# Date 2008-01-16 Time 03:09:02 PST -0800 (1200481742.34 s)
#phil __OFF__

Command line arguments: "../1123.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24246
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1123

-------------------------------------------------------------------------------
  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: (71.655, 46.4607, 84.6622, 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: 3.34, per 1000 atoms: 1.18


================================== 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: (71.655, 46.4607, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96112
Completeness in resolution range: 0.939565
Completeness with d_max=infinity: 0.93678

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1240
                             d_min =   1.9611

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: (71.655, 46.4607, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96112
Completeness in resolution range: 0.939565
Completeness with d_max=infinity: 0.93678

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1245 -  4.1978 [2179/2208]  1966   213   9.8%
  bin  2:  4.1978 -  3.3438 [2107/2123]  1893   214  10.2%
  bin  3:  3.3438 -  2.9246 [2070/2089]  1860   210  10.1%
  bin  4:  2.9246 -  2.6588 [2065/2095]  1865   200   9.7%
  bin  5:  2.6588 -  2.4691 [2039/2058]  1835   204  10.0%
  bin  6:  2.4691 -  2.3240 [2048/2073]  1835   213  10.4%
  bin  7:  2.3240 -  2.2080 [2021/2055]  1817   204  10.1%
  bin  8:  2.2080 -  2.1122 [2012/2042]  1816   196   9.7%
  bin  9:  2.1122 -  2.0311 [1992/2048]  1801   191   9.6%
  bin 10:  2.0311 -  1.9611 [1056/2058]   942   114  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1123/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:
        1.75 -     2.38: 27
        2.38 -     3.01: 2000
        3.01 -     3.64: 4666
        3.64 -     4.27: 9183
        4.27 -     4.90: 12621
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.745 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.804 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.857 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.892 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28492 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_1123/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1123/model_refine_001.geo

CPU time processing inputs: 9.32


============================ 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 = 71.655 46.4607 84.6622 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 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4909   r_free= 0.4766   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.288853                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6827 0.99   1417  161 0.4056 0.4290      6.6004      6.6274|
|  2:  4.6827 -  3.7353 0.99   1370  144 0.4184 0.4113      6.8166      6.8323|
|  3:  3.7353 -  3.2685 0.99   1335  150 0.4604 0.4173      6.6808      6.7228|
|  4:  3.2685 -  2.9722 0.99   1345  155 0.4769 0.4521      6.5379      6.5128|
|  5:  2.9722 -  2.7605 0.99   1323  144 0.5145 0.5082      6.3739      6.3391|
|  6:  2.7605 -  2.5986 0.99   1315  149 0.5238 0.5397      6.2833      6.2794|
|  7:  2.5986 -  2.4691 0.99   1314  138 0.5373 0.4586      6.2655      6.1791|
|  8:  2.4691 -  2.3620 0.98   1296  152 0.5409 0.5128      6.1722      6.1941|
|  9:  2.3620 -  2.2714 0.98   1309  149 0.5268 0.4694      6.1316      6.0573|
| 10:  2.2714 -  2.1932 0.99   1297  141 0.5267 0.5522      6.0894      6.1155|
| 11:  2.1932 -  2.1249 0.99   1307  138 0.5316 0.5395      6.0496      6.0674|
| 12:  2.1249 -  2.0643 0.97   1271  148 0.5143 0.5445       5.942      5.9732|
| 13:  2.0643 -  2.0101 0.91   1199  139 0.5556 0.4997      5.8884      5.8284|
| 14:  2.0101 -  1.9611 0.40    532   51 0.5603 0.5641      5.8231      5.8305|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6827  1417   161  0.66  37.91   0.79     0.71      83604.31|
|  2:  4.6827 -  3.7353  1370   144  0.68  36.91   0.87     0.77     116968.66|
|  3:  3.7353 -  3.2685  1335   150  0.57  46.61   0.83     0.71     124873.34|
|  4:  3.2685 -  2.9722  1345   155  0.48  53.18   0.80     0.61     110640.77|
|  5:  2.9722 -  2.7605  1323   144  0.38  61.24   0.72     0.46      89203.10|
|  6:  2.7605 -  2.5986  1315   149  0.36  62.56   0.72     0.44      75543.94|
|  7:  2.5986 -  2.4691  1314   138  0.37  62.60   0.73     0.42      64769.81|
|  8:  2.4691 -  2.3620  1296   152  0.38  61.22   0.71     0.46      57388.29|
|  9:  2.3620 -  2.2714  1309   149  0.38  61.71   0.74     0.45      51972.78|
| 10:  2.2714 -  2.1932  1297   141  0.35  64.03   0.74     0.42      49884.86|
| 11:  2.1932 -  2.1249  1307   138  0.29  68.12   0.77     0.37      49110.49|
| 12:  2.1249 -  2.0643  1271   148  0.25  71.77   0.75     0.31      46050.41|
| 13:  2.0643 -  2.0101  1199   139  0.20  75.05   0.73     0.27      41443.79|
| 14:  2.0101 -  1.9611   532    51  0.17  77.09   0.68     0.21      35814.62|
|alpha:            min =        0.21 max =            0.77 mean =         0.49|
|beta:             min =    35814.62 max =       124873.34 mean =     73469.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.88|
|phase err.(test): min =        0.00 max =           89.98 mean =        58.88|
|-----------------------------------------------------------------------------|

============================== 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 = 16.649321             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.880   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.376489              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.858   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      176 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      709 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1512 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2681 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3933 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5098 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6632 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7731 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.468 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.870 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.785)------------------------------------------|
|    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 = 11.785)------------------------------------------|
