# Date 2008-01-16 Time 00:45:27 PST -0800 (1200473127.44 s)
#phil __OFF__

Command line arguments: "../136.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18520
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 136

-------------------------------------------------------------------------------
  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: (68.845, 45.9914, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7541 1.96025
Completeness in resolution range: 0.971677
Completeness with d_max=infinity: 0.96865

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7541
                             d_min =   1.9603

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: (68.845, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7541 1.96025
Completeness in resolution range: 0.971677
Completeness with d_max=infinity: 0.96865

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7545 -  4.1939 [2125/2149]  1910   215  10.1%
  bin  2:  4.1939 -  3.3416 [2032/2052]  1833   199   9.8%
  bin  3:  3.3416 -  2.9229 [2011/2030]  1810   201  10.0%
  bin  4:  2.9229 -  2.6574 [1966/1996]  1765   201  10.2%
  bin  5:  2.6574 -  2.4678 [1994/2013]  1795   199  10.0%
  bin  6:  2.4678 -  2.3229 [1966/1991]  1771   195   9.9%
  bin  7:  2.3229 -  2.2070 [1946/1974]  1751   195  10.0%
  bin  8:  2.2070 -  2.1112 [1963/1999]  1768   195   9.9%
  bin  9:  2.1112 -  2.0301 [1929/1971]  1733   196  10.2%
  bin 10:  2.0301 -  1.9603 [1657/1985]  1494   163   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_136/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.36 -     2.07: 21
        2.07 -     2.78: 607
        2.78 -     3.48: 4665
        3.48 -     4.19: 9611
        4.19 -     4.90: 14105
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.358 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.372 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.642 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.642 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.691 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29004 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_136/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_136/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 = 68.845 45.9914 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4972   r_free= 0.4947   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| 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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.296072                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7545 -  4.6774 0.99   1382  152 0.4171 0.4173      6.6159      6.6523|
|  2:  4.6774 -  3.7324 0.99   1312  151 0.4258 0.4032       6.827      6.8146|
|  3:  3.7324 -  3.2664 0.99   1299  141 0.4640 0.4436      6.7198      6.7486|
|  4:  3.2664 -  2.9704 0.99   1296  141 0.4835 0.4409      6.5601      6.4894|
|  5:  2.9704 -  2.7590 0.99   1270  144 0.5270 0.5184      6.3944      6.4181|
|  6:  2.7590 -  2.5973 0.99   1288  145 0.5263 0.5474      6.3028      6.2228|
|  7:  2.5973 -  2.4678 0.99   1266  141 0.5260 0.5126      6.2605      6.2048|
|  8:  2.4678 -  2.3609 0.98   1270  137 0.5454 0.5334      6.2068      6.2168|
|  9:  2.3609 -  2.2703 0.98   1249  143 0.5257 0.5989      6.1236      6.1835|
| 10:  2.2703 -  2.1922 1.00   1277  138 0.5385 0.5442      6.1319      6.1288|
| 11:  2.1922 -  2.1239 0.97   1249  138 0.5368 0.5377      6.0463      6.0761|
| 12:  2.1239 -  2.0633 0.98   1250  139 0.5321 0.5359      5.9893       6.051|
| 13:  2.0633 -  2.0092 0.99   1251  139 0.5524 0.5298      5.9128      5.8562|
| 14:  2.0092 -  1.9603 0.77    971  110 0.5386 0.5145      5.8775      5.7875|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7545 -  4.6774  1382   152  0.62  40.98   0.79     0.68      95652.86|
|  2:  4.6774 -  3.7324  1312   151  0.66  38.81   0.87     0.74     125714.93|
|  3:  3.7324 -  3.2664  1299   141  0.56  47.51   0.86     0.69     130259.98|
|  4:  3.2664 -  2.9704  1296   141  0.47  54.36   0.80     0.57     113108.58|
|  5:  2.9704 -  2.7590  1270   144  0.35  63.89   0.74     0.43      92805.85|
|  6:  2.7590 -  2.5973  1288   145  0.30  67.78   0.72     0.34      81475.80|
|  7:  2.5973 -  2.4678  1266   141  0.20  74.77   0.75     0.24      77941.95|
|  8:  2.4678 -  2.3609  1270   137  0.18  76.73   0.73     0.21      71663.24|
|  9:  2.3609 -  2.2703  1249   143  0.17  77.64   0.73     0.20      66652.20|
| 10:  2.2703 -  2.1922  1277   138  0.20  74.74   0.76     0.25      57398.05|
| 11:  2.1922 -  2.1239  1249   138  0.19  76.13   0.76     0.23      54626.34|
| 12:  2.1239 -  2.0633  1250   139  0.21  74.71   0.78     0.26      48708.09|
| 13:  2.0633 -  2.0092  1251   139  0.24  72.54   0.74     0.30      40891.31|
| 14:  2.0092 -  1.9603   971   110  0.36  63.51   0.73     0.40      29221.06|
|alpha:            min =        0.20 max =            0.74 mean =         0.40|
|beta:             min =    29221.06 max =       130259.98 mean =     78877.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           90.00 mean =        64.30|
|phase err.(test): min =        0.00 max =           89.98 mean =        64.40|
|-----------------------------------------------------------------------------|

