.2296       5.266      5.5803|
|  7:  2.5851 -  2.4562 0.98   1328  160 0.1372 0.1723      5.2269      5.3903|
|  8:  2.4562 -  2.3497 0.99   1353  142 0.1253 0.1767       5.132      5.3182|
|  9:  2.3497 -  2.2596 0.99   1356  147 0.1242 0.1944      5.0567      5.3684|
| 10:  2.2596 -  2.1819 0.98   1347  147 0.1190 0.1877      5.0034      5.2473|
| 11:  2.1819 -  2.1139 0.97   1315  152 0.1224 0.1920      4.9516      5.3113|
| 12:  2.1139 -  2.0536 0.99   1323  149 0.1196 0.1649      4.9107      5.1288|
| 13:  2.0536 -  1.9997 0.75   1030  107 0.1172 0.1917      4.8021      5.0124|
| 14:  1.9997 -  1.9510 0.17    231   29 0.1117 0.1650      4.7596      4.9702|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8788 -  4.6571  1463   161  0.93  10.03   0.97     0.95       8408.47|
|  2:  4.6571 -  3.7154  1419   155  0.95   8.87   1.02     1.00      10125.20|
|  3:  3.7154 -  3.2513  1370   159  0.93  12.41   1.02     1.02      11613.88|
|  4:  3.2513 -  2.9566  1380   144  0.91  14.96   1.01     1.00      10956.69|
|  5:  2.9566 -  2.7461  1359   152  0.88  17.78   1.00     0.98      10011.04|
|  6:  2.7461 -  2.5851  1356   155  0.89  17.72   0.97     0.92       7913.55|
|  7:  2.5851 -  2.4562  1328   160  0.89  17.28   0.99     0.95       7141.35|
|  8:  2.4562 -  2.3497  1353   142  0.89  17.01   1.00     0.97       6176.57|
|  9:  2.3497 -  2.2596  1356   147  0.89  16.98   0.99     0.95       5370.13|
| 10:  2.2596 -  2.1819  1347   147  0.89  17.17   1.00     0.98       5073.77|
| 11:  2.1819 -  2.1139  1315   152  0.88  18.06   0.99     0.95       4723.40|
| 12:  2.1139 -  2.0536  1323   149  0.89  17.17   1.00     1.00       4329.97|
| 13:  2.0536 -  1.9997  1030   107  0.89  17.40   0.98     0.96       3517.31|
| 14:  1.9997 -  1.9510   231    29  0.92  14.13   0.97     0.94       2873.55|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2873.55 max =        11613.88 mean =      7386.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.48|
|phase err.(test): min =        0.00 max =           89.99 mean =        14.97|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1674   ksol= 0.32   Bsol= 52.74   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-0.04,1.38,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206620                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1674   ksol= 0.32   Bsol= 52.74   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-0.04,1.38,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206620                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8788 -  4.6571 0.99   1463  161 0.0988 0.1390      5.4143       5.616|
|  2:  4.6571 -  3.7154 0.99   1419  155 0.0846 0.1122      5.4518      5.6803|
|  3:  3.7154 -  3.2513 0.99   1370  159 0.1137 0.1606      5.5232      5.8441|
|  4:  3.2513 -  2.9566 0.99   1380  144 0.1288 0.1708      5.4699      5.6672|
|  5:  2.9566 -  2.7461 0.98   1359  152 0.1433 0.1653      5.3989      5.5559|
|  6:  2.7461 -  2.5851 0.99   1356  155 0.1310 0.2295      5.2671      5.5811|
|  7:  2.5851 -  2.4562 0.98   1328  160 0.1373 0.1726      5.2282      5.3917|
|  8:  2.4562 -  2.3497 0.99   1353  142 0.1253 0.1765      5.1327      5.3185|
|  9:  2.3497 -  2.2596 0.99   1356  147 0.1243 0.1946      5.0574      5.3697|
| 10:  2.2596 -  2.1819 0.98   1347  147 0.1190 0.1876      5.0037      5.2473|
| 11:  2.1819 -  2.1139 0.97   1315  152 0.1224 0.1920      4.9519      5.3114|
| 12:  2.1139 -  2.0536 0.99   1323  149 0.1196 0.1651      4.9111      5.1297|
| 13:  2.0536 -  1.9997 0.75   1030  107 0.1173 0.1916      4.8027      5.0119|
| 14:  1.9997 -  1.9510 0.17    231   29 0.1117 0.1651      4.7605      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: 14.8788 -  4.6571  1463   161  0.93  10.01   0.97     0.95       8373.46|
|  2:  4.6571 -  3.7154  1419   155  0.95   8.85   1.02     1.00      10076.94|
|  3:  3.7154 -  3.2513  1370   159  0.93  12.39   1.03     1.02      11577.97|
|  4:  3.2513 -  2.9566  1380   144  0.91  14.98   1.01     1.00      10977.78|
|  5:  2.9566 -  2.7461  1359   152  0.88  17.81   1.00     0.98      10045.07|
|  6:  2.7461 -  2.5851  1356   155  0.89  17.74   0.97     0.92       7937.95|
|  7:  2.5851 -  2.4562  1328   160  0.89  17.31   0.99     0.95       7160.07|
|  8:  2.4562 -  2.3497  1353   142  0.89  17.03   1.01     0.97       6188.71|
|  9:  2.3497 -  2.2596  1356   147  0.89  17.00   1.00     0.96       5380.78|
| 10:  2.2596 -  2.1819  1347   147  0.89  17.18   1.00     0.98       5078.15|
| 11:  2.1819 -  2.1139  1315   152  0.88  18.07   1.00     0.95       4727.65|
| 12:  2.1139 -  2.0536  1323   149  0.89  17.18   1.00     1.01       4334.98|
| 13:  2.0536 -  1.9997  1030   107  0.89  17.41   0.98     0.96       3520.64|
| 14:  1.9997 -  1.9510   231    29  0.92  14.15   0.98     0.94       2876.75|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2876.75 max =        11577.97 mean =      7387.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.91 mean =        15.49|
|phase err.(test): min =        0.00 max =           89.99 mean =        14.98|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    87.54   15.54    None  None   None       |
|    all(noH): 2823   0      0.78    87.54   15.54    None  None   None       |
|    Sol.    : 438    0      4.33    87.54   39.62    None  None   None       |
|    Mac.    : 2385   0      0.78    85.69   11.12    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:     0.782 -   9.457: 1305   |   5:    44.159 -  52.834:  100        |
|      1:     9.457 -  18.133:  878   |   6:    52.834 -  61.510:   58        |
|      2:    18.133 -  26.808:  199   |   7:    61.510 -  70.185:   31        |
|      3:    26.808 -  35.484:  119   |   8:    70.185 -  78.861:   19        |
|      4:    35.484 -  44.159:  106   |   9:    78.861 -  87.536:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.547 - 4.749
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 321 from: 327
   mapped sites are within: 0.752 - 4.749

peak=   10.870 closest distance to " CB  VAL A 230 " =    1.494
peak=    6.530 closest distance to " O   HOH Z 255 " =    1.214
peak=    5.866 closest distance to " O   HOH Z 169 " =    1.054
peak=    5.758 closest distance to " CG  LEU A   5 " =    1.249
peak=    5.714 closest distance to " CB  VAL A 296 " =    1.121