|    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 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4948   r_free= 0.4832   ksol= 0.00   Bsol= 0.00   scale= 0.759    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.290756                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4827   r_free= 0.4688   ksol= 0.33   Bsol= 1.49   scale= 0.962    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.89,7.07,7.54,0.00,0.00,0.00); trace/3= 7.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.109141                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.742982             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.303   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.200160              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.795   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4827      final r-factor (work) = 0.4083          |
| start r-factor (free) = 0.4688      final r-factor (free) = 0.4328          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.6510 = 13.74 * 0.50 * 6.2843 + 1.00 * 53.4683                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.6279 = 13.74 * 0.50 * 6.0367 + 1.00 * 0.1468                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4083      final r-factor (work) = 0.3684          |
| start r-factor (free) = 0.4328      final r-factor (free) = 0.4239          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2594 = 1.20 * 1.00 * 6.0367 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3880 = 1.20 * 1.00 * 6.1430 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.785)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.35   13.89    None  None   None       |
|    all(noH): 2823   0      0.00    99.35   13.89    None  None   None       |
|    Sol.    : 438    0      0.00    79.65   25.78    None  None   None       |
|    Mac.    : 2385   0      0.00    99.35   11.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.935: 1325   |   5:    49.674 -  59.609:   29        |
|      1:     9.935 -  19.870:  824   |   6:    59.609 -  69.543:   10        |
|      2:    19.870 -  29.804:  390   |   7:    69.543 -  79.478:    2        |
|      3:    29.804 -  39.739:  161   |   8:    79.478 -  89.413:    1        |
|      4:    39.739 -  49.674:   78   |   9:    89.413 -  99.347:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3684 r_free = 0.4239             target_work(ml) = 6.130         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3680 r_free = 0.4242             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3680   r_free= 0.4242   ksol= 0.33   Bsol= 1.49   scale= 1.083    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.89,7.07,7.54,0.00,0.00,0.00); trace/3= 7.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.128970                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3666   r_free= 0.4193   ksol= 0.34   Bsol= 36.70   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.61,3.82,5.17,0.00,0.00,0.00); trace/3= 4.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.128509                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.682212             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.043   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.584090              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.590  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3666      final r-factor (work) = 0.2652          |
| start r-factor (free) = 0.4193      final r-factor (free) = 0.3218          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.9365 = 10.68 * 0.50 * 6.1391 + 1.00 * 0.1468                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.1981 = 10.68 * 0.50 * 6.0102 + 1.00 * 0.0968                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2652      final r-factor (work) = 0.2356          |
| start r-factor (free) = 0.3218      final r-factor (free) = 0.3026          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5260 = 0.58 * 1.00 * 6.0102 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4125 = 0.58 * 1.00 * 5.8220 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.785)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.66   13.80    None  None   None       |
|    all(noH): 2823   0      0.00    91.66   13.80    None  None   None       |
|    Sol.    : 438    0      1.11    78.63   34.04    None  None   None       |
|    Mac.    : 2385   0      0.00    91.66   10.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.167: 1423   |   5:    45.832 -  54.999:   71        |
|      1:     9.167 -  18.333:  739   |   6:    54.999 -  64.165:   27        |
|      2:    18.333 -  27.499:  256   |   7:    64.165 -  73.332:    6        |
|      3:    27.499 -  36.666:  154   |   8:    73.332 -  82.498:    2        |
|      4:    36.666 -  45.832:  142   |   9:    82.498 -  91.665:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2356 r_free = 0.3026             target_work(ml) = 5.789         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2355 r_free = 0.3027             target_work(ml) = 5.789         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2355   r_free= 0.3027   ksol= 0.34   Bsol= 36.70   scale= 1.061   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.61,3.82,5.17,0.00,0.00,0.00); trace/3= 4.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.789264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2337   r_free= 0.3001   ksol= 0.35   Bsol= 46.81   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.64,1.83,3.03,0.00,0.00,0.00); trace/3= 2.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.788019                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.243567              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.068  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.647793              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.523  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2337      final r-factor (work) = 0.1675          |
| start r-factor (free) = 0.3001      final r-factor (free) = 0.2200          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3766 = 5.24 * 0.50 * 5.8280 + 1.00 * 0.0968                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9395 = 5.24 * 0.50 * 5.6716 + 1.00 * 0.0698                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1675      final r-factor (work) = 0.1505          |
| start r-factor (free) = 0.2200      final r-factor (free) = 0.2017          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6860 = 0.65 * 1.00 * 5.6716 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5386 = 0.65 * 1.00 * 5.4438 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.785)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.38   14.29    None  None   None       |
|    all(noH): 2823   0      0.00    91.38   14.29    None  None   None       |
|    Sol.    : 438    0      2.50    83.71   38.95    None  None   None       |