============================== 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 = 22.263912             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.538   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.004624              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.735   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.104 -  1.484:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.484 -  1.863:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.863 -  2.243:      152 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.243 -  2.622:      627 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.622 -  3.002:     1467 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.002 -  3.382:     2606 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.382 -  3.761:     4065 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.761 -  4.141:     5255 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.141 -  4.520:     6793 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.520 -  4.900:     8056 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.733 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.085    4.900  1.104 |       2.963 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.319)------------------------------------------|
|    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 = 11.319)------------------------------------------|
|    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: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5019   r_free= 0.4959   ksol= 0.00   Bsol= 0.00   scale= 0.763    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.296553                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4885   r_free= 0.4843   ksol= 0.41   Bsol= 20.00   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.96,9.51,7.00,0.00,0.00,0.00); trace/3= 7.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.288725                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.062041             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.469   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.916117              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.359   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4885      final r-factor (work) = 0.4243          |
| start r-factor (free) = 0.4843      final r-factor (free) = 0.4483          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 106.4242 = 17.06 * 0.50 * 6.2936 + 1.00 * 52.7330                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.3461 = 17.06 * 0.50 * 6.2353 + 1.00 * 0.1525                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4243      final r-factor (work) = 0.3806          |
| start r-factor (free) = 0.4483      final r-factor (free) = 0.4375          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.9620 = 1.92 * 1.00 * 6.2353 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.8573 = 1.92 * 1.00 * 6.1767 + 1.00 * 0.0221                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.85   14.54    None  None   None       |
|    all(noH): 2823   0      0.00    77.85   14.54    None  None   None       |
|    Sol.    : 438    0      0.00    73.67   23.86    None  None   None       |
|    Mac.    : 2385   0      0.00    77.85   12.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.785: 1031   |   5:    38.927 -  46.712:   91        |
|      1:     7.785 -  15.571:  743   |   6:    46.712 -  54.498:   37        |
|      2:    15.571 -  23.356:  448   |   7:    54.498 -  62.283:   16        |
|      3:    23.356 -  31.142:  316   |   8:    62.283 -  70.068:    8        |
|      4:    31.142 -  38.927:  129   |   9:    70.068 -  77.854:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3806 r_free = 0.4375             target_work(ml) = 6.164         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3798 r_free = 0.4378             target_work(ml) = 6.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3798   r_free= 0.4378   ksol= 0.41   Bsol= 20.00   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.96,9.51,7.00,0.00,0.00,0.00); trace/3= 7.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.162872                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3785   r_free= 0.4338   ksol= 0.34   Bsol= 20.00   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.38,6.06,4.89,0.00,0.00,0.00); trace/3= 5.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.161912                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.763984             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.947  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.858803              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.428  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3785      final r-factor (work) = 0.3037          |
| start r-factor (free) = 0.4338      final r-factor (free) = 0.3649          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.6255 = 13.76 * 0.50 * 6.1716 + 1.00 * 0.1525                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.9614 = 13.76 * 0.50 * 6.0816 + 1.00 * 0.1082                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3037      final r-factor (work) = 0.2779          |
| start r-factor (free) = 0.3649      final r-factor (free) = 0.3479          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2460 = 0.86 * 1.00 * 6.0816 + 1.00 * 0.0232                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1392 = 0.86 * 1.00 * 5.9575 + 1.00 * 0.0228                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.13   14.10    None  None   None       |
|    all(noH): 2823   0      0.00    84.13   14.10    None  None   None       |
|    Sol.    : 438    0      0.00    83.27   29.62    None  None   None       |
|    Mac.    : 2385   0      0.00    84.13   11.25    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 -   8.413: 1203   |   5:    42.063 -  50.475:   62        |
|      1:     8.413 -  16.825:  763   |   6:    50.475 -  58.888:   29        |
|      2:    16.825 -  25.238:  369   |   7:    58.888 -  67.300:   11        |
|      3:    25.238 -  33.650:  241   |   8:    67.300 -  75.713:    4        |
|      4:    33.650 -  42.063:  138   |   9:    75.713 -  84.125:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2779 r_free = 0.3479             target_work(ml) = 5.935         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2778 r_free = 0.3486             target_work(ml) = 5.935         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2778   r_free= 0.3486   ksol= 0.34   Bsol= 20.00   scale= 1.076   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.38,6.06,4.89,0.00,0.00,0.00); trace/3= 5.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.934897                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2763   r_free= 0.3476   ksol= 0.34   Bsol= 50.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,3.46,3.48,0.00,0.00,0.00); trace/3= 3.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.933621                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.735467              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.096  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.366314              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.361   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2763      final r-factor (work) = 0.2060          |
| start r-factor (free) = 0.3476      final r-factor (free) = 0.2617          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1482 = 7.74 * 0.50 * 5.9570 + 1.00 * 0.1082                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6076 = 7.74 * 0.50 * 5.8235 + 1.00 * 0.0837                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2060      final r-factor (work) = 0.1801          |
| start r-factor (free) = 0.2617      final r-factor (free) = 0.2344          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1490 = 0.37 * 1.00 * 5.8235 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0606 = 0.37 * 1.00 * 5.5969 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.07   13.62    None  None   None       |
|    all(noH): 2823   0      0.00    86.07   13.62    None  None   None       |
|    Sol.    : 438    0      2.41    77.54   35.54    None  None   None       |
|    Mac.    : 2385   0      0.00    86.07   9.59     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 -   8.607: 1462   |   5:    43.033 -  51.639:  100        |
|      1:     8.607 -  17.213:  700   |   6:    51.639 -  60.246:   43        |
|      2:    17.213 -  25.820:  214   |   7:    60.246 -  68.852:   22        |
|      3:    25.820 -  34.426:  157   |   8:    68.852 -  77.459:    5        |
|      4:    34.426 -  43.033:  118   |   9:    77.459 -  86.065:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1801 r_free = 0.2344             target_work(ml) = 5.541         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1795 r_free = 0.2337             target_work(ml) = 5.539         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1795   r_free= 0.2337   ksol= 0.34   Bsol= 50.00   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,3.46,3.48,0.00,0.00,0.00); trace/3= 3.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.539196                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1785   r_free= 0.2326   ksol= 0.33   Bsol= 39.48   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.30,1.89,2.74,0.00,0.00,0.00); trace/3= 1.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.536180                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.864957              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.037  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.134660              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.968  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1785      final r-factor (work) = 0.1424          |
| start r-factor (free) = 0.2326      final r-factor (free) = 0.1910          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1045 = 2.86 * 0.50 * 5.5992 + 1.00 * 0.0837                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8647 = 2.86 * 0.50 * 5.4460 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1424      final r-factor (work) = 0.1372          |