peak=    5.604 closest distance to " O   HOH Z 188 " =    1.542
peak=    5.570 closest distance to " O   HOH Z 248 " =    1.500
peak=    5.490 closest distance to " O   HOH Z  43 " =    1.742
peak=    5.252 closest distance to " NH2 ARG A  56 " =    2.178
peak=    5.117 closest distance to " CG  PRO A  54 " =    1.341
peak=    5.096 closest distance to " NE2 GLN A  11 " =    1.120
peak=    5.061 closest distance to " O   HOH Z 403 " =    1.781
peak=    4.888 closest distance to " CG1 VAL A 296 " =    1.230
peak=    4.861 closest distance to " O   HOH Z 251 " =    1.669
peak=    4.771 closest distance to " CD2 LEU A   5 " =    1.167
peak=    4.712 closest distance to " CB  ARG A 275 " =    0.936
peak=    4.697 closest distance to " O   HOH Z 238 " =    1.767
peak=    4.679 closest distance to " CG  LEU A 228 " =    1.208
peak=    4.646 closest distance to " CZ  PHE A 218 " =    1.168
peak=    4.644 closest distance to " CB  GLN A 223 " =    1.524
peak=    4.589 closest distance to " O   HOH Z 193 " =    2.148
peak=    4.563 closest distance to " O   HOH Z 126 " =    1.538
peak=    4.519 closest distance to " O   HOH Z 368 " =    2.211
peak=    4.502 closest distance to " O   HOH Z 209 " =    2.349
peak=    4.494 closest distance to " CB  SER A  63 " =    1.066
peak=    4.467 closest distance to " O   HOH Z  85 " =    1.816
peak=    4.464 closest distance to " O   HOH Z  76 " =    1.207
peak=    4.463 closest distance to " O   HOH Z 406 " =    1.588
peak=    4.462 closest distance to " O   HOH Z 124 " =    1.252
peak=    4.460 closest distance to " CG2 VAL A 296 " =    1.050
peak=    4.418 closest distance to " CA  ALA A  51 " =    1.035
peak=    4.381 closest distance to " CD2 TRP A 179 " =    1.357
peak=    4.380 closest distance to " CB  VAL A 230 " =    1.211
peak=    4.352 closest distance to " CB  GLU A 152 " =    1.213
peak=    4.350 closest distance to " O   HOH Z 142 " =    1.608
peak=    4.332 closest distance to " O   HOH Z 128 " =    1.481
peak=    4.316 closest distance to " O   HOH Z 210 " =    1.013
peak=    4.292 closest distance to " O   HOH Z 425 " =    1.488
peak=    4.288 closest distance to " O   HOH Z 359 " =    1.837
peak=    4.272 closest distance to " O   HOH Z 394 " =    1.595
peak=    4.271 closest distance to " CB  SER A  26 " =    1.857
peak=    4.232 closest distance to " O   HOH Z 346 " =    1.532
peak=    4.227 closest distance to " CB  GLN A 183 " =    1.281
peak=    4.223 closest distance to " CB  ASN A 148 " =    1.322
peak=    4.222 closest distance to " O   HOH Z 154 " =    1.864
peak=    4.209 closest distance to " CD1AILE A 234 " =    0.974
peak=    4.194 closest distance to " CA  TYR A  30 " =    0.934
peak=    4.188 closest distance to " O   HOH Z 258 " =    1.185
peak=    4.172 closest distance to " O   HOH Z 272 " =    1.860
peak=    4.170 closest distance to " O   HOH Z  80 " =    1.893
peak=    4.162 closest distance to " O   HOH Z 421 " =    1.936
peak=    4.161 closest distance to " O   HOH Z 232 " =    2.332
peak=    4.161 closest distance to " CD2 LEU A 228 " =    1.224
peak=    4.154 closest distance to " CB  GLU A 277 " =    3.644
peak=    4.151 closest distance to " O   HOH Z 411 " =    3.936
peak=    4.120 closest distance to " O   HOH Z 188 " =    2.515
peak=    4.116 closest distance to " CB  PRO A  54 " =    0.965
peak=    4.109 closest distance to " O   HOH Z 375 " =    0.995
peak=    4.095 closest distance to " O   HOH Z 130 " =    2.542
peak=    4.091 closest distance to " O   HOH Z 234 " =    3.455
peak=    4.083 closest distance to " CB  ARG A  79 " =    1.498
peak=    4.055 closest distance to " O   HOH Z 102 " =    1.403
peak=    4.045 closest distance to " CD  LYS A  76 " =    1.805
peak=    4.043 closest distance to " O   PRO A 198 " =    1.567
peak=    4.033 closest distance to " CD  ARG A 159 " =    0.759
peak=    4.032 closest distance to " O   HOH Z 375 " =    1.304
peak=    4.016 closest distance to " O   HOH Z 422 " =    2.629
peak=    3.992 closest distance to " O   HOH Z  63 " =    1.943
peak=    3.986 closest distance to " O   HOH Z 313 " =    1.909
peak=    3.977 closest distance to " CB  ASP A 298 " =    1.155
peak=    3.973 closest distance to " O   HOH Z 246 " =    1.275
peak=    3.960 closest distance to " O   HOH Z 214 " =    3.132
peak=    3.955 closest distance to " CG  GLN A  58 " =    0.923
peak=    3.949 closest distance to " O   HOH Z 142 " =    2.508
peak=    3.947 closest distance to " CB  ASN A 142 " =    1.161
peak=    3.945 closest distance to " O   SER A  87 " =    2.314
peak=    3.929 closest distance to " O   HOH Z 117 " =    1.197
peak=    3.918 closest distance to " O   HOH Z 404 " =    1.610
peak=    3.911 closest distance to " O   HOH Z  97 " =    1.337
peak=    3.903 closest distance to " CG  PRO A 243 " =    1.105
peak=    3.893 closest distance to " ND2 ASN A 187 " =    1.625
peak=    3.887 closest distance to " O   HOH Z 287 " =    1.802
peak=    3.874 closest distance to " O   HOH Z  40 " =    1.765
peak=    3.866 closest distance to " O   HOH Z 414 " =    1.444
peak=    3.865 closest distance to " O   HOH Z 419 " =    1.816
peak=    3.847 closest distance to " O   ASN A  74 " =    1.526
peak=    3.827 closest distance to " CG2 ILE A 234 " =    1.253
peak=    3.814 closest distance to " O   HOH Z 126 " =    1.789
peak=    3.802 closest distance to " O   HOH Z 327 " =    1.654
peak=    3.797 closest distance to " CD  LYS A 166 " =    1.386
peak=    3.786 closest distance to " CB  ALA A   9 " =    1.666
peak=    3.779 closest distance to " N   ASN A  39 " =    1.393
peak=    3.779 closest distance to " O   HOH Z 303 " =    2.246
peak=    3.777 closest distance to " O   HOH Z  35 " =    2.241
peak=    3.776 closest distance to " CB  SER A   3 " =    1.323
peak=    3.772 closest distance to " O   HOH Z 265 " =    1.968
peak=    3.749 closest distance to " CD  PRO A  54 " =    0.999
peak=    3.748 closest distance to " O   HOH Z 130 " =    1.167
peak=    3.729 closest distance to " O   HOH Z  78 " =    1.737
peak=    3.721 closest distance to " CB  ARG A  79 " =    1.018
peak=    3.717 closest distance to " O   HOH Z 316 " =    3.085
peak=    3.713 closest distance to " CB  THR A  52 " =    0.932
peak=    3.708 closest distance to " CA  ARG A  36 " =    1.052
peak=    3.698 closest distance to " CA  ASP A 162 " =    1.004