|    Mac.    : 2385   0      0.00    91.38   9.76     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.138: 1522   |   5:    45.691 -  54.830:  104        |
|      1:     9.138 -  18.277:  690   |   6:    54.830 -  63.968:   58        |
|      2:    18.277 -  27.415:  176   |   7:    63.968 -  73.106:   20        |
|      3:    27.415 -  36.553:  129   |   8:    73.106 -  82.244:   10        |
|      4:    36.553 -  45.691:  111   |   9:    82.244 -  91.382:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1505 r_free = 0.2017             target_work(ml) = 5.399         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1503 r_free = 0.2010             target_work(ml) = 5.398         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1503   r_free= 0.2010   ksol= 0.35   Bsol= 46.81   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.64,1.83,3.03,0.00,0.00,0.00); trace/3= 2.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.397632                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1499   r_free= 0.2003   ksol= 0.33   Bsol= 45.39   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.77,1.05,1.94,0.00,0.00,0.00); trace/3= 1.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.394991                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.985925              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.779  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.300894              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.979  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1499      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.2003      final r-factor (free) = 0.1786          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4810 = 1.99 * 0.50 * 5.4496 + 1.00 * 0.0698                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3667 = 1.99 * 0.50 * 5.3481 + 1.00 * 0.0563                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1329      final r-factor (work) = 0.1295          |
| start r-factor (free) = 0.1786      final r-factor (free) = 0.1742          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6212 = 0.30 * 1.00 * 5.3481 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5971 = 0.30 * 1.00 * 5.2733 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.785)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.67   14.02    None  None   None       |
|    all(noH): 2823   0      0.00    91.67   14.02    None  None   None       |
|    Sol.    : 438    0      3.57    82.94   37.82    None  None   None       |
|    Mac.    : 2385   0      0.00    91.67   9.64     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.167: 1543   |   5:    45.835 -  55.002:   90        |
|      1:     9.167 -  18.334:  698   |   6:    55.002 -  64.169:   49        |
|      2:    18.334 -  27.501:  180   |   7:    64.169 -  73.336:   20        |
|      3:    27.501 -  36.668:  123   |   8:    73.336 -  82.503:    8        |
|      4:    36.668 -  45.835:  109   |   9:    82.503 -  91.670:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1295 r_free = 0.1742             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1294 r_free = 0.1739             target_work(ml) = 5.257         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1739   ksol= 0.33   Bsol= 45.39   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.77,1.05,1.94,0.00,0.00,0.00); trace/3= 1.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.257061                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1293   r_free= 0.1737   ksol= 0.33   Bsol= 45.39   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.38,0.82,1.59,0.00,0.00,0.00); trace/3= 1.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.256907                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.313335              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.282  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.181024              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.560  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1293      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1737      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1561 = 2.31 * 0.50 * 5.2736 + 1.00 * 0.0563                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1058 = 2.31 * 0.50 * 5.2197 + 1.00 * 0.0683                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1189          |
| start r-factor (free) = 0.1659      final r-factor (free) = 0.1644          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9552 = 0.18 * 1.00 * 5.2197 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9494 = 0.18 * 1.00 * 5.1964 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.785)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.50   13.58    None  None   None       |
|    all(noH): 2823   0      0.00    89.50   13.58    None  None   None       |
|    Sol.    : 438    0      3.71    81.22   35.60    None  None   None       |
|    Mac.    : 2385   0      0.00    89.50   9.54     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 -   8.950: 1510   |   5:    44.752 -  53.702:   79        |
|      1:     8.950 -  17.901:  745   |   6:    53.702 -  62.652:   39        |
|      2:    17.901 -  26.851:  166   |   7:    62.652 -  71.603:   20        |
|      3:    26.851 -  35.801:  144   |   8:    71.603 -  80.553:    7        |
|      4:    35.801 -  44.752:  110   |   9:    80.553 -  89.503:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1189 r_free = 0.1644             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1187 r_free = 0.1640             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1640   ksol= 0.33   Bsol= 45.39   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.38,0.82,1.59,0.00,0.00,0.00); trace/3= 1.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.190487                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6827 0.99   1417  161 0.1018 0.1375      5.4106      5.5936|
|  2:  4.6827 -  3.7353 0.99   1370  144 0.0921 0.1190      5.4924      5.6958|
|  3:  3.7353 -  3.2685 0.99   1335  150 0.1149 0.1638      5.5301      5.8731|
|  4:  3.2685 -  2.9722 0.99   1345  155 0.1336 0.1592      5.5163       5.621|
|  5:  2.9722 -  2.7605 0.99   1323  144 0.1391 0.1750      5.3634      5.5555|
|  6:  2.7605 -  2.5986 0.99   1315  149 0.1288 0.1901      5.2364      5.4879|
|  7:  2.5986 -  2.4691 0.99   1314  138 0.1325 0.1709      5.2111      5.3771|
|  8:  2.4691 -  2.3620 0.98   1296  152 0.1203 0.1808      5.0753      5.3793|
|  9:  2.3620 -  2.2714 0.98   1309  149 0.1236 0.1924      5.0625      5.3615|
| 10:  2.2714 -  2.1932 0.99   1297  141 0.1181 0.1806      4.9835       5.222|