| start r-factor (free) = 0.1910      final r-factor (free) = 0.1819          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7437 = 0.13 * 1.00 * 5.4460 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7255 = 0.13 * 1.00 * 5.3262 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.46   13.09    None  None   None       |
|    all(noH): 2823   0      0.00    83.46   13.09    None  None   None       |
|    Sol.    : 438    0      2.85    74.28   34.60    None  None   None       |
|    Mac.    : 2385   0      0.00    83.46   9.14     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.346: 1479   |   5:    41.731 -  50.077:   83        |
|      1:     8.346 -  16.692:  734   |   6:    50.077 -  58.423:   55        |
|      2:    16.692 -  25.039:  185   |   7:    58.423 -  66.769:   18        |
|      3:    25.039 -  33.385:  141   |   8:    66.769 -  75.116:    8        |
|      4:    33.385 -  41.731:  119   |   9:    75.116 -  83.462:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1372 r_free = 0.1819             target_work(ml) = 5.300         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1368 r_free = 0.1812             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1368   r_free= 0.1812   ksol= 0.33   Bsol= 39.48   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.30,1.89,2.74,0.00,0.00,0.00); trace/3= 1.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.297190                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1368   r_free= 0.1804   ksol= 0.32   Bsol= 32.61   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.91,1.35,2.61,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.296096                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.630816              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.579   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.586481              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.024   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1368      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0682 = 2.63 * 0.50 * 5.3252 + 1.00 * 0.0634                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9607 = 2.63 * 0.50 * 5.2438 + 1.00 * 0.0629                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1222      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1666      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0836 = 0.59 * 1.00 * 5.2438 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0571 = 0.59 * 1.00 * 5.1854 + 1.00 * 0.0160                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.01   13.51    None  None   None       |
|    all(noH): 2823   0      0.00    88.01   13.51    None  None   None       |
|    Sol.    : 438    0      2.53    79.81   37.33    None  None   None       |
|    Mac.    : 2385   0      0.00    88.01   9.13     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 -   8.801: 1588   |   5:    44.003 -  52.804:   85        |
|      1:     8.801 -  17.601:  652   |   6:    52.804 -  61.604:   70        |
|      2:    17.601 -  26.402:  163   |   7:    61.604 -  70.405:   26        |
|      3:    26.402 -  35.202:  124   |   8:    70.405 -  79.205:    8        |
|      4:    35.202 -  44.003:  104   |   9:    79.205 -  88.006:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1653             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1177 r_free = 0.1652             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1652   ksol= 0.32   Bsol= 32.61   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.91,1.35,2.61,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.179631                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7545 -  4.6774 0.99   1382  152 0.1036 0.1332      5.4121      5.5488|
|  2:  4.6774 -  3.7324 0.99   1312  151 0.0894 0.1202      5.4805      5.6991|
|  3:  3.7324 -  3.2664 0.99   1299  141 0.1130 0.1468      5.5391       5.855|
|  4:  3.2664 -  2.9704 0.99   1296  141 0.1290 0.1826      5.5054       5.696|
|  5:  2.9704 -  2.7590 0.99   1270  144 0.1369 0.1836      5.3676      5.5797|
|  6:  2.7590 -  2.5973 0.99   1288  145 0.1289 0.2002      5.2544      5.5188|
|  7:  2.5973 -  2.4678 0.99   1266  141 0.1295 0.1676      5.1899      5.3689|
|  8:  2.4678 -  2.3609 0.98   1270  137 0.1251 0.1718      5.1277      5.3812|
|  9:  2.3609 -  2.2703 0.98   1249  143 0.1226 0.1705      5.0588      5.2858|
| 10:  2.2703 -  2.1922 1.00   1277  138 0.1197 0.1793      5.0068       5.245|
| 11:  2.1922 -  2.1239 0.97   1249  138 0.1180 0.1884      4.9849      5.2989|
| 12:  2.1239 -  2.0633 0.98   1250  139 0.1238 0.1798      4.9452      5.2765|
| 13:  2.0633 -  2.0092 0.99   1251  139 0.1126 0.1918      4.8151      5.1342|
| 14:  2.0092 -  1.9603 0.77    971  110 0.0985 0.1582      4.6405      4.8846|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7545 -  4.6774  1382   152  0.94   9.42   0.99     0.96       7486.21|
|  2:  4.6774 -  3.7324  1312   151  0.95   8.48   1.04     1.02       9843.64|
|  3:  3.7324 -  3.2664  1299   141  0.93  12.29   1.05     1.04      11696.88|
|  4:  3.2664 -  2.9704  1296   141  0.91  14.50   1.02     1.01      11343.46|
|  5:  2.9704 -  2.7590  1270   144  0.90  16.33   1.01     0.97       8929.14|
|  6:  2.7590 -  2.5973  1288   145  0.89  16.61   0.99     0.95       7509.41|
|  7:  2.5973 -  2.4678  1266   141  0.90  16.56   1.00     0.96       6572.49|
|  8:  2.4678 -  2.3609  1270   137  0.90  15.64   1.01     1.00       5789.69|
|  9:  2.3609 -  2.2703  1249   143  0.90  15.82   1.01     0.98       5231.80|
| 10:  2.2703 -  2.1922  1277   138  0.90  16.25   1.01     0.97       4725.00|
| 11:  2.1922 -  2.1239  1249   138  0.90  16.90   1.01     0.98       4932.54|
| 12:  2.1239 -  2.0633  1250   139  0.89  17.41   1.03     1.01       4591.07|
| 13:  2.0633 -  2.0092  1251   139  0.90  16.26   1.02     1.00       3567.58|
| 14:  2.0092 -  1.9603   971   110  0.93  13.37   1.01     0.98       2410.26|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2410.26 max =        11696.88 mean =      6869.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.67|
|phase err.(test): min =        0.00 max =           89.63 mean =        14.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1652   ksol= 0.32   Bsol= 37.16   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.71,-0.32,1.03,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.178858                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1652   ksol= 0.32   Bsol= 37.16   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.71,-0.32,1.03,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.178858                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7545 -  4.6774 0.99   1382  152 0.1035 0.1328      5.4076      5.5437|
|  2:  4.6774 -  3.7324 0.99   1312  151 0.0899 0.1207      5.4826      5.7036|
|  3:  3.7324 -  3.2664 0.99   1299  141 0.1133 0.1473      5.5415      5.8585|
|  4:  3.2664 -  2.9704 0.99   1296  141 0.1290 0.1827      5.5058      5.6949|
|  5:  2.9704 -  2.7590 0.99   1270  144 0.1367 0.1832      5.3667      5.5783|
|  6:  2.7590 -  2.5973 0.99   1288  145 0.1286 0.1997      5.2528      5.5163|
|  7:  2.5973 -  2.4678 0.99   1266  141 0.1294 0.1674      5.1885      5.3686|
|  8:  2.4678 -  2.3609 0.98   1270  137 0.1250 0.1715      5.1263      5.3799|
|  9:  2.3609 -  2.2703 0.98   1249  143 0.1225 0.1703      5.0579      5.2852|
| 10:  2.2703 -  2.1922 1.00   1277  138 0.1196 0.1790      5.0058      5.2446|
| 11:  2.1922 -  2.1239 0.97   1249  138 0.1179 0.1881      4.9841      5.2978|
| 12:  2.1239 -  2.0633 0.98   1250  139 0.1236 0.1798      4.9446      5.2773|
| 13:  2.0633 -  2.0092 0.99   1251  139 0.1125 0.1915      4.8143      5.1324|
| 14:  2.0092 -  1.9603 0.77    971  110 0.0983 0.1581      4.6389      4.8834|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7545 -  4.6774  1382   152  0.94   9.36   0.99     0.96       7395.45|
|  2:  4.6774 -  3.7324  1312   151  0.95   8.48   1.04     1.02       9836.50|
|  3:  3.7324 -  3.2664  1299   141  0.93  12.34   1.05     1.04      11764.22|
|  4:  3.2664 -  2.9704  1296   141  0.91  14.51   1.02     1.01      11350.83|
|  5:  2.9704 -  2.7590  1270   144  0.90  16.32   1.01     0.97       8907.31|
|  6:  2.7590 -  2.5973  1288   145  0.90  16.58   0.99     0.96       7485.30|
|  7:  2.5973 -  2.4678  1266   141  0.90  16.54   1.00     0.97       6552.91|
|  8:  2.4678 -  2.3609  1270   137  0.90  15.61   1.01     1.00       5772.16|
|  9:  2.3609 -  2.2703  1249   143  0.91  15.79   1.01     0.98       5220.94|
| 10:  2.2703 -  2.1922  1277   138  0.90  16.22   1.01     0.97       4715.16|
| 11:  2.1922 -  2.1239  1249   138  0.90  16.90   1.02     0.98       4926.16|
| 12:  2.1239 -  2.0633  1250   139  0.89  17.40   1.03     1.01       4585.45|
| 13:  2.0633 -  2.0092  1251   139  0.90  16.25   1.02     1.01       3561.48|
| 14:  2.0092 -  1.9603   971   110  0.93  13.34   1.01     0.98       2400.93|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2400.93 max =        11764.22 mean =      6858.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.65|
|phase err.(test): min =        0.00 max =           89.54 mean =        14.08|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.64    89.65   15.15    None  None   None       |
|    all(noH): 2823   0      1.64    89.65   15.15    None  None   None       |
|    Sol.    : 438    0      4.17    81.45   38.97    None  None   None       |
|    Mac.    : 2385   0      1.64    89.65   10.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.641 -  10.442: 1588   |   5:    45.644 -  54.444:   85        |
|      1:    10.442 -  19.242:  652   |   6:    54.444 -  63.245:   70        |
|      2:    19.242 -  28.043:  163   |   7:    63.245 -  72.046:   26        |
|      3:    28.043 -  36.843:  124   |   8:    72.046 -  80.846:    8        |
|      4:    36.843 -  45.644:  104   |   9:    80.846 -  89.647:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.738 - 4.372
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 317
   mapped sites are within: 0.738 - 4.372