peak=    3.677 closest distance to " CG2AVAL A 121 " =    2.167
peak=    3.676 closest distance to " O   HOH Z   1 " =    2.277
peak=    3.675 closest distance to " O   HOH Z 423 " =    2.766
peak=    3.675 closest distance to " O   HOH Z 298 " =    4.317
peak=    3.666 closest distance to " O   HOH Z 365 " =    2.546
peak=    3.658 closest distance to " O   HOH Z 120 " =    2.642
peak=    3.657 closest distance to " CB  TRP A 266 " =    1.098
peak=    3.657 closest distance to " CB  ARG A 190 " =    1.626
peak=    3.652 closest distance to " O   HOH Z  30 " =    1.341
peak=    3.651 closest distance to " O   HOH Z 369 " =    2.312
peak=    3.649 closest distance to " O   HOH Z 423 " =    1.814
peak=    3.642 closest distance to " CA  TYR A 116 " =    1.438
peak=    3.637 closest distance to " CA  ALA A 158 " =    1.479
peak=    3.631 closest distance to " O   HOH Z 236 " =    1.585
peak=    3.629 closest distance to " CG1 ILE A  20 " =    1.380
peak=    3.624 closest distance to " O   HOH Z  95 " =    1.185
peak=    3.622 closest distance to " O   HOH Z  15 " =    2.109
peak=    3.620 closest distance to " ND2 ASN A 249 " =    0.907
peak=    3.615 closest distance to " CA  ASN A 217 " =    1.070
peak=    3.606 closest distance to " CB  ASN A 110 " =    1.035
peak=    3.595 closest distance to " CB  PHE A 204 " =    0.844
peak=    3.588 closest distance to " O   HOH Z  59 " =    2.153
peak=    3.579 closest distance to " O   HOH Z 298 " =    2.546
peak=    3.579 closest distance to " CB  ALA A 248 " =    1.341
peak=    3.577 closest distance to " O   HOH Z 427 " =    2.579
peak=    3.577 closest distance to " O   ALA A 165 " =    1.457
peak=    3.574 closest distance to " O   ASP A 124 " =    1.418
peak=    3.572 closest distance to " NZ  LYS A 117 " =    2.787
peak=    3.569 closest distance to " NH2BARG A 145 " =    2.365
peak=    3.561 closest distance to " O   HOH Z 402 " =    1.354
peak=    3.559 closest distance to " CD  ARG A 269 " =    1.004
peak=    3.557 closest distance to " CZ3 TRP A 266 " =    1.038
peak=    3.556 closest distance to " OG BSER A 212 " =    2.633
peak=    3.551 closest distance to " O   HOH Z 416 " =    2.720
peak=    3.543 closest distance to " O   HOH Z 213 " =    1.723
peak=    3.543 closest distance to " CG AARG A 102 " =    1.133
peak=    3.523 closest distance to " CZ  PHE A  38 " =    1.121
peak=    3.518 closest distance to " O   HOH Z 132 " =    2.655
peak=    3.517 closest distance to " CD1 ILE A 199 " =    1.100
peak=    3.516 closest distance to " O   HOH Z 344 " =    1.803
peak=    3.513 closest distance to " O   HOH Z  61 " =    1.719
peak=    3.511 closest distance to " O   HOH Z 263 " =    1.803
peak=    3.505 closest distance to " CD  LYS A 119 " =    1.909
peak=    3.505 closest distance to " O   HOH Z 371 " =    2.781
peak=    3.504 closest distance to " O   HOH Z 415 " =    3.658
peak=    3.497 closest distance to " O   HOH Z 361 " =    2.562
peak=    3.494 closest distance to " CA  SER A  32 " =    1.756
peak=    3.488 closest distance to " O   HOH Z 345 " =    1.652
peak=    3.473 closest distance to " CB  THR A  31 " =    1.602
peak=    3.468 closest distance to " CA  ALA A 291 " =    0.863
peak=    3.465 closest distance to " O   HOH Z 385 " =    3.823
peak=    3.458 closest distance to " CE  LYS A  76 " =    0.871
peak=    3.456 closest distance to " CG  PHE A 204 " =    0.879
peak=    3.453 closest distance to " CG  PRO A 213 " =    1.219
peak=    3.445 closest distance to " NH1AARG A 145 " =    1.421
peak=    3.444 closest distance to " O   HOH Z 438 " =    2.886
peak=    3.442 closest distance to " O   HOH Z 368 " =    4.749
peak=    3.441 closest distance to " OG BSER A 164 " =    2.319
peak=    3.440 closest distance to " O   HOH Z 173 " =    2.250
peak=    3.436 closest distance to " CG  LEU A 167 " =    1.197
peak=    3.435 closest distance to " NH1AARG A 275 " =    0.937
peak=    3.434 closest distance to " O   HOH Z 403 " =    1.426
peak=    3.430 closest distance to " O   HOH Z 337 " =    1.947
peak=    3.428 closest distance to " O   HOH Z 361 " =    3.282
peak=    3.425 closest distance to " CG  MET A 185 " =    1.126
peak=    3.424 closest distance to " O   HOH Z 148 " =    3.274
peak=    3.414 closest distance to " O   HOH Z 107 " =    0.861
peak=    3.409 closest distance to " CB  ASN A 215 " =    1.084
peak=    3.406 closest distance to " O   HOH Z 298 " =    1.689
peak=    3.405 closest distance to " CB  ARG A 156 " =    1.097
peak=    3.404 closest distance to " O   HOH Z 404 " =    2.133
peak=    3.404 closest distance to " CB  SER A  97 " =    0.831
peak=    3.399 closest distance to " CA  ALA A 160 " =    0.957
peak=    3.397 closest distance to " O   HOH Z 162 " =    1.695
peak=    3.394 closest distance to " O   HOH Z 325 " =    2.223
peak=    3.388 closest distance to " O   HOH Z   9 " =    2.273
peak=    3.386 closest distance to " O   HOH Z 193 " =    1.482
peak=    3.383 closest distance to " O   HOH Z 245 " =    1.462
peak=    3.383 closest distance to " CB  TYR A 169 " =    0.810
peak=    3.382 closest distance to " CB  PRO A 198 " =    1.182
peak=    3.378 closest distance to " O   HOH Z 409 " =    1.595
peak=    3.371 closest distance to " CA  ARG A 195 " =    1.211
peak=    3.368 closest distance to " CD  ARG A 195 " =    0.855
peak=    3.366 closest distance to " CB  SER A 141 " =    1.120
peak=    3.363 closest distance to " O   HOH Z 126 " =    1.552
peak=    3.361 closest distance to " O   HOH Z   4 " =    1.575
peak=    3.358 closest distance to " O   HOH Z 200 " =    2.489
peak=    3.356 closest distance to " O   HOH Z 137 " =    1.582
peak=    3.355 closest distance to " CG2 THR A 221 " =    1.258
peak=    3.353 closest distance to " O   HOH Z  88 " =    2.881
peak=    3.353 closest distance to " O   HOH Z 357 " =    2.014
peak=    3.352 closest distance to " O   HOH Z 313 " =    1.516
peak=    3.349 closest distance to " CB  ASP A 191 " =    1.152
peak=    3.347 closest distance to " CA  PHE A 283 " =    1.104
peak=    3.346 closest distance to " N   GLN A 194 " =    1.676
peak=    3.343 closest distance to " O   HOH Z 132 " =    2.608
peak=    3.338 closest distance to " O   HOH Z 158 " =    3.259
peak=    3.336 closest distance to " O   HOH Z 425 " =    1.882
peak=    3.335 closest distance to " O   THR A 182 " =    1.474