| 11:  2.1932 -  2.1249 0.99   1307  138 0.1226 0.1830      4.9831      5.3233|
| 12:  2.1249 -  2.0643 0.97   1271  148 0.1155 0.1734      4.9068      5.1203|
| 13:  2.0643 -  2.0101 0.91   1199  139 0.1260 0.1747        4.83      5.0565|
| 14:  2.0101 -  1.9611 0.40    532   51 0.1099 0.1550      4.6559      4.9212|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6827  1417   161  0.94   9.23   0.98     0.97       7690.78|
|  2:  4.6827 -  3.7353  1370   144  0.95   8.50   1.02     1.00       9784.05|
|  3:  3.7353 -  3.2685  1335   150  0.93  12.32   1.03     1.02      11471.57|
|  4:  3.2685 -  2.9722  1345   155  0.91  14.98   1.01     0.98      11413.67|
|  5:  2.9722 -  2.7605  1323   144  0.90  16.36   0.99     0.97       8675.59|
|  6:  2.7605 -  2.5986  1315   149  0.90  16.55   0.98     0.96       7320.73|
|  7:  2.5986 -  2.4691  1314   138  0.90  15.87   1.00     0.98       6632.74|
|  8:  2.4691 -  2.3620  1296   152  0.90  15.71   0.98     0.95       5350.18|
|  9:  2.3620 -  2.2714  1309   149  0.90  16.33   1.02     0.99       5274.71|
| 10:  2.2714 -  2.1932  1297   141  0.91  15.42   1.01     0.98       4503.19|
| 11:  2.1932 -  2.1249  1307   138  0.89  17.31   1.00     0.96       4716.52|
| 12:  2.1249 -  2.0643  1271   148  0.90  16.22   1.02     1.03       4285.20|
| 13:  2.0643 -  2.0101  1199   139  0.90  16.52   1.01     1.00       3461.84|
| 14:  2.0101 -  1.9611   532    51  0.91  15.04   1.00     0.98       2507.53|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2507.53 max =        11471.57 mean =      6895.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        14.66|
|phase err.(test): min =        0.00 max =           89.06 mean =        14.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1639   ksol= 0.32   Bsol= 43.98   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.11,-0.43,0.31,-0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.190443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1639   ksol= 0.32   Bsol= 43.98   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.11,-0.43,0.31,-0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.190443                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6827 0.99   1417  161 0.1002 0.1356      5.3969      5.5942|
|  2:  4.6827 -  3.7353 0.99   1370  144 0.0925 0.1192      5.4961      5.7073|
|  3:  3.7353 -  3.2685 0.99   1335  150 0.1154 0.1641      5.5333      5.8728|
|  4:  3.2685 -  2.9722 0.99   1345  155 0.1341 0.1595        5.52      5.6257|
|  5:  2.9722 -  2.7605 0.99   1323  144 0.1397 0.1740      5.3654      5.5548|
|  6:  2.7605 -  2.5986 0.99   1315  149 0.1293 0.1890      5.2364      5.4849|
|  7:  2.5986 -  2.4691 0.99   1314  138 0.1325 0.1714      5.2113      5.3788|
|  8:  2.4691 -  2.3620 0.98   1296  152 0.1203 0.1811      5.0768      5.3818|
|  9:  2.3620 -  2.2714 0.98   1309  149 0.1233 0.1919       5.062      5.3615|
| 10:  2.2714 -  2.1932 0.99   1297  141 0.1180 0.1806       4.983      5.2218|
| 11:  2.1932 -  2.1249 0.99   1307  138 0.1223 0.1831      4.9825       5.324|
| 12:  2.1249 -  2.0643 0.97   1271  148 0.1154 0.1735      4.9075      5.1211|
| 13:  2.0643 -  2.0101 0.91   1199  139 0.1261 0.1753      4.8306      5.0573|
| 14:  2.0101 -  1.9611 0.40    532   51 0.1101 0.1550      4.6562      4.9208|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6827  1417   161  0.94   9.22   0.98     0.96       7595.62|
|  2:  4.6827 -  3.7353  1370   144  0.95   8.56   1.01     1.00       9837.52|
|  3:  3.7353 -  3.2685  1335   150  0.93  12.37   1.03     1.02      11595.79|
|  4:  3.2685 -  2.9722  1345   155  0.91  15.03   1.00     0.98      11488.10|
|  5:  2.9722 -  2.7605  1323   144  0.90  16.31   0.99     0.97       8645.94|
|  6:  2.7605 -  2.5986  1315   149  0.90  16.56   0.98     0.96       7310.08|
|  7:  2.5986 -  2.4691  1314   138  0.90  15.86   0.99     0.97       6631.59|
|  8:  2.4691 -  2.3620  1296   152  0.90  15.76   0.98     0.95       5388.63|
|  9:  2.3620 -  2.2714  1309   149  0.90  16.36   1.01     0.98       5282.65|
| 10:  2.2714 -  2.1932  1297   141  0.91  15.44   1.00     0.97       4510.04|
| 11:  2.1932 -  2.1249  1307   138  0.89  17.33   0.99     0.96       4719.52|
| 12:  2.1249 -  2.0643  1271   148  0.90  16.23   1.01     1.02       4292.11|
| 13:  2.0643 -  2.0101  1199   139  0.90  16.53   1.00     0.99       3465.85|
| 14:  2.0101 -  1.9611   532    51  0.91  15.05   0.99     0.97       2507.30|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2507.30 max =        11595.79 mean =      6908.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.67|
|phase err.(test): min =        0.00 max =           88.53 mean =        14.07|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.785)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.11    90.61   14.69    None  None   None       |
|    all(noH): 2823   0      1.11    90.61   14.69    None  None   None       |
|    Sol.    : 438    0      4.82    82.33   36.71    None  None   None       |
|    Mac.    : 2385   0      1.11    90.61   10.65    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:     1.108 -  10.059: 1510   |   5:    45.860 -  54.810:   79        |
|      1:    10.059 -  19.009:  745   |   6:    54.810 -  63.761:   39        |
|      2:    19.009 -  27.959:  166   |   7:    63.761 -  72.711:   20        |
|      3:    27.959 -  36.910:  144   |   8:    72.711 -  81.661:    7        |
|      4:    36.910 -  45.860:  110   |   9:    81.661 -  90.612:    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)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.461 - 5.911
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 329
   mapped sites are within: 0.702 - 5.911

peak=   10.391 closest distance to " CB  VAL A 230 " =    1.451
peak=    8.395 closest distance to " CG2 VAL A 296 " =    1.266
peak=    7.269 closest distance to " CG  ARG A 138 " =    1.164
peak=    6.222 closest distance to " NH2 ARG A  56 " =    2.264
peak=    6.050 closest distance to " O   HOH Z 278 " =    1.391
peak=    5.909 closest distance to " O   HOH Z   7 " =    1.558
peak=    5.878 closest distance to " O   HOH Z  37 " =    1.522
peak=    5.572 closest distance to " CG  LEU A   5 " =    1.235
peak=    5.539 closest distance to " NE2 GLN A  11 " =    1.232
peak=    5.424 closest distance to " CD2 LEU A   5 " =    1.227
peak=    5.190 closest distance to " O   HOH Z 183 " =    1.458
peak=    5.076 closest distance to " CB  GLN A 223 " =    1.354
peak=    5.072 closest distance to " CD1AILE A 234 " =    1.063
peak=    4.888 closest distance to " CG  PRO A 213 " =    1.260
peak=    4.843 closest distance to " O   HOH Z 232 " =    2.292