peak=   10.741 closest distance to " CB  VAL A 296 " =    1.519
peak=   10.080 closest distance to " CB  VAL A 230 " =    1.392
peak=    7.854 closest distance to " O   HOH Z 130 " =    1.776
peak=    6.033 closest distance to " O   HOH Z  65 " =    1.625
peak=    5.996 closest distance to " CD2 LEU A   5 " =    1.303
peak=    5.939 closest distance to " O   HOH Z 375 " =    1.273
peak=    5.871 closest distance to " O   HOH Z 424 " =    1.509
peak=    5.792 closest distance to " O   HOH Z 142 " =    1.934
peak=    5.766 closest distance to " NE2 GLN A  11 " =    1.148
peak=    5.516 closest distance to " CG  LEU A   5 " =    1.208
peak=    5.410 closest distance to " O   HOH Z 193 " =    1.703
peak=    5.396 closest distance to " O   HOH Z 236 " =    1.492
peak=    5.287 closest distance to " O   HOH Z  28 " =    1.438
peak=    5.244 closest distance to " CB  ARG A 275 " =    1.023
peak=    5.225 closest distance to " O   HOH Z   9 " =    1.374
peak=    5.170 closest distance to " O   HOH Z 112 " =    1.478
peak=    5.138 closest distance to " CG  PRO A  54 " =    1.357
peak=    5.136 closest distance to " O   HOH Z 124 " =    1.473
peak=    5.042 closest distance to " O   HOH Z 369 " =    2.409
peak=    4.996 closest distance to " O   HOH Z 423 " =    1.714
peak=    4.966 closest distance to " O   HOH Z 427 " =    2.273
peak=    4.942 closest distance to " O   HOH Z 385 " =    1.124
peak=    4.927 closest distance to " CB  PRO A  54 " =    1.054
peak=    4.923 closest distance to " O   HOH Z  78 " =    1.646
peak=    4.796 closest distance to " CB  VAL A 230 " =    1.177
peak=    4.795 closest distance to " CB  SER A   3 " =    1.220
peak=    4.788 closest distance to " CG  LEU A 228 " =    1.043
peak=    4.730 closest distance to " O   HOH Z 352 " =    1.427
peak=    4.708 closest distance to " O   HOH Z 250 " =    2.391
peak=    4.684 closest distance to " O   HOH Z 126 " =    1.885
peak=    4.641 closest distance to " CD1AILE A 234 " =    0.924
peak=    4.605 closest distance to " O   HOH Z 123 " =    1.391
peak=    4.586 closest distance to " O   HOH Z 417 " =    1.380
peak=    4.519 closest distance to " O   HOH Z 418 " =    1.002
peak=    4.510 closest distance to " NH2 ARG A  56 " =    1.915
peak=    4.497 closest distance to " O   HOH Z 272 " =    1.823
peak=    4.487 closest distance to " O   HOH Z 211 " =    1.201
peak=    4.478 closest distance to " O   HOH Z 380 " =    1.918
peak=    4.436 closest distance to " CB  GLN A 223 " =    1.632
peak=    4.430 closest distance to " O   SER A  87 " =    2.419
peak=    4.428 closest distance to " CG  ARG A 138 " =    0.921
peak=    4.425 closest distance to " O   HOH Z 414 " =    1.315
peak=    4.386 closest distance to " O   HOH Z 289 " =    1.636
peak=    4.360 closest distance to " O   HOH Z  92 " =    1.275
peak=    4.340 closest distance to " O   HOH Z 403 " =    1.944
peak=    4.324 closest distance to " O   HOH Z  11 " =    1.913
peak=    4.309 closest distance to " CD2 LEU A 228 " =    1.179
peak=    4.309 closest distance to " O   HOH Z  69 " =    1.219
peak=    4.292 closest distance to " O   HOH Z 422 " =    2.206
peak=    4.279 closest distance to " O   HOH Z 358 " =    1.302
peak=    4.271 closest distance to " O   HOH Z   7 " =    1.390
peak=    4.250 closest distance to " NH1 ARG A 138 " =    0.987
peak=    4.238 closest distance to " CB  GLN A 183 " =    1.239
peak=    4.236 closest distance to " O   HOH Z 389 " =    1.454
peak=    4.211 closest distance to " CB  SER A  63 " =    1.247
peak=    4.203 closest distance to " O   HOH Z  85 " =    1.548
peak=    4.193 closest distance to " O   HOH Z  51 " =    1.902
peak=    4.192 closest distance to " O   HOH Z 287 " =    1.719
peak=    4.189 closest distance to " CG  PRO A 213 " =    1.194
peak=    4.155 closest distance to " NZ  LYS A 117 " =    3.126
peak=    4.119 closest distance to " O   HOH Z  39 " =    1.539
peak=    4.109 closest distance to " O   HOH Z 366 " =    2.579
peak=    4.104 closest distance to " O   HOH Z 130 " =    1.848
peak=    4.048 closest distance to " O   HOH Z 371 " =    3.019
peak=    4.046 closest distance to " O   HOH Z  30 " =    1.789
peak=    4.039 closest distance to " CB  ASN A 148 " =    1.296
peak=    3.998 closest distance to " O   HOH Z 427 " =    1.182
peak=    3.961 closest distance to " O   HOH Z 213 " =    1.686
peak=    3.959 closest distance to " O   HOH Z 425 " =    2.001
peak=    3.918 closest distance to " O   HOH Z 371 " =    1.890
peak=    3.917 closest distance to " O   HOH Z 298 " =    1.758
peak=    3.908 closest distance to " CB  VAL A 202 " =    1.649
peak=    3.903 closest distance to " CG  GLN A  11 " =    2.004
peak=    3.900 closest distance to " O   HOH Z 114 " =    1.797
peak=    3.873 closest distance to " CB  SER A 276 " =    1.342
peak=    3.861 closest distance to " O   HOH Z  93 " =    2.246
peak=    3.851 closest distance to " O   HOH Z 128 " =    2.027
peak=    3.849 closest distance to " O   HOH Z 415 " =    1.179
peak=    3.844 closest distance to " O   HOH Z 137 " =    1.577
peak=    3.839 closest distance to " O   HOH Z 176 " =    1.688
peak=    3.839 closest distance to " CG2 VAL A 257 " =    0.916
peak=    3.835 closest distance to " CA  PHE A 283 " =    1.231
peak=    3.814 closest distance to " O   HOH Z 250 " =    1.452
peak=    3.813 closest distance to " O   HOH Z  44 " =    1.844
peak=    3.809 closest distance to " O   HOH Z 435 " =    2.012
peak=    3.799 closest distance to " O   HOH Z 405 " =    1.494
peak=    3.795 closest distance to " CB  THR A  31 " =    1.601
peak=    3.791 closest distance to " CB  ALA A 114 " =    1.480
peak=    3.791 closest distance to " O   HOH Z 368 " =    2.066
peak=    3.789 closest distance to " O   HOH Z 423 " =    1.748
peak=    3.788 closest distance to " CB  SER A  26 " =    1.673
peak=    3.784 closest distance to " CB  TRP A 266 " =    1.139
peak=    3.780 closest distance to " N   PHE A 130 " =    1.226
peak=    3.774 closest distance to " O   HOH Z 145 " =    1.938
peak=    3.772 closest distance to " O   HOH Z 419 " =    2.002
peak=    3.770 closest distance to " NH2BARG A 190 " =    1.516
peak=    3.761 closest distance to " O   HOH Z  58 " =    1.842
peak=    3.754 closest distance to " CB BVAL A  41 " =    1.242
peak=    3.753 closest distance to " O   HOH Z 244 " =    1.770
peak=    3.753 closest distance to " O   HOH Z 128 " =    2.113
peak=    3.750 closest distance to " O   HOH Z  59 " =    1.504
peak=    3.742 closest distance to " OD2 ASP A 286 " =    2.405
peak=    3.742 closest distance to " CG  PRO A 243 " =    1.204
peak=    3.739 closest distance to " O   HOH Z  63 " =    1.472
peak=    3.737 closest distance to " O   HOH Z 384 " =    1.261
peak=    3.731 closest distance to " NH2BARG A 145 " =    1.278
peak=    3.730 closest distance to " O   HOH Z 143 " =    1.552
peak=    3.730 closest distance to " O   HOH Z 189 " =    2.687
peak=    3.719 closest distance to " OG BSER A 164 " =    2.193
peak=    3.717 closest distance to " CE AMET A  47 " =    1.356
peak=    3.707 closest distance to " O   HOH Z 152 " =    2.258
peak=    3.691 closest distance to " CB  GLU A 277 " =    3.384
peak=    3.685 closest distance to " CA  ASN A 127 " =    1.060
peak=    3.684 closest distance to " O   HOH Z 222 " =    1.224
peak=    3.679 closest distance to " CB  ARG A  79 " =    1.410
peak=    3.672 closest distance to " CG  LYS A  76 " =    1.474
peak=    3.668 closest distance to " CG  TRP A 179 " =    2.243
peak=    3.665 closest distance to " O   HOH Z 316 " =    2.907
peak=    3.656 closest distance to " O   HOH Z 410 " =    1.305
peak=    3.648 closest distance to " O   HOH Z  59 " =    2.210
peak=    3.645 closest distance to " O   HOH Z  61 " =    1.676
peak=    3.642 closest distance to " O   HOH Z  47 " =    1.513
peak=    3.642 closest distance to " O   HOH Z  69 " =    2.075
peak=    3.637 closest distance to " O   HOH Z 344 " =    1.246
peak=    3.635 closest distance to " O   HOH Z 411 " =    3.642
peak=    3.629 closest distance to " CB  ASN A 187 " =    1.069
peak=    3.623 closest distance to " O   HOH Z 327 " =    1.613
peak=    3.622 closest distance to " O   HOH Z 128 " =    1.858
peak=    3.619 closest distance to " O   HOH Z 234 " =    3.509
peak=    3.613 closest distance to " CB  ALA A 248 " =    1.453
peak=    3.612 closest distance to " CG1 VAL A 153 " =    0.841
peak=    3.609 closest distance to " O   HOH Z 106 " =    2.602
peak=    3.603 closest distance to " O   HOH Z 362 " =    2.196
peak=    3.598 closest distance to " CB  VAL A 265 " =    1.305
peak=    3.595 closest distance to " O   HOH Z 425 " =    1.445
peak=    3.586 closest distance to " CD  GLN A 194 " =    1.354
peak=    3.581 closest distance to " O   HOH Z  61 " =    1.478
peak=    3.573 closest distance to " O   HOH Z  68 " =    2.015
peak=    3.571 closest distance to " OG BSER A 212 " =    2.737
peak=    3.571 closest distance to " OG  SER A  62 " =    2.931
peak=    3.568 closest distance to " CA  ASN A 215 " =    1.014
peak=    3.561 closest distance to " O   HOH Z 261 " =    2.273
peak=    3.555 closest distance to " O   HOH Z 117 " =    1.927
peak=    3.549 closest distance to " CG  PRO A 198 " =    1.128
peak=    3.545 closest distance to " CB  ARG A 139 " =    1.047
peak=    3.545 closest distance to " O   HOH Z  88 " =    2.411
peak=    3.544 closest distance to " NH2AARG A 190 " =    1.795
peak=    3.539 closest distance to " O   HOH Z 227 " =    2.138
peak=    3.535 closest distance to " O   HOH Z  55 " =    1.982
peak=    3.535 closest distance to " CB  LEU A 255 " =    0.765
peak=    3.531 closest distance to " O   HOH Z 365 " =    1.695
peak=    3.526 closest distance to " O   HOH Z 203 " =    1.426
peak=    3.523 closest distance to " O   HOH Z 257 " =    2.208
peak=    3.516 closest distance to " O   HOH Z 334 " =    1.448
peak=    3.515 closest distance to " CG2 THR A 221 " =    1.281
peak=    3.504 closest distance to " OG BSER A 210 " =    1.417
peak=    3.493 closest distance to " CG2 ILE A  20 " =    1.715
peak=    3.488 closest distance to " O   HOH Z 305 " =    3.335
peak=    3.487 closest distance to " O   HOH Z 214 " =    2.355