peak=    3.332 closest distance to " O   HOH Z 380 " =    2.012
peak=    3.332 closest distance to " O   HOH Z  94 " =    2.436
peak=    3.332 closest distance to " CZ2 TRP A 150 " =    1.109
peak=    3.331 closest distance to " O   HOH Z 189 " =    2.390
peak=    3.327 closest distance to " O   HOH Z 388 " =    2.282
peak=    3.324 closest distance to " CG1 ILE A  49 " =    1.525
peak=    3.324 closest distance to " N   PHE A 130 " =    1.417
peak=    3.323 closest distance to " O   HOH Z 366 " =    2.391
peak=    3.321 closest distance to " CB  THR A 235 " =    1.259
peak=    3.320 closest distance to " O   HOH Z 345 " =    2.941
peak=    3.319 closest distance to " CB  ALA A 295 " =    1.305
peak=    3.317 closest distance to " OE1 GLU A   2 " =    2.018
peak=    3.313 closest distance to " CA  ALA A 295 " =    0.993
peak=    3.309 closest distance to " CB  SER A  62 " =    0.955
peak=    3.301 closest distance to " N   ASP A 162 " =    1.245
peak=    3.296 closest distance to " CB  ASP A 124 " =    0.805
peak=    3.295 closest distance to " OD2 ASP A 298 " =    3.888
peak=    3.295 closest distance to " O   HOH Z 438 " =    2.425
peak=    3.293 closest distance to " O   HOH Z 193 " =    1.519
peak=    3.293 closest distance to " CA  ASP A 149 " =    1.128
peak=    3.292 closest distance to " CD2 LEU A 297 " =    0.929
peak=    3.291 closest distance to " O   HOH Z  54 " =    1.532
peak=    3.291 closest distance to " O  BHOH Z  74 " =    1.470
peak=    3.290 closest distance to " O   HOH Z 383 " =    1.682
peak=    3.289 closest distance to " CE  LYS A 119 " =    1.008
peak=    3.288 closest distance to " O   HOH Z  97 " =    1.915
peak=    3.285 closest distance to " CG1 VAL A 174 " =    1.396
peak=    3.285 closest distance to " O   HOH Z 141 " =    1.629
peak=    3.282 closest distance to " N   CYS A 260 " =    0.752
peak=    3.281 closest distance to " CB  SER A  99 " =    1.296
peak=    3.280 closest distance to " CE1 TYR A 186 " =    1.195
peak=    3.277 closest distance to " CB  GLN A  55 " =    0.870
peak=    3.276 closest distance to " O   HOH Z 371 " =    1.296
peak=    3.270 closest distance to " O   HOH Z 410 " =    3.246
peak=    3.269 closest distance to " CB  TRP A 179 " =    1.320
peak=    3.269 closest distance to " OG  SER A 135 " =    1.379
peak=    3.268 closest distance to " CG  GLN A  55 " =    2.408
peak=    3.264 closest distance to " CB  ASP A 107 " =    1.218
peak=    3.262 closest distance to " CG2 VAL A 197 " =    1.015
peak=    3.262 closest distance to " CB  VAL A 265 " =    1.275
peak=    3.258 closest distance to " OH  TYR A 116 " =    1.195
peak=    3.256 closest distance to " O   HOH Z 380 " =    1.960
peak=    3.254 closest distance to " O   HOH Z  83 " =    1.533
peak=    3.253 closest distance to " CB  ALA A 114 " =    0.940
peak=    3.252 closest distance to " CG AARG A 275 " =    1.176
peak=    3.251 closest distance to " CG  LYS A 289 " =    1.451
peak=    3.251 closest distance to " CB  ALA A  71 " =    1.307
peak=    3.250 closest distance to " CG2 ILE A 120 " =    1.536
peak=    3.245 closest distance to " CB  PRO A  90 " =    1.199
peak=    3.242 closest distance to " N   ARG A 156 " =    1.344
peak=    3.237 closest distance to " CD1 LEU A  96 " =    0.879
peak=    3.237 closest distance to " O   HOH Z 209 " =    2.654
peak=    3.235 closest distance to " O   HOH Z 197 " =    1.971
peak=    3.235 closest distance to " CE3 TRP A 150 " =    1.110
peak=    3.232 closest distance to " CG2 THR A  18 " =    1.460
peak=    3.230 closest distance to " CD1 LEU A 228 " =    1.940
peak=    3.227 closest distance to " CB  ASN A  39 " =    0.790
peak=    3.227 closest distance to " CE1 HIS A 108 " =    1.172
peak=    3.224 closest distance to " O   ASN A 284 " =    1.826
peak=    3.224 closest distance to " O   HOH Z 247 " =    1.629
peak=    3.222 closest distance to " O   HOH Z 214 " =    1.270
peak=    3.219 closest distance to " NE2 GLN A  77 " =    3.292
peak=    3.216 closest distance to " O   HOH Z 350 " =    1.827
peak=    3.214 closest distance to " CG  GLN A  88 " =    1.147
peak=    3.211 closest distance to " CB  SER A  62 " =    1.081
peak=    3.210 closest distance to " O   HOH Z 322 " =    2.065
peak=    3.208 closest distance to " O   ALA A 158 " =    1.120
peak=    3.206 closest distance to " O   HOH Z 279 " =    2.107
peak=    3.199 closest distance to " CB  GLN A  89 " =    1.278
peak=    3.196 closest distance to " O   HOH Z  99 " =    1.764
peak=    3.195 closest distance to " O   HOH Z 353 " =    2.744
peak=    3.194 closest distance to " CB  LYS A 290 " =    1.060
peak=    3.192 closest distance to " CB  ARG A 139 " =    1.168
peak=    3.191 closest distance to " O   HOH Z   4 " =    1.785
peak=    3.189 closest distance to " CA  ILE A 106 " =    0.808
peak=    3.187 closest distance to " O   HOH Z 285 " =    2.373
peak=    3.185 closest distance to " O   HOH Z 146 " =    1.441
peak=    3.180 closest distance to " O   HOH Z 130 " =    2.251
peak=    3.167 closest distance to " O   HOH Z 428 " =    3.757
peak=    3.165 closest distance to " O   HOH Z 329 " =    4.172
peak=    3.163 closest distance to " CG  LEU A 237 " =    1.321
peak=    3.158 closest distance to " O   HOH Z 299 " =    4.179
peak=    3.156 closest distance to " CA  LEU A 282 " =    1.262
peak=    3.153 closest distance to " O   HOH Z 147 " =    1.739
peak=    3.149 closest distance to " CB  ASP A 140 " =    1.259
peak=    3.147 closest distance to " CA  ILE A 234 " =    0.952
peak=    3.145 closest distance to " CB  VAL A 202 " =    1.494
peak=    3.144 closest distance to " CD  ARG A  79 " =    1.798
peak=    3.139 closest distance to " O   HOH Z 334 " =    1.364
peak=    3.134 closest distance to " O   HOH Z 185 " =    1.666
peak=    3.132 closest distance to " O   HOH Z 256 " =    2.434
peak=    3.128 closest distance to " CB  ARG A 219 " =    1.166
peak=    3.126 closest distance to " CA  ASN A 176 " =    1.199
peak=    3.122 closest distance to " CA  LYS A 117 " =    1.234
peak=    3.119 closest distance to " O   HOH Z 151 " =    1.710
peak=    3.118 closest distance to " O   HOH Z  28 " =    1.673
peak=    3.118 closest distance to " O   HOH Z 134 " =    1.255
peak=    3.116 closest distance to " O   HOH Z  44 " =    2.219
peak=    3.115 closest distance to " CD2 TYR A 186 " =    1.093