peak=    4.831 closest distance to " CG  PRO A 198 " =    1.315
peak=    4.809 closest distance to " O   HOH Z 144 " =    1.733
peak=    4.801 closest distance to " O   HOH Z 132 " =    1.059
peak=    4.788 closest distance to " NH2BARG A 102 " =    0.980
peak=    4.752 closest distance to " CB  SER A  63 " =    1.310
peak=    4.748 closest distance to " O   HOH Z 202 " =    1.507
peak=    4.718 closest distance to " CG  LEU A 228 " =    1.268
peak=    4.635 closest distance to " O   HOH Z 427 " =    2.960
peak=    4.620 closest distance to " O   HOH Z 124 " =    1.418
peak=    4.612 closest distance to " O   HOH Z 344 " =    1.261
peak=    4.600 closest distance to " O   HOH Z 108 " =    1.716
peak=    4.599 closest distance to " O   HOH Z 193 " =    1.769
peak=    4.521 closest distance to " O   HOH Z 186 " =    1.289
peak=    4.501 closest distance to " O   HOH Z 126 " =    1.832
peak=    4.493 closest distance to " NH1 ARG A 138 " =    1.023
peak=    4.490 closest distance to " CB  GLN A 183 " =    1.178
peak=    4.470 closest distance to " O   HOH Z 368 " =    2.047
peak=    4.465 closest distance to " O   HOH Z  78 " =    2.457
peak=    4.446 closest distance to " O   HOH Z 236 " =    1.959
peak=    4.440 closest distance to " O   HOH Z 260 " =    1.351
peak=    4.414 closest distance to " CB  GLU A 152 " =    1.255
peak=    4.407 closest distance to " O   HOH Z  48 " =    1.719
peak=    4.388 closest distance to " CB  ASN A 148 " =    1.388
peak=    4.371 closest distance to " O   PRO A 198 " =    1.549
peak=    4.366 closest distance to " O   HOH Z 298 " =    1.939
peak=    4.342 closest distance to " CB  SER A   3 " =    1.520
peak=    4.340 closest distance to " O   HOH Z 303 " =    2.273
peak=    4.327 closest distance to " OD2 ASP A 286 " =    2.842
peak=    4.299 closest distance to " NH1 ARG A  56 " =    0.999
peak=    4.285 closest distance to " CB  VAL A 230 " =    1.228
peak=    4.250 closest distance to " O   HOH Z 217 " =    3.086
peak=    4.240 closest distance to " O   HOH Z   9 " =    2.121
peak=    4.234 closest distance to " O   HOH Z 369 " =    1.949
peak=    4.218 closest distance to " O   HOH Z 411 " =    3.611
peak=    4.213 closest distance to " CD2 LEU A 228 " =    1.279
peak=    4.192 closest distance to " O   HOH Z 316 " =    2.996
peak=    4.179 closest distance to " CB  TYR A 169 " =    0.951
peak=    4.170 closest distance to " O   HOH Z 214 " =    1.344
peak=    4.168 closest distance to " O   HOH Z 263 " =    1.605
peak=    4.164 closest distance to " O   HOH Z 227 " =    1.728
peak=    4.154 closest distance to " O   HOH Z 272 " =    1.920
peak=    4.147 closest distance to " O   HOH Z 126 " =    1.594
peak=    4.124 closest distance to " O   HOH Z   2 " =    1.812
peak=    4.119 closest distance to " O   HOH Z 117 " =    1.900
peak=    4.114 closest distance to " O   HOH Z 371 " =    2.775
peak=    4.109 closest distance to " O   HOH Z   3 " =    2.051
peak=    4.098 closest distance to " CA  LEU A 282 " =    1.129
peak=    4.097 closest distance to " O   HOH Z 133 " =    1.790
peak=    4.073 closest distance to " O   HOH Z 132 " =    2.328
peak=    4.064 closest distance to " CD1 LEU A 300 " =    1.255
peak=    4.061 closest distance to " O   HOH Z 112 " =    1.244
peak=    4.057 closest distance to " CB  VAL A 265 " =    1.274
peak=    4.052 closest distance to " O   HOH Z 246 " =    1.456
peak=    4.047 closest distance to " O   HOH Z  58 " =    1.737
peak=    4.036 closest distance to " O   HOH Z 425 " =    1.443
peak=    4.034 closest distance to " OD1 ASN A  69 " =    2.676
peak=    4.029 closest distance to " CD  ARG A 138 " =    1.093
peak=    4.014 closest distance to " O   HOH Z 126 " =    1.552
peak=    4.002 closest distance to " O   HOH Z 410 " =    1.570
peak=    3.998 closest distance to " CB  GLU A 128 " =    1.074
peak=    3.990 closest distance to " CB  ARG A 275 " =    0.871
peak=    3.894 closest distance to " O   HOH Z  80 " =    1.663
peak=    3.893 closest distance to " CD1 ILE A  33 " =    1.677
peak=    3.887 closest distance to " O   HOH Z 357 " =    1.631
peak=    3.881 closest distance to " O   HOH Z 184 " =    1.510
peak=    3.877 closest distance to " CG2 THR A 221 " =    1.068
peak=    3.877 closest distance to " O   HOH Z  40 " =    2.658
peak=    3.874 closest distance to " O   HOH Z 134 " =    1.498
peak=    3.872 closest distance to " CB  LEU A 228 " =    1.207
peak=    3.872 closest distance to " O   HOH Z 193 " =    1.910
peak=    3.849 closest distance to " CB  LEU A 143 " =    1.077
peak=    3.832 closest distance to " CG  PRO A 243 " =    1.140
peak=    3.830 closest distance to " O   SER A  87 " =    2.430
peak=    3.826 closest distance to " CA  ALA A 154 " =    1.086
peak=    3.826 closest distance to " O   HOH Z  21 " =    1.691
peak=    3.823 closest distance to " CB  ARG A  79 " =    1.458
peak=    3.823 closest distance to " O   HOH Z 281 " =    1.791
peak=    3.818 closest distance to " O   HOH Z 255 " =    1.660
peak=    3.809 closest distance to " O   HOH Z 234 " =    3.755
peak=    3.805 closest distance to " CA  ALA A  51 " =    1.081
peak=    3.805 closest distance to " CA  GLY A 267 " =    1.048
peak=    3.803 closest distance to " O   HOH Z 346 " =    1.542
peak=    3.800 closest distance to " O   HOH Z 132 " =    2.328
peak=    3.800 closest distance to " O   HOH Z 284 " =    1.800
peak=    3.799 closest distance to " O   HOH Z  61 " =    1.660
peak=    3.780 closest distance to " O   HOH Z  88 " =    3.358
peak=    3.776 closest distance to " CG  LEU A 167 " =    1.158
peak=    3.772 closest distance to " CG  GLN A  88 " =    1.118
peak=    3.767 closest distance to " CB  ILE A 234 " =    0.889
peak=    3.766 closest distance to " CD  ARG A 159 " =    0.775
peak=    3.754 closest distance to " CA  ALA A  21 " =    1.200
peak=    3.753 closest distance to " CG2 VAL A 257 " =    0.928
peak=    3.753 closest distance to " CB  THR A 157 " =    1.053
peak=    3.751 closest distance to " CB  ASN A 187 " =    1.026
peak=    3.735 closest distance to " CB  VAL A 202 " =    1.527
peak=    3.735 closest distance to " O   HOH Z 271 " =    2.041
peak=    3.725 closest distance to " ND2 ASN A 187 " =    1.605
peak=    3.719 closest distance to " CB  ALA A 291 " =    1.430
peak=    3.719 closest distance to " O   HOH Z 193 " =    1.867
peak=    3.717 closest distance to " NH1AARG A 145 " =    1.140
peak=    3.716 closest distance to " O   HOH Z 180 " =    2.120
peak=    3.696 closest distance to " O   HOH Z 143 " =    1.089
peak=    3.694 closest distance to " CB  ARG A 139 " =    1.008
peak=    3.692 closest distance to " O   HOH Z 295 " =    1.535
peak=    3.690 closest distance to " CG BARG A 102 " =    1.883
peak=    3.682 closest distance to " O   HOH Z  49 " =    1.892