peak=    3.483 closest distance to " CB  TYR A 169 " =    0.805
peak=    3.479 closest distance to " CB  GLU A 128 " =    1.001
peak=    3.473 closest distance to " O   HOH Z 126 " =    1.508
peak=    3.469 closest distance to " C   PRO A 198 " =    1.577
peak=    3.469 closest distance to " CB  GLU A 152 " =    1.262
peak=    3.462 closest distance to " O   HOH Z 438 " =    2.445
peak=    3.444 closest distance to " O   HOH Z 166 " =    1.517
peak=    3.442 closest distance to " O   HOH Z   1 " =    4.372
peak=    3.433 closest distance to " O   HOH Z   4 " =    1.323
peak=    3.432 closest distance to " CG1 ILE A  33 " =    1.293
peak=    3.430 closest distance to " O   HOH Z 222 " =    2.256
peak=    3.430 closest distance to " CG1BVAL A  72 " =    1.078
peak=    3.428 closest distance to " O   HOH Z 130 " =    1.531
peak=    3.426 closest distance to " O   HOH Z 193 " =    1.791
peak=    3.421 closest distance to " N   ARG A 156 " =    1.246
peak=    3.418 closest distance to " O   HOH Z 390 " =    2.223
peak=    3.417 closest distance to " O   HOH Z  65 " =    1.512
peak=    3.416 closest distance to " OG BSER A  99 " =    2.155
peak=    3.415 closest distance to " CB  ALA A   1 " =    1.025
peak=    3.412 closest distance to " O   GLN A  58 " =    1.409
peak=    3.412 closest distance to " NH1 ARG A  14 " =    1.048
peak=    3.411 closest distance to " ND1 HIS A  81 " =    1.472
peak=    3.409 closest distance to " O   HOH Z 392 " =    1.151
peak=    3.407 closest distance to " O   HOH Z 181 " =    2.264
peak=    3.406 closest distance to " O   HOH Z 148 " =    1.557
peak=    3.401 closest distance to " CB  TRP A 179 " =    1.258
peak=    3.400 closest distance to " O   HOH Z 109 " =    2.366
peak=    3.383 closest distance to " O   HOH Z  78 " =    2.175
peak=    3.382 closest distance to " O   HOH Z 194 " =    1.956
peak=    3.380 closest distance to " O   HOH Z   9 " =    1.911
peak=    3.380 closest distance to " O   HOH Z 193 " =    1.938
peak=    3.380 closest distance to " N   ASN A 148 " =    1.066
peak=    3.370 closest distance to " O   HOH Z 424 " =    1.879
peak=    3.370 closest distance to " CA  ARG A 195 " =    1.302
peak=    3.367 closest distance to " CB  ASN A 142 " =    1.025
peak=    3.364 closest distance to " O   HOH Z 272 " =    2.120
peak=    3.361 closest distance to " CA  ALA A 299 " =    0.988
peak=    3.359 closest distance to " CG  GLN A  88 " =    1.067
peak=    3.354 closest distance to " CA  TYR A  30 " =    0.968
peak=    3.342 closest distance to " CE  MET A  93 " =    1.754
peak=    3.338 closest distance to " O   HOH Z 291 " =    1.720
peak=    3.334 closest distance to " O   HOH Z 215 " =    1.446
peak=    3.330 closest distance to " O   GLY A 147 " =    1.552
peak=    3.321 closest distance to " O   HOH Z 128 " =    2.440
peak=    3.321 closest distance to " O   HOH Z 375 " =    2.152
peak=    3.316 closest distance to " CD1 ILE A 263 " =    1.408
peak=    3.315 closest distance to " CG BARG A 102 " =    1.890
peak=    3.314 closest distance to " CG2 ILE A 106 " =    0.909
peak=    3.313 closest distance to " O   HOH Z 337 " =    3.421
peak=    3.311 closest distance to " O   HOH Z 368 " =    3.599
peak=    3.310 closest distance to " CA  ALA A  51 " =    1.082
peak=    3.309 closest distance to " O   HOH Z 355 " =    1.711
peak=    3.308 closest distance to " CB  ASN A 148 " =    1.886
peak=    3.307 closest distance to " SD AMET A  47 " =    0.880
peak=    3.305 closest distance to " O   HOH Z 212 " =    1.463
peak=    3.305 closest distance to " O   HOH Z  50 " =    1.459
peak=    3.301 closest distance to " O   HOH Z 389 " =    2.857
peak=    3.301 closest distance to " CD1 LEU A   5 " =    1.793
peak=    3.301 closest distance to " OE1 GLU A   2 " =    2.114
peak=    3.298 closest distance to " NE1 TRP A 274 " =    0.950
peak=    3.294 closest distance to " O   HOH Z 383 " =    2.203
peak=    3.293 closest distance to " O   HOH Z 145 " =    2.177
peak=    3.288 closest distance to " NE2 GLN A  73 " =    1.505
peak=    3.287 closest distance to " O   HOH Z  80 " =    1.831
peak=    3.285 closest distance to " NE2 GLN A  58 " =    3.864
peak=    3.280 closest distance to " N   VAL A 126 " =    1.191
peak=    3.280 closest distance to " O   HOH Z 322 " =    1.940
peak=    3.280 closest distance to " CB  ASN A 215 " =    1.070
peak=    3.278 closest distance to " CB  ILE A 234 " =    1.092
peak=    3.277 closest distance to " O   HOH Z 156 " =    2.934
peak=    3.277 closest distance to " O   HOH Z 392 " =    1.873
peak=    3.272 closest distance to " O   HOH Z 366 " =    2.005
peak=    3.271 closest distance to " NH1AARG A 145 " =    1.152
peak=    3.271 closest distance to " O   HOH Z 158 " =    2.836
peak=    3.268 closest distance to " CG2 ILE A  20 " =    1.188
peak=    3.261 closest distance to " CG  LEU A 281 " =    0.941
peak=    3.261 closest distance to " O   HOH Z 345 " =    3.057
peak=    3.259 closest distance to " O   HOH Z 253 " =    1.328
peak=    3.257 closest distance to " O   HOH Z 222 " =    2.165
peak=    3.256 closest distance to " OE2 GLU A   2 " =    1.957
peak=    3.253 closest distance to " O   HOH Z 251 " =    1.692
peak=    3.245 closest distance to " O   HOH Z 356 " =    1.227
peak=    3.242 closest distance to " NE  ARG A  56 " =    3.355
peak=    3.241 closest distance to " OG ASER A  99 " =    1.471
peak=    3.241 closest distance to " O   HOH Z 147 " =    1.395
peak=    3.240 closest distance to " N   VAL A 257 " =    1.624
peak=    3.238 closest distance to " O   HOH Z 426 " =    1.778
peak=    3.237 closest distance to " O   HOH Z 263 " =    1.558
peak=    3.235 closest distance to " O   HOH Z 245 " =    1.428
peak=    3.233 closest distance to " N   ALA A   1 " =    3.083
peak=    3.229 closest distance to " O   HOH Z 261 " =    1.607
peak=    3.229 closest distance to " OG1 THR A 294 " =    2.354
peak=    3.225 closest distance to " O   HOH Z  43 " =    2.573
peak=    3.223 closest distance to " CA  ALA A 158 " =    1.309
peak=    3.222 closest distance to " CE  LYS A  48 " =    1.063
peak=    3.222 closest distance to " NE2 GLN A 278 " =    3.428
peak=    3.220 closest distance to " O   HOH Z  47 " =    1.730
peak=    3.215 closest distance to " O   HOH Z  66 " =    2.136
peak=    3.212 closest distance to " CB  PHE A 130 " =    0.832
peak=    3.210 closest distance to " CB  HIS A 108 " =    0.783
peak=    3.208 closest distance to " CB  ASN A 110 " =    1.078
peak=    3.206 closest distance to " O   HOH Z 367 " =    2.168
peak=    3.204 closest distance to " O   HOH Z 412 " =    1.895
peak=    3.203 closest distance to " CB  TYR A  30 " =    1.753
peak=    3.202 closest distance to " CB  MET A 188 " =    1.654
peak=    3.198 closest distance to " OG ASER A 134 " =    1.512
peak=    3.197 closest distance to " CE ALYS A 290 " =    0.933
peak=    3.191 closest distance to " CE3 TRP A 150 " =    0.926
peak=    3.191 closest distance to " CB  LEU A 300 " =    0.890
peak=    3.190 closest distance to " N   TYR A  15 " =    1.083
peak=    3.184 closest distance to " CD1 ILE A  33 " =    1.776
peak=    3.182 closest distance to " O   HOH Z 388 " =    1.984
peak=    3.180 closest distance to " CE BLYS A 290 " =    0.908
peak=    3.180 closest distance to " O   HOH Z 422 " =    1.000
peak=    3.179 closest distance to " O   HOH Z  89 " =    2.181
peak=    3.177 closest distance to " CB  GLN A 278 " =    0.927
peak=    3.177 closest distance to " CA  SER A  87 " =    1.058
peak=    3.176 closest distance to " O   HOH Z 214 " =    1.233
peak=    3.174 closest distance to " CG1 ILE A 120 " =    1.424
peak=    3.168 closest distance to " N   SER A 135 " =    1.241
peak=    3.168 closest distance to " O   HOH Z 406 " =    1.293
peak=    3.167 closest distance to " O   HOH Z 248 " =    1.767
peak=    3.167 closest distance to " N   ASP A 162 " =    1.132
peak=    3.166 closest distance to " O   HOH Z  10 " =    1.744
peak=    3.165 closest distance to " CB  GLU A 175 " =    1.154
peak=    3.164 closest distance to " O   HOH Z 418 " =    2.123
peak=    3.163 closest distance to " CB  VAL A 121 " =    0.939
peak=    3.158 closest distance to " O   HOH Z 153 " =    3.432
peak=    3.156 closest distance to " CA  LYS A 117 " =    1.200
peak=    3.152 closest distance to " CG  GLN A  77 " =    1.943
peak=    3.151 closest distance to " OG1 THR A 221 " =    1.341
peak=    3.151 closest distance to " O   HOH Z 409 " =    1.558
peak=    3.149 closest distance to " OD1 ASN A  69 " =    2.561
peak=    3.132 closest distance to " CG1BVAL A  72 " =    1.117
peak=    3.130 closest distance to " O   HOH Z 233 " =    2.055
peak=    3.128 closest distance to " CD  ARG A 269 " =    1.021
peak=    3.127 closest distance to " O   HOH Z 368 " =    2.766
peak=    3.123 closest distance to " O   HOH Z 406 " =    1.271
peak=    3.116 closest distance to " O   HOH Z 154 " =    1.929
peak=    3.112 closest distance to " CB  ASN A  39 " =    0.881
peak=    3.112 closest distance to " O   HOH Z  40 " =    2.066
peak=    3.109 closest distance to " NH2 ARG A 156 " =    1.102
peak=    3.099 closest distance to " O   HOH Z 323 " =    1.550
peak=    3.098 closest distance to " O   ARG A 275 " =    1.521
peak=    3.097 closest distance to " O   HOH Z 105 " =    1.688
peak=    3.093 closest distance to " N   GLY A 196 " =    1.024
peak=    3.092 closest distance to " O   HOH Z 407 " =    2.218
peak=    3.092 closest distance to " O   HOH Z 173 " =    2.140
peak=    3.091 closest distance to " O   HOH Z  88 " =    2.317
peak=    3.082 closest distance to " CB  SER A 216 " =    0.738
peak=    3.077 closest distance to " CB  THR A  52 " =    1.139
peak=    3.073 closest distance to " CG2 ILE A 120 " =    1.253
peak=    3.070 closest distance to " O   HOH Z 344 " =    2.741
peak=    3.069 closest distance to " O   HOH Z 353 " =    1.799
peak=    3.060 closest distance to " CD1 ILE A  49 " =    1.411
peak=    3.056 closest distance to " CA  MET A 105 " =    0.858
peak=    3.025 closest distance to " CD  LYS A 119 " =    1.830
peak=    3.011 closest distance to " O   GLY A 302 " =    1.926