peak=    3.111 closest distance to " O   HOH Z 128 " =    2.404
peak=    3.110 closest distance to " NH2AARG A 275 " =    3.445
peak=    3.109 closest distance to " O   HOH Z 109 " =    2.003
peak=    3.105 closest distance to " O   HOH Z 423 " =    3.018
peak=    3.103 closest distance to " CB  PRO A 243 " =    1.115
peak=    3.101 closest distance to " CE2 TYR A 169 " =    1.310
peak=    3.100 closest distance to " CG BARG A 275 " =    1.252
peak=    3.096 closest distance to " CZ3 TRP A  85 " =    0.945
peak=    3.096 closest distance to " OG  SER A  62 " =    2.710
peak=    3.096 closest distance to " OD1 ASN A 301 " =    1.639
peak=    3.072 closest distance to " O   HOH Z  10 " =    1.737
peak=    3.067 closest distance to " O   HOH Z  41 " =    1.958
peak=    3.065 closest distance to " N   ALA A 295 " =    1.717
peak=    3.065 closest distance to " NH2 ARG A  79 " =    1.267
peak=    3.053 closest distance to " O   HOH Z 163 " =    1.963
peak=    3.048 closest distance to " CB  GLU A  46 " =    1.008
peak=    3.041 closest distance to " OD1 ASP A 231 " =    1.959
peak=    3.038 closest distance to " CA  ASP A 140 " =    1.451
peak=    3.036 closest distance to " O   HOH Z 293 " =    1.980

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.737 - 5.912
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.737 - 5.912

peak=   -5.383 closest distance to " CG2 VAL A 230 " =    0.737
peak=   -4.770 closest distance to " O   HOH Z 193 " =    0.942
peak=   -4.728 closest distance to " CD  ARG A  14 " =    3.168
peak=   -4.681 closest distance to " O   VAL A  67 " =    2.667
peak=   -4.550 closest distance to " CD  ARG A 156 " =    1.994
peak=   -4.499 closest distance to " O   HOH Z 169 " =    0.766
peak=   -4.436 closest distance to " CG  GLN A  58 " =    0.949
peak=   -4.335 closest distance to " O   PRO A 163 " =    2.118
peak=   -4.321 closest distance to " CD2 TYR A 293 " =    1.849
peak=   -4.261 closest distance to " CD1 ILE A 263 " =    2.749
peak=   -4.252 closest distance to " OG BSER A 134 " =    1.367
peak=   -4.247 closest distance to " O   HOH Z 210 " =    0.942
peak=   -4.179 closest distance to " CG2 ILE A  49 " =    2.832
peak=   -4.176 closest distance to " O   HOH Z 267 " =    5.542
peak=   -4.173 closest distance to " C   HIS A 108 " =    1.177
peak=   -4.055 closest distance to " OE1 GLN A 223 " =    2.293
peak=   -4.046 closest distance to " NE2 GLN A  88 " =    1.138
peak=   -3.994 closest distance to " CD1 LEU A 101 " =    2.447
peak=   -3.983 closest distance to " O   GLY A 241 " =    2.378
peak=   -3.969 closest distance to " OG  SER A  97 " =    2.361
peak=   -3.967 closest distance to " O   HOH Z 109 " =    0.772
peak=   -3.937 closest distance to " O   ASN A  45 " =    1.888
peak=   -3.931 closest distance to " O   HOH Z 131 " =    4.156
peak=   -3.931 closest distance to " CB  ALA A  43 " =    2.470
peak=   -3.898 closest distance to " O   PRO A 198 " =    1.256
peak=   -3.885 closest distance to " O   HOH Z 166 " =    1.686
peak=   -3.873 closest distance to " CG1 VAL A 112 " =    2.562
peak=   -3.871 closest distance to " O   HOH Z 203 " =    1.461
peak=   -3.844 closest distance to " CB  ALA A 248 " =    2.321
peak=   -3.836 closest distance to " O   ALA A 256 " =    1.805
peak=   -3.786 closest distance to " CE2 TYR A  30 " =    2.711
peak=   -3.783 closest distance to " OXT GLY A 302 " =    2.909
peak=   -3.779 closest distance to " O   HOH Z 196 " =    2.126
peak=   -3.768 closest distance to " O   HOH Z 116 " =    1.315
peak=   -3.760 closest distance to " O   PHE A 218 " =    1.424
peak=   -3.751 closest distance to " O   HOH Z 348 " =    2.279
peak=   -3.744 closest distance to " O   HOH Z 216 " =    1.135
peak=   -3.728 closest distance to " CG2 ILE A  20 " =    2.965
peak=   -3.706 closest distance to " O   VAL A 174 " =    2.235
peak=   -3.700 closest distance to " OH  TYR A 172 " =    1.771
peak=   -3.682 closest distance to " CA  ASP A 298 " =    1.074
peak=   -3.666 closest distance to " CD1 PHE A  59 " =    2.016
peak=   -3.659 closest distance to " O   HOH Z 423 " =    2.517
peak=   -3.656 closest distance to " O   HOH Z 351 " =    1.625
peak=   -3.648 closest distance to " CZ  PHE A  38 " =    2.281
peak=   -3.647 closest distance to " CE BMET A  47 " =    1.264
peak=   -3.631 closest distance to " CH2 TRP A 179 " =    1.255
peak=   -3.617 closest distance to " ND2 ASN A  69 " =    1.937
peak=   -3.600 closest distance to " N   SER A 276 " =    1.478
peak=   -3.599 closest distance to " O   HOH Z 387 " =    2.769
peak=   -3.595 closest distance to " CG  GLN A 103 " =    2.517
peak=   -3.586 closest distance to " O   HOH Z  13 " =    1.884
peak=   -3.577 closest distance to " O   HOH Z 407 " =    2.661
peak=   -3.576 closest distance to " O   HOH Z 100 " =    0.788
peak=   -3.568 closest distance to " O   HOH Z 174 " =    3.789
peak=   -3.564 closest distance to " NE2 GLN A  11 " =    1.693
peak=   -3.540 closest distance to " O   HOH Z 119 " =    2.075
peak=   -3.535 closest distance to " O   HOH Z 290 " =    0.986
peak=   -3.532 closest distance to " O   HOH Z 211 " =    1.306
peak=   -3.532 closest distance to " CE  MET A 105 " =    2.226
peak=   -3.529 closest distance to " O   GLY A  80 " =    2.659
peak=   -3.520 closest distance to " O   ALA A 227 " =    1.301
peak=   -3.514 closest distance to " O   HOH Z 165 " =    2.046
peak=   -3.509 closest distance to " CD2 LEU A 167 " =    1.753
peak=   -3.506 closest distance to " O   HOH Z 179 " =    2.183
peak=   -3.503 closest distance to " NE2 GLN A  88 " =    1.870
peak=   -3.503 closest distance to " O   HOH Z 285 " =    1.875
peak=   -3.502 closest distance to " CG1 VAL A  78 " =    2.445
peak=   -3.499 closest distance to " O   HOH Z  65 " =    0.829
peak=   -3.485 closest distance to " O   HOH Z  28 " =    2.424
peak=   -3.479 closest distance to " ND2 ASN A  45 " =    1.284
peak=   -3.477 closest distance to " O   HOH Z 185 " =    2.438
peak=   -3.471 closest distance to " O   HOH Z 111 " =    1.758
peak=   -3.467 closest distance to " OG  SER A  87 " =    1.519
peak=   -3.466 closest distance to " O   HOH Z 177 " =    1.418
peak=   -3.462 closest distance to " CB  PRO A 163 " =    2.534
peak=   -3.462 closest distance to " CZ  PHE A  38 " =    2.168
peak=   -3.461 closest distance to " CE1 TYR A 247 " =    2.631