peak=    3.679 closest distance to " CG1 ILE A  33 " =    1.335
peak=    3.675 closest distance to " O   HOH Z 403 " =    1.624
peak=    3.670 closest distance to " CD2 LEU A 255 " =    1.524
peak=    3.663 closest distance to " C   ALA A 299 " =    0.947
peak=    3.656 closest distance to " N   PHE A 130 " =    1.338
peak=    3.649 closest distance to " O   HOH Z  64 " =    2.327
peak=    3.643 closest distance to " O   HOH Z 280 " =    3.063
peak=    3.637 closest distance to " CB  ASN A 148 " =    1.888
peak=    3.631 closest distance to " CB  VAL A 296 " =    1.119
peak=    3.626 closest distance to " O   HOH Z  61 " =    1.617
peak=    3.619 closest distance to " CB  TRP A 179 " =    1.422
peak=    3.614 closest distance to " O   HOH Z 113 " =    1.376
peak=    3.613 closest distance to " CB  MET A  40 " =    0.889
peak=    3.604 closest distance to " NH2BARG A 190 " =    1.625
peak=    3.593 closest distance to " O   HOH Z 380 " =    1.696
peak=    3.591 closest distance to " CB  PRO A  54 " =    0.702
peak=    3.581 closest distance to " O   HOH Z 359 " =    3.885
peak=    3.576 closest distance to " O   HOH Z 281 " =    4.337
peak=    3.573 closest distance to " O   HOH Z   9 " =    1.950
peak=    3.572 closest distance to " CG1BVAL A 121 " =    1.099
peak=    3.571 closest distance to " O   HOH Z 145 " =    1.657
peak=    3.570 closest distance to " CA  ASN A 215 " =    1.209
peak=    3.560 closest distance to " O   HOH Z 182 " =    1.366
peak=    3.557 closest distance to " CB  ALA A 161 " =    0.902
peak=    3.555 closest distance to " O   HOH Z 118 " =    1.887
peak=    3.552 closest distance to " CB  GLN A  88 " =    1.264
peak=    3.546 closest distance to " O  BHOH Z 338 " =    2.453
peak=    3.541 closest distance to " ND1 HIS A  86 " =    1.732
peak=    3.540 closest distance to " CD BLYS A 290 " =    1.090
peak=    3.533 closest distance to " CA  TYR A 186 " =    1.506
peak=    3.531 closest distance to " O   HOH Z 189 " =    2.645
peak=    3.531 closest distance to " O   HOH Z 437 " =    2.367
peak=    3.529 closest distance to " CA  TYR A  30 " =    1.019
peak=    3.527 closest distance to " NE AARG A 275 " =    1.432
peak=    3.526 closest distance to " OD1 ASN A 217 " =    1.657
peak=    3.519 closest distance to " CE  MET A  93 " =    1.481
peak=    3.515 closest distance to " CB  TRP A 266 " =    0.998
peak=    3.510 closest distance to " O   HOH Z  15 " =    1.564
peak=    3.506 closest distance to " O   HOH Z 145 " =    3.364
peak=    3.504 closest distance to " CA  SER A  87 " =    0.863
peak=    3.497 closest distance to " CA  VAL A  41 " =    0.938
peak=    3.488 closest distance to " CA  THR A 221 " =    0.931
peak=    3.488 closest distance to " CB  GLU A 236 " =    0.857
peak=    3.485 closest distance to " CB  ASN A 142 " =    0.939
peak=    3.479 closest distance to " CB  TYR A  30 " =    1.468
peak=    3.475 closest distance to " O   HOH Z 329 " =    3.715
peak=    3.469 closest distance to " O   HOH Z 419 " =    1.749
peak=    3.466 closest distance to " O   HOH Z 158 " =    2.641
peak=    3.462 closest distance to " O   HOH Z 332 " =    1.527
peak=    3.459 closest distance to " NH2AARG A 190 " =    1.561
peak=    3.458 closest distance to " O   HOH Z 222 " =    2.271
peak=    3.446 closest distance to " CA  ILE A 234 " =    0.869
peak=    3.442 closest distance to " CB  THR A  82 " =    1.263
peak=    3.442 closest distance to " O   HOH Z 303 " =    1.795
peak=    3.437 closest distance to " O   HOH Z 244 " =    1.586
peak=    3.437 closest distance to " ND2 ASN A 249 " =    1.852
peak=    3.434 closest distance to " OG  SER A  22 " =    2.986
peak=    3.431 closest distance to " O   HOH Z  68 " =    2.135
peak=    3.415 closest distance to " O   HOH Z 119 " =    1.493
peak=    3.412 closest distance to " O   HOH Z 139 " =    3.025
peak=    3.412 closest distance to " N   ARG A 156 " =    1.365
peak=    3.410 closest distance to " O   HOH Z  68 " =    1.578
peak=    3.409 closest distance to " O   HOH Z 184 " =    2.127
peak=    3.406 closest distance to " O   HOH Z 276 " =    1.295
peak=    3.403 closest distance to " CB  GLU A 277 " =    3.536
peak=    3.398 closest distance to " CG1 VAL A 153 " =    0.974
peak=    3.396 closest distance to " O   HOH Z 148 " =    3.325
peak=    3.395 closest distance to " NH2 ARG A 219 " =    1.883
peak=    3.391 closest distance to " O   HOH Z 148 " =    1.736
peak=    3.389 closest distance to " CA  VAL A 126 " =    1.077
peak=    3.388 closest distance to " CB BVAL A  41 " =    1.291
peak=    3.384 closest distance to " O   HOH Z  44 " =    2.481
peak=    3.378 closest distance to " CG1BVAL A  72 " =    1.543
peak=    3.377 closest distance to " O   HOH Z 345 " =    3.290
peak=    3.371 closest distance to " CA  ALA A 160 " =    0.892
peak=    3.369 closest distance to " OD1BASN A 224 " =    2.209
peak=    3.368 closest distance to " CB  SER A 212 " =    1.149
peak=    3.365 closest distance to " NE2 GLN A  58 " =    5.449
peak=    3.364 closest distance to " CA  THR A 264 " =    0.783
peak=    3.364 closest distance to " O   HOH Z 115 " =    2.260
peak=    3.361 closest distance to " CB  TRP A 150 " =    1.334
peak=    3.361 closest distance to " O   HOH Z 344 " =    2.796
peak=    3.360 closest distance to " CZ3 TRP A 123 " =    1.310
peak=    3.359 closest distance to " O   HOH Z 271 " =    2.239
peak=    3.356 closest distance to " CB  LEU A 237 " =    0.941
peak=    3.355 closest distance to " CB  SER A 216 " =    0.838
peak=    3.355 closest distance to " CA  ALA A 158 " =    1.135
peak=    3.353 closest distance to " NZ ALYS A 290 " =    1.048
peak=    3.345 closest distance to " CE  LYS A  76 " =    0.949
peak=    3.344 closest distance to " CG  ARG A 159 " =    1.002
peak=    3.343 closest distance to " CD  ARG A 269 " =    0.964
peak=    3.342 closest distance to " CA  ASP A 162 " =    1.012
peak=    3.336 closest distance to " O   HOH Z 128 " =    1.819
peak=    3.335 closest distance to " O   HOH Z 280 " =    1.698
peak=    3.333 closest distance to " O   MET A 105 " =    1.727
peak=    3.332 closest distance to " O   HOH Z 196 " =    1.419
peak=    3.331 closest distance to " O   HOH Z 423 " =    2.629
peak=    3.330 closest distance to " O   HOH Z 435 " =    2.139
peak=    3.325 closest distance to " CA  LYS A 117 " =    1.208
peak=    3.316 closest distance to " O   HOH Z 216 " =    2.331
peak=    3.315 closest distance to " O   HOH Z  18 " =    1.816
peak=    3.308 closest distance to " O   HOH Z 175 " =    2.017
peak=    3.305 closest distance to " O   HOH Z 102 " =    1.023
peak=    3.303 closest distance to " O   HOH Z 287 " =    2.388
peak=    3.299 closest distance to " O   HOH Z 423 " =    1.723