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.690 - 5.381
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.748 - 5.381

peak=   -4.542 closest distance to " O   HOH Z 385 " =    1.142
peak=   -4.501 closest distance to " CG2 VAL A 230 " =    0.835
peak=   -4.353 closest distance to " O   HOH Z 412 " =    5.126
peak=   -4.319 closest distance to " O   HOH Z 429 " =    1.999
peak=   -4.268 closest distance to " CD  ARG A 156 " =    1.976
peak=   -4.259 closest distance to " OG BSER A 134 " =    1.215
peak=   -4.246 closest distance to " O   HOH Z  69 " =    1.653
peak=   -4.138 closest distance to " O   HOH Z 131 " =    3.980
peak=   -4.089 closest distance to " C   HIS A 108 " =    1.234
peak=   -4.065 closest distance to " O   ALA A 292 " =    2.272
peak=   -4.061 closest distance to " CE2 PHE A 218 " =    2.474
peak=   -4.026 closest distance to " CG  GLN A  58 " =    0.982
peak=   -4.019 closest distance to " SG  CYS A 254 " =    3.160
peak=   -4.014 closest distance to " NH2 ARG A  79 " =    1.935
peak=   -4.000 closest distance to " O   HOH Z  37 " =    1.609
peak=   -3.999 closest distance to " CG2 ILE A  20 " =    2.821
peak=   -3.972 closest distance to " O   HOH Z 185 " =    1.909
peak=   -3.955 closest distance to " CD1 LEU A 255 " =    2.752
peak=   -3.951 closest distance to " N   GLN A  58 " =    1.939
peak=   -3.950 closest distance to " O   HOH Z 423 " =    2.455
peak=   -3.918 closest distance to " OD1 ASN A  39 " =    2.136
peak=   -3.910 closest distance to " CB  ALA A  43 " =    2.207
peak=   -3.907 closest distance to " O   HOH Z 427 " =    1.702
peak=   -3.887 closest distance to " O   SER A 135 " =    1.472
peak=   -3.886 closest distance to " O   SER A  22 " =    2.234
peak=   -3.849 closest distance to " O   HOH Z  56 " =    2.065
peak=   -3.841 closest distance to " O   PRO A 198 " =    1.199
peak=   -3.839 closest distance to " O   HOH Z 407 " =    2.679
peak=   -3.827 closest distance to " OD2 ASP A 191 " =    1.342
peak=   -3.818 closest distance to " CD  LYS A 289 " =    2.474
peak=   -3.785 closest distance to " CE2 TYR A  30 " =    2.813
peak=   -3.783 closest distance to " OD2 ASP A  27 " =    1.234
peak=   -3.778 closest distance to " O   HOH Z 234 " =    3.878
peak=   -3.769 closest distance to " O   HOH Z 137 " =    1.500
peak=   -3.767 closest distance to " O   HOH Z  60 " =    2.345
peak=   -3.763 closest distance to " O   HOH Z 313 " =    1.694
peak=   -3.748 closest distance to " O   HOH Z 426 " =    2.314
peak=   -3.741 closest distance to " CA  GLY A  23 " =    1.937
peak=   -3.740 closest distance to " O   HOH Z 406 " =    0.873
peak=   -3.729 closest distance to " OG  SER A   3 " =    1.339
peak=   -3.709 closest distance to " C   ASN A 285 " =    2.015
peak=   -3.698 closest distance to " CG  PHE A 283 " =    2.470
peak=   -3.697 closest distance to " CZ2 TRP A 274 " =    0.916
peak=   -3.690 closest distance to " O   HOH Z 290 " =    1.090
peak=   -3.689 closest distance to " O   HOH Z 130 " =    2.062
peak=   -3.686 closest distance to " O   HOH Z 351 " =    1.414
peak=   -3.665 closest distance to " O   HOH Z  11 " =    1.808
peak=   -3.644 closest distance to " CG2 THR A  52 " =    2.998
peak=   -3.644 closest distance to " CB  ASP A 171 " =    2.370
peak=   -3.642 closest distance to " OG  SER A  87 " =    1.286
peak=   -3.614 closest distance to " CB  SER A 210 " =    1.215
peak=   -3.611 closest distance to " O   HOH Z 191 " =    5.381
peak=   -3.602 closest distance to " NH1 ARG A  56 " =    2.456
peak=   -3.600 closest distance to " O   HOH Z 134 " =    2.936
peak=   -3.593 closest distance to " CA  GLY A  98 " =    1.715
peak=   -3.586 closest distance to " O   HOH Z 114 " =    3.147
peak=   -3.584 closest distance to " CB  ASN A  39 " =    2.034
peak=   -3.573 closest distance to " O   HOH Z 193 " =    1.661
peak=   -3.562 closest distance to " ND2 ASN A 187 " =    1.683
peak=   -3.557 closest distance to " O   PRO A 243 " =    2.517
peak=   -3.554 closest distance to " O   ALA A 161 " =    1.737
peak=   -3.551 closest distance to " O   HOH Z 298 " =    2.589
peak=   -3.547 closest distance to " O   ARG A  24 " =    1.824
peak=   -3.543 closest distance to " OXT GLY A 302 " =    2.890
peak=   -3.541 closest distance to " O   HOH Z  24 " =    1.143
peak=   -3.527 closest distance to " N   ALA A 248 " =    1.577
peak=   -3.520 closest distance to " CG  GLN A 223 " =    1.790
peak=   -3.518 closest distance to " O   HOH Z 339 " =    1.632
peak=   -3.512 closest distance to " CG  GLU A 152 " =    1.169
peak=   -3.503 closest distance to " O   HOH Z 368 " =    2.551
peak=   -3.499 closest distance to " CD2 LEU A 237 " =    2.663
peak=   -3.493 closest distance to " O   PRO A 163 " =    2.012
peak=   -3.478 closest distance to " CB  ALA A   7 " =    1.980
peak=   -3.471 closest distance to " O   HOH Z  60 " =    1.592
peak=   -3.465 closest distance to " O   HOH Z 415 " =    1.166
peak=   -3.464 closest distance to " CB  PHE A 192 " =    1.878
peak=   -3.459 closest distance to " O   HOH Z 266 " =    4.561
peak=   -3.457 closest distance to " O   HOH Z 211 " =    1.467
peak=   -3.440 closest distance to " CB  ASP A 132 " =    2.331
peak=   -3.439 closest distance to " O   VAL A  67 " =    2.780
peak=   -3.435 closest distance to " N   HIS A 115 " =    2.034
peak=   -3.431 closest distance to " O   HOH Z 414 " =    2.442
peak=   -3.429 closest distance to " C   ALA A 158 " =    1.338
peak=   -3.423 closest distance to " CD  GLN A  88 " =    1.049
peak=   -3.418 closest distance to " O   VAL A 189 " =    2.441
peak=   -3.411 closest distance to " CB  ALA A 114 " =    2.328
peak=   -3.407 closest distance to " N   VAL A  72 " =    1.831
peak=   -3.404 closest distance to " O   HOH Z 134 " =    3.537
peak=   -3.398 closest distance to " OG ASER A 134 " =    1.128
peak=   -3.396 closest distance to " OD1 ASN A 301 " =    1.963
peak=   -3.394 closest distance to " O   HOH Z 387 " =    2.413
peak=   -3.388 closest distance to " CD1 LEU A 101 " =    2.191
peak=   -3.383 closest distance to " O   HOH Z 102 " =    1.433
peak=   -3.381 closest distance to " CD2 LEU A   5 " =    1.154
peak=   -3.380 closest distance to " OG ASER A 216 " =    1.383