peak=   -3.454 closest distance to " CH2 TRP A 150 " =    1.099
peak=   -3.451 closest distance to " CG  ARG A 269 " =    2.106
peak=   -3.449 closest distance to " CG  LEU A   5 " =    0.989
peak=   -3.447 closest distance to " O   HOH Z  78 " =    1.698
peak=   -3.444 closest distance to " O   HOH Z   6 " =    1.672
peak=   -3.437 closest distance to " OG ASER A 134 " =    1.337
peak=   -3.420 closest distance to " OD2 ASP A 191 " =    1.491
peak=   -3.417 closest distance to " CE3 TRP A 150 " =    2.262
peak=   -3.414 closest distance to " O   HOH Z 372 " =    0.958
peak=   -3.413 closest distance to " O   HOH Z 110 " =    1.425
peak=   -3.412 closest distance to " O   HOH Z 102 " =    1.648
peak=   -3.412 closest distance to " N   ALA A 226 " =    1.889
peak=   -3.412 closest distance to " ND2 ASN A 209 " =    2.649
peak=   -3.410 closest distance to " O   HOH Z 114 " =    3.403
peak=   -3.409 closest distance to " O   ASN A 187 " =    1.610
peak=   -3.409 closest distance to " O   HOH Z 387 " =    2.912
peak=   -3.406 closest distance to " O   HOH Z 215 " =    3.942
peak=   -3.395 closest distance to " O   HOH Z 107 " =    1.059
peak=   -3.395 closest distance to " CZ  ARG A  66 " =    1.127
peak=   -3.395 closest distance to " O   HOH Z 128 " =    1.327
peak=   -3.392 closest distance to " O   HOH Z 266 " =    1.567
peak=   -3.386 closest distance to " O   HOH Z 252 " =    3.660
peak=   -3.382 closest distance to " O   HOH Z 275 " =    1.476
peak=   -3.380 closest distance to " OD1 ASN A  39 " =    1.381
peak=   -3.379 closest distance to " O   SER A 276 " =    1.737
peak=   -3.371 closest distance to " O   HOH Z 150 " =    2.241
peak=   -3.368 closest distance to " O   HOH Z 433 " =    0.960
peak=   -3.364 closest distance to " O   HOH Z 137 " =    1.558
peak=   -3.362 closest distance to " O   LEU A 282 " =    2.125
peak=   -3.362 closest distance to " CB  SER A 210 " =    1.233
peak=   -3.358 closest distance to " O   HOH Z 218 " =    3.888
peak=   -3.358 closest distance to " O   TRP A  92 " =    1.967
peak=   -3.356 closest distance to " CB  ALA A 248 " =    2.131
peak=   -3.351 closest distance to " O   HOH Z 208 " =    1.801
peak=   -3.351 closest distance to " NE2 GLN A 194 " =    1.913
peak=   -3.338 closest distance to " O   HOH Z 340 " =    1.850
peak=   -3.335 closest distance to " O   HOH Z 426 " =    2.364
peak=   -3.334 closest distance to " CG1 VAL A 112 " =    2.667
peak=   -3.333 closest distance to " ND2BASN A 224 " =    1.770
peak=   -3.330 closest distance to " O   HOH Z 329 " =    1.084
peak=   -3.328 closest distance to " CD1 ILE A 199 " =    2.298
peak=   -3.326 closest distance to " N   PHE A  59 " =    2.105
peak=   -3.322 closest distance to " O   HOH Z 111 " =    4.043
peak=   -3.319 closest distance to " O   HOH Z 377 " =    2.197
peak=   -3.312 closest distance to " CG2 VAL A 296 " =    1.166
peak=   -3.309 closest distance to " O   HOH Z 292 " =    3.093
peak=   -3.309 closest distance to " O   HOH Z 264 " =    1.650
peak=   -3.309 closest distance to " CG  MET A 105 " =    0.895
peak=   -3.306 closest distance to " CD1 PHE A 130 " =    2.299
peak=   -3.305 closest distance to " CE1 PHE A 218 " =    1.622
peak=   -3.303 closest distance to " CD  GLN A  88 " =    0.884
peak=   -3.297 closest distance to " C   THR A 279 " =    1.162
peak=   -3.297 closest distance to " O   HOH Z 427 " =    1.401
peak=   -3.296 closest distance to " CD  PRO A 243 " =    1.866
peak=   -3.295 closest distance to " O   HOH Z 166 " =    2.107
peak=   -3.294 closest distance to " CB  ALA A   9 " =    2.399
peak=   -3.287 closest distance to " CD2 PHE A 192 " =    2.073
peak=   -3.284 closest distance to " O   HOH Z 246 " =    0.893
peak=   -3.281 closest distance to " O   SER A 210 " =    1.820
peak=   -3.279 closest distance to " ND2 ASN A 249 " =    2.196
peak=   -3.271 closest distance to " O   ASN A 252 " =    1.436
peak=   -3.269 closest distance to " CG  PRO A 243 " =    1.640
peak=   -3.269 closest distance to " O   HOH Z 414 " =    1.748
peak=   -3.268 closest distance to " O   HOH Z 423 " =    2.637
peak=   -3.265 closest distance to " O   HOH Z 357 " =    2.130
peak=   -3.261 closest distance to " C   ASN A 285 " =    2.154
peak=   -3.261 closest distance to " ND2 ASN A 187 " =    1.602
peak=   -3.253 closest distance to " CB  ASP A 132 " =    2.389
peak=   -3.249 closest distance to " O   ILE A 106 " =    1.801
peak=   -3.247 closest distance to " O   HOH Z 269 " =    1.198
peak=   -3.246 closest distance to " O   ARG A 219 " =    1.641
peak=   -3.239 closest distance to " CA  GLY A 133 " =    2.063
peak=   -3.235 closest distance to " ND2 ASN A 173 " =    1.262
peak=   -3.233 closest distance to " N   ALA A 248 " =    2.378
peak=   -3.230 closest distance to " O   HOH Z 429 " =    1.390
peak=   -3.228 closest distance to " CB  ALA A 161 " =    2.354
peak=   -3.226 closest distance to " O  BHOH Z 338 " =    1.255
peak=   -3.221 closest distance to " O   ASP A 107 " =    1.777
peak=   -3.218 closest distance to " O   HOH Z 154 " =    1.414
peak=   -3.218 closest distance to " O   HOH Z 214 " =    2.596
peak=   -3.214 closest distance to " N   LYS A 289 " =    1.677
peak=   -3.211 closest distance to " OG1 THR A  52 " =    2.657
peak=   -3.211 closest distance to " O   HOH Z 431 " =    2.039
peak=   -3.209 closest distance to " O   HOH Z 250 " =    2.059
peak=   -3.207 closest distance to " O   GLY A  80 " =    2.675
peak=   -3.201 closest distance to " NE  ARG A  66 " =    4.352
peak=   -3.199 closest distance to " NH2 ARG A  66 " =    5.912
peak=   -3.196 closest distance to " OD1 ASN A 301 " =    1.890
peak=   -3.191 closest distance to " O   HOH Z 153 " =    2.937
peak=   -3.189 closest distance to " OXT GLY A 302 " =    3.622
peak=   -3.181 closest distance to " O   ALA A   1 " =    1.603
peak=   -3.177 closest distance to " CE3 TRP A 274 " =    2.285
peak=   -3.177 closest distance to " OD1 ASN A  39 " =    2.158
peak=   -3.174 closest distance to " CG  ASP A 132 " =    2.214
peak=   -3.174 closest distance to " O   HOH Z 183 " =    1.648
peak=   -3.171 closest distance to " O   HOH Z 411 " =    1.418
peak=   -3.171 closest distance to " OG BSER A 210 " =    1.482
peak=   -3.170 closest distance to " NE2 HIS A 108 " =    1.724
peak=   -3.170 closest distance to " O   SER A  95 " =    1.612