peak=    3.296 closest distance to " CA  GLY A 196 " =    0.914
peak=    3.294 closest distance to " OG  SER A  62 " =    2.891
peak=    3.291 closest distance to " O   HOH Z  59 " =    1.861
peak=    3.287 closest distance to " O   HOH Z 116 " =    3.017
peak=    3.283 closest distance to " O   HOH Z 130 " =    2.158
peak=    3.280 closest distance to " CA  MET A  40 " =    1.123
peak=    3.279 closest distance to " OE1 GLN A  11 " =    2.008
peak=    3.274 closest distance to " O   HOH Z  59 " =    2.032
peak=    3.273 closest distance to " CD1 LEU A 101 " =    1.165
peak=    3.273 closest distance to " CZ  PHE A 192 " =    1.167
peak=    3.272 closest distance to " CB  ASP A 140 " =    0.708
peak=    3.272 closest distance to " O   HOH Z 412 " =    3.551
peak=    3.271 closest distance to " O   HOH Z 148 " =    2.284
peak=    3.269 closest distance to " O   HOH Z 156 " =    2.912
peak=    3.267 closest distance to " CD  ARG A  14 " =    1.171
peak=    3.265 closest distance to " CB  SER A 273 " =    0.878
peak=    3.265 closest distance to " O   HOH Z 273 " =    2.624
peak=    3.262 closest distance to " O   HOH Z 374 " =    2.578
peak=    3.261 closest distance to " CB  ASN A  39 " =    0.788
peak=    3.258 closest distance to " O   HOH Z 302 " =    1.878
peak=    3.258 closest distance to " O   ALA A 291 " =    1.657
peak=    3.258 closest distance to " O   GLN A  58 " =    1.515
peak=    3.257 closest distance to " O   HOH Z 128 " =    1.581
peak=    3.253 closest distance to " CA  ALA A 295 " =    1.014
peak=    3.250 closest distance to " CB  ALA A 104 " =    0.763
peak=    3.249 closest distance to " O   HOH Z 140 " =    2.558
peak=    3.242 closest distance to " O   GLY A  57 " =    2.679
peak=    3.239 closest distance to " CG  LYS A  76 " =    1.481
peak=    3.237 closest distance to " O   HOH Z  89 " =    1.540
peak=    3.234 closest distance to " CB  LEU A 255 " =    0.945
peak=    3.233 closest distance to " O   HOH Z 116 " =    1.686
peak=    3.233 closest distance to " NH2BARG A 145 " =    2.062
peak=    3.230 closest distance to " O   HOH Z 194 " =    2.226
peak=    3.226 closest distance to " O   HOH Z 175 " =    3.508
peak=    3.222 closest distance to " CA  LYS A  48 " =    1.435
peak=    3.220 closest distance to " NE2 GLN A 223 " =    1.744
peak=    3.213 closest distance to " O   HOH Z 394 " =    1.820
peak=    3.211 closest distance to " O   HOH Z 415 " =    5.832
peak=    3.207 closest distance to " CD BARG A 102 " =    1.370
peak=    3.205 closest distance to " N   ASN A  39 " =    1.154
peak=    3.204 closest distance to " O   PRO A 198 " =    1.272
peak=    3.202 closest distance to " OE1 GLU A   2 " =    2.113
peak=    3.201 closest distance to " O   HOH Z 143 " =    0.852
peak=    3.201 closest distance to " O   HOH Z 148 " =    3.698
peak=    3.201 closest distance to " CA  LEU A 101 " =    1.502
peak=    3.200 closest distance to " CD  LYS A 119 " =    1.645
peak=    3.194 closest distance to " CB  SER A 276 " =    1.128
peak=    3.189 closest distance to " N   TYR A  15 " =    0.902
peak=    3.189 closest distance to " CB  ALA A  34 " =    0.972
peak=    3.188 closest distance to " O   HOH Z 200 " =    5.911
peak=    3.187 closest distance to " O   HOH Z 151 " =    1.722
peak=    3.184 closest distance to " O   HOH Z  64 " =    2.019
peak=    3.183 closest distance to " O   HOH Z   1 " =    1.723
peak=    3.183 closest distance to " CH2 TRP A 150 " =    1.026
peak=    3.179 closest distance to " CG BARG A 275 " =    1.508
peak=    3.176 closest distance to " O   HOH Z  55 " =    2.172
peak=    3.174 closest distance to " O   HOH Z 217 " =    1.529
peak=    3.173 closest distance to " O   HOH Z 406 " =    1.762
peak=    3.171 closest distance to " CH2 TRP A  92 " =    2.074
peak=    3.170 closest distance to " CA  ASN A  74 " =    1.177
peak=    3.169 closest distance to " CA  ASN A 127 " =    1.005
peak=    3.168 closest distance to " O   THR A  31 " =    1.417
peak=    3.164 closest distance to " O   HOH Z 189 " =    3.418
peak=    3.164 closest distance to " O   ALA A  10 " =    1.450
peak=    3.164 closest distance to " O   HOH Z  66 " =    2.026
peak=    3.161 closest distance to " O   HOH Z  20 " =    1.869
peak=    3.160 closest distance to " O   HOH Z 227 " =    2.038
peak=    3.158 closest distance to " OG BSER A 164 " =    2.332
peak=    3.152 closest distance to " O   HOH Z 388 " =    2.047
peak=    3.150 closest distance to " O   HOH Z 181 " =    2.188
peak=    3.144 closest distance to " CG2 ILE A  20 " =    1.595
peak=    3.142 closest distance to " O   HOH Z 171 " =    2.067
peak=    3.141 closest distance to " CG1 ILE A  49 " =    1.323
peak=    3.136 closest distance to " O   HOH Z 109 " =    2.710
peak=    3.134 closest distance to " O   HOH Z 409 " =    2.853
peak=    3.130 closest distance to " O   HOH Z 298 " =    2.577
peak=    3.129 closest distance to " O   ASN A 217 " =    1.292
peak=    3.126 closest distance to " O   HOH Z  10 " =    1.783
peak=    3.125 closest distance to " CA  GLU A 152 " =    1.009
peak=    3.124 closest distance to " ND1 HIS A  81 " =    1.652
peak=    3.124 closest distance to " O   HOH Z 236 " =    1.624
peak=    3.120 closest distance to " O   HOH Z 407 " =    1.928
peak=    3.110 closest distance to " O   HOH Z  53 " =    2.544
peak=    3.106 closest distance to " O   HOH Z  97 " =    1.325
peak=    3.105 closest distance to " O   HOH Z 203 " =    1.680
peak=    3.098 closest distance to " O   HOH Z  43 " =    2.078
peak=    3.089 closest distance to " O   HOH Z  88 " =    2.521
peak=    3.089 closest distance to " OD1 ASN A  45 " =    1.462
peak=    3.082 closest distance to " O   ALA A 158 " =    1.377
peak=    3.082 closest distance to " O   ALA A 233 " =    1.826
peak=    3.080 closest distance to " CG  MET A 185 " =    1.222
peak=    3.079 closest distance to " O   HOH Z 383 " =    2.261
peak=    3.067 closest distance to " CG  LYS A 166 " =    1.370
peak=    3.066 closest distance to " CD  LYS A 166 " =    1.288
peak=    3.064 closest distance to " CG2 VAL A 174 " =    1.347
peak=    3.052 closest distance to " O   SER A  87 " =    1.782
peak=    3.017 closest distance to " O   HOH Z 110 " =    1.612

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.337 - 5.397
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 203
   mapped sites are within: 0.721 - 5.397

peak=   -5.936 closest distance to " CG2 VAL A 230 " =    0.754
peak=   -4.691 closest distance to " O   HOH Z 290 " =    0.967
peak=   -4.483 closest distance to " O   HOH Z 102 " =    1.386
peak=   -4.389 closest distance to " CG  ARG A 138 " =    0.921
peak=   -4.354 closest distance to " CD  ARG A  14 " =    3.271
peak=   -4.309 closest distance to " O   HOH Z 377 " =    1.581