peak=   -3.373 closest distance to " O   HOH Z 237 " =    2.344
peak=   -3.372 closest distance to " O   HOH Z   9 " =    1.462
peak=   -3.371 closest distance to " CG  GLN A 278 " =    2.039
peak=   -3.370 closest distance to " CG  ASP A 286 " =    1.565
peak=   -3.364 closest distance to " OE2 GLU A 152 " =    1.118
peak=   -3.358 closest distance to " O   HOH Z 377 " =    1.025
peak=   -3.352 closest distance to " O   HOH Z 165 " =    2.224
peak=   -3.347 closest distance to " O   GLN A 240 " =    1.793
peak=   -3.342 closest distance to " O   SER A  95 " =    1.484
peak=   -3.341 closest distance to " O   HOH Z 385 " =    1.816
peak=   -3.334 closest distance to " O   HOH Z  63 " =    2.191
peak=   -3.329 closest distance to " O   HOH Z 140 " =    1.680
peak=   -3.329 closest distance to " CG  ARG A 219 " =    2.322
peak=   -3.328 closest distance to " O   ASN A 187 " =    1.424
peak=   -3.326 closest distance to " CA  TYR A  30 " =    2.857
peak=   -3.324 closest distance to " N   ALA A 226 " =    1.940
peak=   -3.323 closest distance to " N   PRO A 163 " =    1.542
peak=   -3.323 closest distance to " OE1 GLU A 277 " =    2.171
peak=   -3.319 closest distance to " OD2 ASP A 270 " =    1.231
peak=   -3.307 closest distance to " OG  SER A  97 " =    2.159
peak=   -3.307 closest distance to " N   THR A 157 " =    1.432
peak=   -3.303 closest distance to " O   HOH Z 158 " =    1.978
peak=   -3.301 closest distance to " O   HOH Z 231 " =    1.898
peak=   -3.295 closest distance to " O   HOH Z 100 " =    1.226
peak=   -3.289 closest distance to " O   HOH Z 326 " =    1.598
peak=   -3.288 closest distance to " CA  GLY A  35 " =    1.955
peak=   -3.286 closest distance to " CB  ALA A 291 " =    2.112
peak=   -3.283 closest distance to " O   HOH Z 235 " =    1.152
peak=   -3.279 closest distance to " CB  VAL A 230 " =    0.960
peak=   -3.272 closest distance to " O   THR A 235 " =    1.438
peak=   -3.271 closest distance to " O   HOH Z 364 " =    1.482
peak=   -3.268 closest distance to " O   HOH Z 125 " =    3.353
peak=   -3.264 closest distance to " O   HOH Z 210 " =    1.877
peak=   -3.258 closest distance to " CG  ARG A 219 " =    2.699
peak=   -3.257 closest distance to " O   HOH Z 166 " =    1.668
peak=   -3.248 closest distance to " CB  ASN A  39 " =    1.846
peak=   -3.248 closest distance to " CE  LYS A  76 " =    2.928
peak=   -3.244 closest distance to " O   HOH Z 389 " =    1.951
peak=   -3.238 closest distance to " N   MET A 188 " =    1.847
peak=   -3.237 closest distance to " CA  GLY A 133 " =    1.948
peak=   -3.236 closest distance to " O   ASN A 301 " =    1.466
peak=   -3.235 closest distance to " ND2 ASN A 209 " =    2.026
peak=   -3.234 closest distance to " ND2 ASN A  45 " =    1.159
peak=   -3.233 closest distance to " CG1 VAL A 230 " =    1.747
peak=   -3.228 closest distance to " O   HOH Z 183 " =    1.711
peak=   -3.227 closest distance to " OD2 ASP A 171 " =    1.521
peak=   -3.227 closest distance to " O   ALA A 292 " =    1.977
peak=   -3.227 closest distance to " CG1 VAL A 197 " =    2.214
peak=   -3.226 closest distance to " O   ASP A 298 " =    2.043
peak=   -3.223 closest distance to " O   SER A 271 " =    2.038
peak=   -3.220 closest distance to " N   ASN A 127 " =    1.415
peak=   -3.218 closest distance to " N   ALA A   1 " =    1.371
peak=   -3.213 closest distance to " O   ALA A  51 " =    1.157
peak=   -3.209 closest distance to " CZ  TYR A 169 " =    1.803
peak=   -3.201 closest distance to " CB  GLN A  55 " =    1.188
peak=   -3.196 closest distance to " O   HOH Z  42 " =    1.881
peak=   -3.196 closest distance to " CG  ASP A 231 " =    0.748
peak=   -3.196 closest distance to " O   HOH Z 166 " =    1.716
peak=   -3.195 closest distance to " OG  SER A 245 " =    1.280
peak=   -3.194 closest distance to " O   HOH Z 426 " =    1.767
peak=   -3.193 closest distance to " CZ  PHE A  59 " =    1.311
peak=   -3.193 closest distance to " CD1 LEU A   5 " =    2.582
peak=   -3.191 closest distance to " C   ASP A 231 " =    2.484
peak=   -3.191 closest distance to " CE1 TYR A 247 " =    2.582
peak=   -3.190 closest distance to " O   HOH Z  15 " =    1.456
peak=   -3.189 closest distance to " O   HOH Z 111 " =    4.589
peak=   -3.185 closest distance to " OG  SER A  62 " =    4.264
peak=   -3.185 closest distance to " O   HOH Z 192 " =    1.037
peak=   -3.185 closest distance to " O   HOH Z  13 " =    1.756
peak=   -3.183 closest distance to " O   HOH Z 213 " =    1.403
peak=   -3.183 closest distance to " CZ3 TRP A 123 " =    1.894
peak=   -3.182 closest distance to " CG  MET A 105 " =    0.834
peak=   -3.175 closest distance to " C   ASP A 124 " =    2.038
peak=   -3.173 closest distance to " OE1 GLN A  88 " =    1.131
peak=   -3.169 closest distance to " O   HOH Z 359 " =    1.796
peak=   -3.158 closest distance to " NE2 GLN A  55 " =    0.899
peak=   -3.156 closest distance to " CE BMET A  47 " =    1.398
peak=   -3.154 closest distance to " C   MET A 188 " =    1.596
peak=   -3.148 closest distance to " N   ALA A 244 " =    1.400
peak=   -3.144 closest distance to " CG  GLU A 152 " =    2.156
peak=   -3.142 closest distance to " O   HOH Z 128 " =    1.687
peak=   -3.139 closest distance to " CA  TYR A  68 " =    1.073
peak=   -3.137 closest distance to " O   HOH Z 414 " =    2.506
peak=   -3.131 closest distance to " CB  TYR A 172 " =    2.400
peak=   -3.123 closest distance to " O   ILE A  49 " =    1.698
peak=   -3.119 closest distance to " O   GLU A 152 " =    1.406
peak=   -3.118 closest distance to " NE  ARG A  36 " =    1.836
peak=   -3.114 closest distance to " O   HOH Z 147 " =    1.117
peak=   -3.095 closest distance to " O   HOH Z 389 " =    1.406
peak=   -3.095 closest distance to " CG  LEU A 228 " =    0.988
peak=   -3.094 closest distance to " O   HOH Z 113 " =    2.477
peak=   -3.092 closest distance to " O   LYS A 117 " =    1.537
peak=   -3.090 closest distance to " OG1 THR A  82 " =    1.833
peak=   -3.089 closest distance to " O   ILE A 106 " =    2.033
peak=   -3.077 closest distance to " O   ALA A   8 " =    1.809
peak=   -3.066 closest distance to " ND2 ASN A  45 " =    2.092
peak=   -3.065 closest distance to " CB  PHE A  38 " =    2.890
peak=   -3.047 closest distance to " CD2 LEU A 143 " =    2.618