peak=   -3.169 closest distance to " O   HOH Z 139 " =    5.121
peak=   -3.168 closest distance to " CG  GLU A 277 " =    1.167
peak=   -3.167 closest distance to " NH2AARG A 275 " =    4.683
peak=   -3.164 closest distance to " N   ALA A  43 " =    2.743
peak=   -3.161 closest distance to " OD2 ASP A 298 " =    1.824
peak=   -3.155 closest distance to " O   HOH Z  71 " =    2.707
peak=   -3.154 closest distance to " O   HOH Z 191 " =    5.817
peak=   -3.149 closest distance to " O   HOH Z 199 " =    2.474
peak=   -3.146 closest distance to " CZ  TYR A 169 " =    1.707
peak=   -3.144 closest distance to " CG1 VAL A 296 " =    1.043
peak=   -3.137 closest distance to " O   HOH Z  10 " =    1.415
peak=   -3.136 closest distance to " CG2 ILE A 263 " =    2.299
peak=   -3.134 closest distance to " CD1 LEU A  83 " =    2.755
peak=   -3.133 closest distance to " O   HOH Z 423 " =    1.047
peak=   -3.133 closest distance to " CD1 ILE A 109 " =    2.599
peak=   -3.130 closest distance to " N   VAL A  41 " =    1.823
peak=   -3.130 closest distance to " O   GLY A  75 " =    1.888
peak=   -3.128 closest distance to " O   HOH Z 313 " =    1.888
peak=   -3.123 closest distance to " CG2AVAL A  72 " =    2.619
peak=   -3.117 closest distance to " CB  HIS A  86 " =    1.182
peak=   -3.114 closest distance to " CB  TRP A  85 " =    2.750
peak=   -3.110 closest distance to " O   HOH Z 190 " =    1.093
peak=   -3.082 closest distance to " OD2 ASP A  50 " =    1.432
peak=   -3.075 closest distance to " O   SER A 273 " =    1.180
peak=   -3.072 closest distance to " O   HOH Z  58 " =    1.077
peak=   -3.071 closest distance to " O   HOH Z 297 " =    2.712
peak=   -3.062 closest distance to " O   HOH Z 353 " =    1.205
peak=   -3.044 closest distance to " O   SER A 141 " =    1.872
peak=   -3.026 closest distance to " O   HOH Z 262 " =    2.630
peak=   -3.025 closest distance to " CG  ARG A 219 " =    2.638
peak=   -3.011 closest distance to " N   ILE A  20 " =    1.840

================= 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    :  0.5036 0.4947   6.300064e+00   6.298040e+00
   1_bss:  0.4957 0.4908   6.293785e+00   6.295510e+00
   1_xyz:  0.4257 0.4498   6.213659e+00   6.251435e+00
   1_adp:  0.3831 0.4442   6.158088e+00   6.237791e+00
   1_occ:  0.3828 0.4443   6.157608e+00   6.238491e+00
   2_bss:  0.3794 0.4401   6.158572e+00   6.238746e+00
   2_xyz:  0.2941 0.3525   5.952424e+00   6.097394e+00
   2_adp:  0.2681 0.3274   5.882528e+00   6.037364e+00
   2_occ:  0.2679 0.3272   5.882085e+00   6.036733e+00
   3_bss:  0.2653 0.3245   5.881061e+00   6.034561e+00
   3_xyz:  0.1935 0.2452   5.610064e+00   5.800730e+00
   3_adp:  0.1773 0.2295   5.531537e+00   5.733494e+00
   3_occ:  0.1771 0.2295   5.530503e+00   5.732422e+00
   4_bss:  0.1754 0.2278   5.528666e+00   5.730464e+00
   4_xyz:  0.1455 0.1916   5.363577e+00   5.570557e+00
   4_adp:  0.1347 0.1827   5.306595e+00   5.529333e+00
   4_occ:  0.1343 0.1830   5.305270e+00   5.529648e+00
   5_bss:  0.1346 0.1838   5.306646e+00   5.531026e+00
   5_xyz:  0.1205 0.1709   5.224621e+00   5.468814e+00
   5_adp:  0.1182 0.1675   5.207021e+00   5.447104e+00
   5_occ:  0.1181 0.1674   5.206508e+00   5.446596e+00
   5_bss:  0.1180 0.1674   5.206620e+00   5.446762e+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:  0.317   1.311   7.966   8.772  10.935   0.000   0.000   0.000
   1_xyz:  0.317   1.311   7.966   8.772  10.935   0.000   0.000   0.000
   1_adp:  0.317   1.311   7.966   8.772  10.935   0.000   0.000   0.000
   1_occ:  0.317   1.311   7.966   8.772  10.935   0.000   0.000   0.000
   2_bss:  0.331  37.633   3.692   4.608   6.603   0.000   0.000   0.000
   2_xyz:  0.331  37.633   3.692   4.608   6.603   0.000   0.000   0.000
   2_adp:  0.331  37.633   3.692   4.608   6.603   0.000   0.000   0.000
   2_occ:  0.331  37.633   3.692   4.608   6.603   0.000   0.000   0.000
   3_bss:  0.340  57.336   1.245   2.589   3.911   0.000   0.000   0.000
   3_xyz:  0.340  57.336   1.245   2.589   3.911   0.000   0.000   0.000
   3_adp:  0.340  57.336   1.245   2.589   3.911   0.000   0.000   0.000
   3_occ:  0.340  57.336   1.245   2.589   3.911   0.000   0.000   0.000
   4_bss:  0.338  57.336  -0.348   1.131   2.440   0.000   0.000   0.000
   4_xyz:  0.338  57.336  -0.348   1.131   2.440   0.000   0.000   0.000
   4_adp:  0.338  57.336  -0.348   1.131   2.440   0.000   0.000   0.000
   4_occ:  0.338  57.336  -0.348   1.131   2.440   0.000   0.000   0.000
   5_bss:  0.328  57.336  -0.655   0.736   2.116   0.000   0.000   0.000
   5_xyz:  0.328  57.336  -0.655   0.736   2.116   0.000   0.000   0.000
   5_adp:  0.328  57.336  -0.655   0.736   2.116   0.000   0.000   0.000
   5_occ:  0.328  57.336  -0.655   0.736   2.116   0.000   0.000   0.000
   5_bss:  0.323  52.737  -1.339  -0.039   1.378   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.907 0.3559  0.4238    80513.630
   1_bss:  64.115 0.3386  0.5228    80433.423
   1_xyz:  54.103 0.4674  0.7139    62465.595
   1_adp:  51.193 0.5045  0.8404    58889.789
   1_occ:  51.262 0.5036  0.8374    58936.850
   2_bss:  50.808 0.5096  0.7377    58677.590
   2_xyz:  38.412 0.6604  0.9282    34931.485
   2_adp:  34.613 0.7056  0.9802    29719.134
   2_occ:  34.559 0.7063  0.9811    29685.544
   3_bss:  34.307 0.7092  0.9045    29404.692
   3_xyz:  24.577 0.8155  0.9962    15715.336
   3_adp:  22.302 0.8394  1.0158    13735.253
   3_occ:  22.272 0.8397  1.0160    13704.469
   4_bss:  22.175 0.8405  0.9636    13585.741
   4_xyz:  18.183 0.8788  0.9789     9489.225
   4_adp:  17.209 0.8877  0.9785     8701.966
   4_occ:  17.211 0.8876  0.9781     8696.729
   5_bss:  17.236 0.8875  0.9663     8750.314
   5_xyz:  15.889 0.8992  0.9737     7665.793
   5_adp:  15.438 0.9033  0.9719     7394.455
   5_occ:  15.427 0.9034  0.9719     7386.449
   5_bss:  15.435 0.9033  0.9734     7387.444
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3654e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3654e+01
   1_xyz:   1.798  0.014  0.111 18.485  0.007  4.107   1.5907e-01
   1_adp:   1.798  0.014  0.111 18.485  0.007  4.107   1.5907e-01
   1_occ:   1.798  0.014  0.111 18.485  0.007  4.107   1.5907e-01
   2_bss:   1.798  0.014  0.111 18.485  0.007  4.107   1.5907e-01
   2_xyz:   1.280  0.010  0.082 16.727  0.005  4.108   9.7335e-02