================= 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    :  0.4972 0.4947   6.296072e+00   6.288951e+00
   1_bss:  0.4885 0.4843   6.288725e+00   6.279758e+00
   1_xyz:  0.4243 0.4483   6.215353e+00   6.242406e+00
   1_adp:  0.3806 0.4375   6.163717e+00   6.232435e+00
   1_occ:  0.3798 0.4378   6.162872e+00   6.232881e+00
   2_bss:  0.3785 0.4338   6.161912e+00   6.230342e+00
   2_xyz:  0.3037 0.3649   5.992379e+00   6.120533e+00
   2_adp:  0.2779 0.3479   5.934739e+00   6.079828e+00
   2_occ:  0.2778 0.3486   5.934897e+00   6.080635e+00
   3_bss:  0.2763 0.3476   5.933621e+00   6.077814e+00
   3_xyz:  0.2060 0.2617   5.663297e+00   5.847236e+00
   3_adp:  0.1801 0.2344   5.541121e+00   5.746726e+00
   3_occ:  0.1795 0.2337   5.539196e+00   5.744825e+00
   4_bss:  0.1785 0.2326   5.536180e+00   5.742154e+00
   4_xyz:  0.1424 0.1910   5.340364e+00   5.559634e+00
   4_adp:  0.1372 0.1819   5.299648e+00   5.511829e+00
   4_occ:  0.1368 0.1812   5.297190e+00   5.508328e+00
   5_bss:  0.1368 0.1804   5.296096e+00   5.506591e+00
   5_xyz:  0.1222 0.1666   5.203496e+00   5.434750e+00
   5_adp:  0.1179 0.1653   5.180647e+00   5.425103e+00
   5_occ:  0.1177 0.1652   5.179631e+00   5.424161e+00
   5_bss:  0.1176 0.1652   5.178858e+00   5.423588e+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:  0.407  19.999   6.956   9.511   7.004   0.000   0.000   0.000
   1_xyz:  0.407  19.999   6.956   9.511   7.004   0.000   0.000   0.000
   1_adp:  0.407  19.999   6.956   9.511   7.004   0.000   0.000   0.000
   1_occ:  0.407  19.999   6.956   9.511   7.004   0.000   0.000   0.000
   2_bss:  0.345  20.001   4.376   6.058   4.891   0.000   0.000   0.000
   2_xyz:  0.345  20.001   4.376   6.058   4.891   0.000   0.000   0.000
   2_adp:  0.345  20.001   4.376   6.058   4.891   0.000   0.000   0.000
   2_occ:  0.345  20.001   4.376   6.058   4.891   0.000   0.000   0.000
   3_bss:  0.345  50.000   2.331   3.463   3.485   0.000   0.000   0.000
   3_xyz:  0.345  50.000   2.331   3.463   3.485   0.000   0.000   0.000
   3_adp:  0.345  50.000   2.331   3.463   3.485   0.000   0.000   0.000
   3_occ:  0.345  50.000   2.331   3.463   3.485   0.000   0.000   0.000
   4_bss:  0.330  39.480   1.304   1.889   2.744   0.000   0.000   0.000
   4_xyz:  0.330  39.480   1.304   1.889   2.744   0.000   0.000   0.000
   4_adp:  0.330  39.480   1.304   1.889   2.744   0.000   0.000   0.000
   4_occ:  0.330  39.480   1.304   1.889   2.744   0.000   0.000   0.000
   5_bss:  0.322  32.613   0.908   1.351   2.607   0.000   0.000   0.000
   5_xyz:  0.322  32.613   0.908   1.351   2.607   0.000   0.000   0.000
   5_adp:  0.322  32.613   0.908   1.351   2.607   0.000   0.000   0.000
   5_occ:  0.322  32.613   0.908   1.351   2.607   0.000   0.000   0.000
   5_bss:  0.318  37.160  -0.711  -0.322   1.033  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.307 0.3375  0.4006    78875.280
   1_bss:  63.936 0.3409  0.5027    75923.895
   1_xyz:  55.109 0.4546  0.6678    62646.765
   1_adp:  52.158 0.4926  0.7714    59568.463
   1_occ:  52.191 0.4922  0.7689    59570.727
   2_bss:  51.843 0.4962  0.7040    58610.012
   2_xyz:  40.126 0.6407  0.9005    38563.240
   2_adp:  37.050 0.6776  0.9442    34031.491
   2_occ:  37.102 0.6771  0.9430    34091.933
   3_bss:  36.806 0.6804  0.8818    33719.799
   3_xyz:  26.121 0.7994  0.9945    17575.758
   3_adp:  22.517 0.8372  1.0135    13855.593
   3_occ:  22.447 0.8379  1.0139    13771.118
   4_bss:  22.390 0.8384  0.9729    13664.597
   4_xyz:  17.805 0.8823  0.9945     9147.229
   4_adp:  16.520 0.8942  0.9978     8348.170
   4_occ:  16.452 0.8948  0.9979     8271.002
   5_bss:  16.420 0.8950  0.9840     8203.461
   5_xyz:  14.826 0.9084  0.9921     7023.033
   5_adp:  14.620 0.9102  0.9891     6881.620
   5_occ:  14.609 0.9102  0.9890     6869.210
   5_bss:  14.594 0.9103  0.9899     6857.774
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.085   5.2733e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.085   5.2733e+01
   1_xyz:   1.748  0.014  0.108 18.213  0.007  4.104   1.5248e-01
   1_adp:   1.748  0.014  0.108 18.213  0.007  4.104   1.5248e-01
   1_occ:   1.748  0.014  0.108 18.213  0.007  4.104   1.5248e-01
   2_bss:   1.748  0.014  0.108 18.213  0.007  4.104   1.5248e-01
   2_xyz:   1.363  0.010  0.089 16.483  0.006  4.100   1.0821e-01
   2_adp:   1.363  0.010  0.089 16.483  0.006  4.100   1.0821e-01
   2_occ:   1.363  0.010  0.089 16.483  0.006  4.100   1.0821e-01
   3_bss:   1.363  0.010  0.089 16.483  0.006  4.100   1.0821e-01
   3_xyz:   1.184  0.009  0.085 16.372  0.004  4.105   8.3704e-02
   3_adp:   1.184  0.009  0.085 16.372  0.004  4.105   8.3704e-02
   3_occ:   1.184  0.009  0.085 16.372  0.004  4.105   8.3704e-02
   4_bss:   1.184  0.009  0.085 16.372  0.004  4.105   8.3704e-02
   4_xyz:   0.996  0.006  0.068 15.756  0.004  4.112   6.3418e-02
   4_adp:   0.996  0.006  0.068 15.756  0.004  4.112   6.3418e-02
   4_occ:   0.996  0.006  0.068 15.756  0.004  4.112   6.3418e-02
   5_bss:   0.996  0.006  0.068 15.756  0.004  4.112   6.3418e-02
   5_xyz:   1.018  0.006  0.073 15.757  0.004  4.107   6.2934e-02
   5_adp:   1.018  0.006  0.073 15.757  0.004  4.107   6.2934e-02
   5_occ:   1.018  0.006  0.073 15.757  0.004  4.107   6.2934e-02
   5_bss:   1.018  0.006  0.073 15.757  0.004  4.107   6.2934e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.104   6.8276e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.104   6.8276e+00
   1_xyz:  15.244  0.172  0.476 88.009  0.037  2.028   1.0067e-01
   1_adp:  15.244  0.172  0.476 88.009  0.037  2.028   1.0067e-01
   1_occ:  15.244  0.172  0.476 88.009  0.037  2.028   1.0067e-01
   2_bss:  15.244  0.172  0.476 88.009  0.037  2.028   1.0067e-01
   2_xyz:   8.527  0.104  0.314 83.326  0.041  2.082   7.6433e-02
   2_adp:   8.527  0.104  0.314 83.326  0.041  2.082   7.6433e-02
   2_occ:   8.527  0.104  0.314 83.326  0.041  2.082   7.6433e-02
   3_bss:   8.527  0.104  0.314 83.326  0.041  2.082   7.6433e-02
   3_xyz:   8.691  0.069  0.322 80.848  0.036  2.263   7.3776e-02
   3_adp:   8.691  0.069  0.322 80.848  0.036  2.263   7.3776e-02
   3_occ:   8.691  0.069  0.322 80.848  0.036  2.263   7.3776e-02
   4_bss:   8.691  0.069  0.322 80.848  0.036  2.263   7.3776e-02
   4_xyz:   7.679  0.041  0.209 83.117  0.028  2.322   1.0276e-01
   4_adp:   7.679  0.041  0.209 83.117  0.028  2.322   1.0276e-01
   4_occ:   7.679  0.041  0.209 83.117  0.028  2.322   1.0276e-01
   5_bss:   7.679  0.041  0.209 83.117  0.028  2.322   1.0276e-01
   5_xyz:   7.680  0.040  0.228 84.842  0.037  2.293   4.4018e-02
   5_adp:   7.680  0.040  0.228 84.842  0.037  2.293   4.4018e-02
   5_occ:   7.680  0.040  0.228 84.842  0.037  2.293   4.4018e-02
   5_bss:   7.680  0.040  0.228 84.842  0.037  2.293   4.4018e-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:  77.85   0.00  14.54  77.85   0.00  12.83  73.67   0.00  23.86
   1_occ:  77.85   0.00  14.54  77.85   0.00  12.83  73.67   0.00  23.86
   2_bss:  77.85   0.00  14.54  77.85   0.00  12.83  73.67   0.00  23.86
   2_xyz:  77.85   0.00  14.54  77.85   0.00  12.83  73.67   0.00  23.86
   2_adp:  84.13   0.00  14.10  84.13   0.00  11.25  83.27   0.00  29.62
   2_occ:  84.13   0.00  14.10  84.13   0.00  11.25  83.27   0.00  29.62
   3_bss:  84.13   0.00  14.10  84.13   0.00  11.25  83.27   0.00  29.62
   3_xyz:  84.13   0.00  14.10  84.13   0.00  11.25  83.27   0.00  29.62
   3_adp:  86.07   0.00  13.62  86.07   0.00   9.59  77.54   2.41  35.54
   3_occ:  86.07   0.00  13.62  86.07   0.00   9.59  77.54   2.41  35.54
   4_bss:  86.07   0.00  13.62  86.07   0.00   9.59  77.54   2.41  35.54
   4_xyz:  86.07   0.00  13.62  86.07   0.00   9.59  77.54   2.41  35.54
   4_adp:  83.46   0.00  13.09  83.46   0.00   9.14  74.28   2.85  34.60
   4_occ:  83.46   0.00  13.09  83.46   0.00   9.14  74.28   2.85  34.60
   5_bss:  83.46   0.00  13.09  83.46   0.00   9.14  74.28   2.85  34.60
   5_xyz:  83.46   0.00  13.09  83.46   0.00   9.14  74.28   2.85  34.60
   5_adp:  88.01   0.00  13.51  88.01   0.00   9.13  79.81   2.53  37.33
   5_occ:  88.01   0.00  13.51  88.01   0.00   9.13  79.81   2.53  37.33
   5_bss:  89.65   1.64  15.15  89.65   1.64  10.77  81.45   4.17  38.97
------------------------------------------------------------------------
 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:    1.258    0.028    0.415
   1_adp:    1.258    0.028    0.415
   1_occ:    1.258    0.028    0.415
   2_bss:    1.258    0.028    0.415
   2_xyz:    1.576    0.029    0.598
   2_adp:    1.576    0.029    0.598
   2_occ:    1.576    0.029    0.598
   3_bss:    1.576    0.029    0.598
   3_xyz:    1.637    0.016    0.754
   3_adp:    1.637    0.016    0.754
   3_occ:    1.637    0.016    0.754
   4_bss:    1.637    0.016    0.754
   4_xyz:    1.773    0.048    0.809
   4_adp:    1.773    0.048    0.809
   4_occ:    1.773    0.048    0.809
   5_bss:    1.773    0.048    0.809
   5_xyz:    1.853    0.023    0.832
   5_adp:    1.853    0.023    0.832
   5_occ:    1.853    0.023    0.832
   5_bss:    1.853    0.023    0.832
------------------------------------------------------------------------

CPU time actual refinement: 354.08


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_136/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_136/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_136/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_136/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_136/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.92 
  Macro-tasks:
    bulk solvent and scale       = 46.45  
    individual site refinement   = 145.95 
    weights calculation          = 31.87  
    collect and process          = 6.42   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 230.80 
  Micro-tasks:
    mask                            = 2.41   
    f_calc                          = 109.58 
    alpha_beta                      = 8.25   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 120.12 
    fmodel                         = 8.20   
    r_factors                      = 0.29   
    phase_errors                   = 10.17  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 260.47 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.944 micro seconds
Total CPU time: 6.12 minutes
from_scatterers_fft:    665 calls, 109.26 s
gradients_fft:          610 calls, 106.93 s

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

# Date 2008-01-16 Time 00:51:34 PST -0800 (1200473494.96 s)
Start R-work = 0.4972, R-free = 0.4947 (no bulk solvent and anisotropic scale)
Final R-work = 0.1349, R-free = 0.1792 (no bulk solvent and anisotropic scale)

Start R-work = 0.4885, R-free = 0.4843
Final R-work = 0.1176, R-free = 0.1652