   2_adp:   1.280  0.010  0.082 16.727  0.005  4.108   9.7335e-02
   2_occ:   1.280  0.010  0.082 16.727  0.005  4.108   9.7335e-02
   3_bss:   1.280  0.010  0.082 16.727  0.005  4.108   9.7335e-02
   3_xyz:   1.178  0.008  0.084 15.933  0.004  4.111   7.9137e-02
   3_adp:   1.178  0.008  0.084 15.933  0.004  4.111   7.9137e-02
   3_occ:   1.178  0.008  0.084 15.933  0.004  4.111   7.9137e-02
   4_bss:   1.178  0.008  0.084 15.933  0.004  4.111   7.9137e-02
   4_xyz:   1.076  0.008  0.078 15.513  0.004  4.121   6.7830e-02
   4_adp:   1.076  0.008  0.078 15.513  0.004  4.121   6.7830e-02
   4_occ:   1.076  0.008  0.078 15.513  0.004  4.121   6.7830e-02
   5_bss:   1.076  0.008  0.078 15.513  0.004  4.121   6.7830e-02
   5_xyz:   1.215  0.010  0.092 15.720  0.004  4.113   8.4220e-02
   5_adp:   1.215  0.010  0.092 15.720  0.004  4.113   8.4220e-02
   5_occ:   1.215  0.010  0.092 15.720  0.004  4.113   8.4220e-02
   5_bss:   1.215  0.010  0.092 15.720  0.004  4.113   8.4220e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.835   6.9450e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.835   6.9450e+00
   1_xyz:  16.096  0.179  0.515 86.267  0.044  2.061   1.0817e-01
   1_adp:  16.096  0.179  0.515 86.267  0.044  2.061   1.0817e-01
   1_occ:  16.096  0.179  0.515 86.267  0.044  2.061   1.0817e-01
   2_bss:  16.096  0.179  0.515 86.267  0.044  2.061   1.0817e-01
   2_xyz:   8.252  0.110  0.279 88.131  0.059  2.240   8.8732e-02
   2_adp:   8.252  0.110  0.279 88.131  0.059  2.240   8.8732e-02
   2_occ:   8.252  0.110  0.279 88.131  0.059  2.240   8.8732e-02
   3_bss:   8.252  0.110  0.279 88.131  0.059  2.240   8.8732e-02
   3_xyz:   8.082  0.054  0.338 88.143  0.040  2.180   5.6884e-02
   3_adp:   8.082  0.054  0.338 88.143  0.040  2.180   5.6884e-02
   3_occ:   8.082  0.054  0.338 88.143  0.040  2.180   5.6884e-02
   4_bss:   8.082  0.054  0.338 88.143  0.040  2.180   5.6884e-02
   4_xyz:   7.479  0.043  0.370 83.119  0.044  2.273   4.2316e-02
   4_adp:   7.479  0.043  0.370 83.119  0.044  2.273   4.2316e-02
   4_occ:   7.479  0.043  0.370 83.119  0.044  2.273   4.2316e-02
   5_bss:   7.479  0.043  0.370 83.119  0.044  2.273   4.2316e-02
   5_xyz:   8.082  0.054  0.515 83.144  0.039  2.234   6.8333e-02
   5_adp:   8.082  0.054  0.515 83.144  0.039  2.234   6.8333e-02
   5_occ:   8.082  0.054  0.515 83.144  0.039  2.234   6.8333e-02
   5_bss:   8.082  0.054  0.515 83.144  0.039  2.234   6.8333e-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:  78.94   0.00  15.50  78.94   0.00  13.45  78.85   0.00  26.67
   1_occ:  78.94   0.00  15.50  78.94   0.00  13.45  78.85   0.00  26.67
   2_bss:  78.94   0.00  15.50  78.94   0.00  13.45  78.85   0.00  26.67
   2_xyz:  78.94   0.00  15.50  78.94   0.00  13.45  78.85   0.00  26.67
   2_adp:  81.05   0.00  15.04  81.05   0.00  11.69  79.65   0.00  33.28
   2_occ:  81.05   0.00  15.04  81.05   0.00  11.69  79.65   0.00  33.28
   3_bss:  81.05   0.00  15.04  81.05   0.00  11.69  79.65   0.00  33.28
   3_xyz:  81.05   0.00  15.04  81.05   0.00  11.69  79.65   0.00  33.28
   3_adp:  80.02   0.00  14.67  80.02   0.00  10.88  76.98   3.01  35.32
   3_occ:  80.02   0.00  14.67  80.02   0.00  10.88  76.98   3.01  35.32
   4_bss:  80.02   0.00  14.67  80.02   0.00  10.88  76.98   3.01  35.32
   4_xyz:  80.02   0.00  14.67  80.02   0.00  10.88  76.98   3.01  35.32
   4_adp:  86.54   0.00  15.21  86.54   0.00  10.57  82.48   3.11  40.52
   4_occ:  86.54   0.00  15.21  86.54   0.00  10.57  82.48   3.11  40.52
   5_bss:  86.54   0.00  15.21  86.54   0.00  10.57  82.48   3.11  40.52
   5_xyz:  86.54   0.00  15.21  86.54   0.00  10.57  82.48   3.11  40.52
   5_adp:  86.75   0.00  14.76  84.91   0.00  10.34  86.75   3.55  38.84
   5_occ:  86.75   0.00  14.76  84.91   0.00  10.34  86.75   3.55  38.84
   5_bss:  87.54   0.78  15.54  85.69   0.78  11.12  87.54   4.33  39.62
------------------------------------------------------------------------
 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:    1.317    0.017    0.419
   1_adp:    1.317    0.017    0.419
   1_occ:    1.317    0.017    0.419
   2_bss:    1.317    0.017    0.419
   2_xyz:    1.946    0.031    0.614
   2_adp:    1.946    0.031    0.614
   2_occ:    1.946    0.031    0.614
   3_bss:    1.946    0.031    0.614
   3_xyz:    1.888    0.058    0.730
   3_adp:    1.888    0.058    0.730
   3_occ:    1.888    0.058    0.730
   4_bss:    1.888    0.058    0.730
   4_xyz:    1.961    0.045    0.781
   4_adp:    1.961    0.045    0.781
   4_occ:    1.961    0.045    0.781
   5_bss:    1.961    0.045    0.781
   5_xyz:    1.997    0.082    0.811
   5_adp:    1.997    0.082    0.811
   5_occ:    1.997    0.082    0.811
   5_bss:    1.997    0.082    0.811
------------------------------------------------------------------------

CPU time actual refinement: 351.00


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_86/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_86/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_86/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_86/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_86/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.85 
  Macro-tasks:
    bulk solvent and scale       = 40.41  
    individual site refinement   = 155.29 
    weights calculation          = 31.72  
    collect and process          = 6.55   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 234.08 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 110.22 
    alpha_beta                      = 8.26   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 122.69 
    fmodel                         = 7.27   
    r_factors                      = 0.27   
    phase_errors                   = 10.32  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 262.97 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.863 micro seconds
Total CPU time: 6.07 minutes
from_scatterers_fft:    652 calls, 109.88 s
gradients_fft:          596 calls, 108.78 s

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

# Date 2008-01-16 Time 00:45:10 PST -0800 (1200473110.09 s)
Start R-work = 0.5036, R-free = 0.4947 (no bulk solvent and anisotropic scale)
Final R-work = 0.1366, R-free = 0.1818 (no bulk solvent and anisotropic scale)

Start R-work = 0.4957, R-free = 0.4908
Final R-work = 0.1180, R-free = 0.1674