peak=   -4.235 closest distance to " O   HOH Z 231 " =    0.812
peak=   -4.176 closest distance to " O   HOH Z 231 " =    1.212
peak=   -4.162 closest distance to " CD  ARG A 156 " =    1.990
peak=   -4.123 closest distance to " CD2 LEU A 143 " =    2.637
peak=   -4.095 closest distance to " CD  ARG A 138 " =    1.164
peak=   -4.070 closest distance to " SG  CYS A 254 " =    3.112
peak=   -4.023 closest distance to " O   HOH Z 166 " =    1.479
peak=   -3.947 closest distance to " O   HOH Z 388 " =    1.969
peak=   -3.917 closest distance to " CG  ASP A 231 " =    0.728
peak=   -3.912 closest distance to " OE1 GLN A  88 " =    1.043
peak=   -3.899 closest distance to " CD1 LEU A 228 " =    2.330
peak=   -3.893 closest distance to " O   PRO A 163 " =    1.852
peak=   -3.885 closest distance to " N   HIS A 115 " =    2.189
peak=   -3.869 closest distance to " CG  PRO A 163 " =    2.416
peak=   -3.856 closest distance to " CD  LYS A 289 " =    2.640
peak=   -3.832 closest distance to " CB  PRO A 243 " =    2.677
peak=   -3.819 closest distance to " O   PRO A 198 " =    1.349
peak=   -3.815 closest distance to " O   HOH Z 143 " =    1.024
peak=   -3.810 closest distance to " O   HOH Z  98 " =    1.890
peak=   -3.804 closest distance to " C   ALA A 158 " =    1.239
peak=   -3.797 closest distance to " NH2 ARG A  79 " =    1.888
peak=   -3.791 closest distance to " CB  PRO A 163 " =    2.567
peak=   -3.784 closest distance to " CG2 VAL A 296 " =    1.377
peak=   -3.762 closest distance to " CG1 VAL A 250 " =    2.712
peak=   -3.743 closest distance to " N   GLN A  58 " =    1.747
peak=   -3.732 closest distance to " O   ASP A 231 " =    2.520
peak=   -3.730 closest distance to " NH2AARG A 275 " =    5.397
peak=   -3.707 closest distance to " CB  TYR A  15 " =    2.139
peak=   -3.701 closest distance to " C   ASN A 285 " =    2.491
peak=   -3.695 closest distance to " O   HOH Z 266 " =    4.567
peak=   -3.682 closest distance to " OG ASER A 134 " =    1.310
peak=   -3.667 closest distance to " CB  TYR A 172 " =    2.358
peak=   -3.665 closest distance to " CB  ASP A  27 " =    2.452
peak=   -3.665 closest distance to " N   THR A 157 " =    1.642
peak=   -3.659 closest distance to " CD  GLN A  88 " =    0.799
peak=   -3.646 closest distance to " O   HOH Z  13 " =    1.137
peak=   -3.640 closest distance to " O   HOH Z  43 " =    1.654
peak=   -3.623 closest distance to " CG  PHE A 283 " =    2.597
peak=   -3.600 closest distance to " O   HOH Z 274 " =    2.817
peak=   -3.600 closest distance to " O   HOH Z  97 " =    1.333
peak=   -3.593 closest distance to " OG BSER A 134 " =    1.671
peak=   -3.591 closest distance to " CE1 TYR A 169 " =    2.589
peak=   -3.588 closest distance to " O   ILE A 109 " =    2.628
peak=   -3.579 closest distance to " O   HOH Z  56 " =    0.735
peak=   -3.574 closest distance to " CG  GLN A 223 " =    1.977
peak=   -3.572 closest distance to " CD2 LEU A 237 " =    2.815
peak=   -3.565 closest distance to " CD1 LEU A 101 " =    2.755
peak=   -3.561 closest distance to " CG  MET A 105 " =    0.936
peak=   -3.549 closest distance to " CB  ASN A  39 " =    2.055
peak=   -3.542 closest distance to " O   HOH Z 275 " =    1.605
peak=   -3.522 closest distance to " CA  GLY A 241 " =    2.229
peak=   -3.520 closest distance to " O   HOH Z 389 " =    1.788
peak=   -3.520 closest distance to " O   GLY A 211 " =    1.368
peak=   -3.499 closest distance to " OG1 THR A 178 " =    1.159
peak=   -3.499 closest distance to " O   HOH Z  71 " =    1.109
peak=   -3.494 closest distance to " O   GLY A  80 " =    2.537
peak=   -3.485 closest distance to " CB  ALA A 244 " =    2.021
peak=   -3.485 closest distance to " CD1 PHE A  59 " =    1.958
peak=   -3.480 closest distance to " O   HOH Z  98 " =    1.463
peak=   -3.475 closest distance to " O   HOH Z  97 " =    0.908
peak=   -3.462 closest distance to " CD2 PHE A 225 " =    2.741
peak=   -3.452 closest distance to " CG2 THR A   4 " =    1.966
peak=   -3.441 closest distance to " O   HOH Z 281 " =    3.116
peak=   -3.440 closest distance to " O   HOH Z 350 " =    2.047
peak=   -3.436 closest distance to " CG1 VAL A 296 " =    1.413
peak=   -3.433 closest distance to " CZ3 TRP A 179 " =    1.227
peak=   -3.423 closest distance to " O   HOH Z  44 " =    1.881
peak=   -3.421 closest distance to " CG  LYS A 193 " =    2.367
peak=   -3.401 closest distance to " O   HOH Z  51 " =    0.993
peak=   -3.400 closest distance to " OG  SER A  87 " =    1.332
peak=   -3.398 closest distance to " O   HOH Z 103 " =    2.050
peak=   -3.398 closest distance to " CG  TRP A 266 " =    1.637
peak=   -3.398 closest distance to " CD  GLN A  58 " =    0.959
peak=   -3.397 closest distance to " CB  ALA A  43 " =    2.382
peak=   -3.394 closest distance to " O   HOH Z 435 " =    2.860
peak=   -3.390 closest distance to " CB  ALA A 248 " =    1.899
peak=   -3.389 closest distance to " OG BSER A 134 " =    1.242
peak=   -3.388 closest distance to " OG  SER A  87 " =    1.497
peak=   -3.386 closest distance to " CB  TRP A  85 " =    2.472
peak=   -3.384 closest distance to " O   PRO A 198 " =    1.247
peak=   -3.377 closest distance to " O   HOH Z 111 " =    4.311
peak=   -3.375 closest distance to " CB  GLN A  55 " =    1.464
peak=   -3.373 closest distance to " O   HOH Z  63 " =    1.110
peak=   -3.370 closest distance to " O   ALA A   1 " =    1.173
peak=   -3.369 closest distance to " O   HOH Z 407 " =    3.137
peak=   -3.358 closest distance to " O   HOH Z 298 " =    1.220
peak=   -3.355 closest distance to " OG  SER A 206 " =    1.688
peak=   -3.352 closest distance to " N   SER A  12 " =    1.239
peak=   -3.349 closest distance to " O   VAL A 153 " =    2.264
peak=   -3.347 closest distance to " ND2 ASN A  60 " =    1.670
peak=   -3.344 closest distance to " C   MET A 188 " =    1.591
peak=   -3.330 closest distance to " CB  CYS A 254 " =    2.200
peak=   -3.328 closest distance to " CD  GLN A  88 " =    2.250
peak=   -3.325 closest distance to " O   HOH Z 241 " =    1.398
peak=   -3.320 closest distance to " O   HOH Z 256 " =    1.543
peak=   -3.319 closest distance to " O   HOH Z 211 " =    1.527
peak=   -3.317 closest distance to " CE2 PHE A 218 " =    2.537
peak=   -3.316 closest distance to " N   ALA A  43 " =    2.562
peak=   -3.316 closest distance to " NH1 ARG A  56 " =    2.426
peak=   -3.314 closest distance to " CG  GLU A 152 " =    0.804
peak=   -3.312 closest distance to " O   HOH Z 111 " =    0.929
peak=   -3.304 closest distance to " O   ALA A 161 " =    1.655
peak=   -3.303 closest distance to " O   HOH Z  92 " =    1.206
peak=   -3.300 closest distance to " N   ALA A   9 " =    1.415
peak=   -3.300 closest distance to " CA  SER A 146 " =    2.358
peak=   -3.294 closest distance to " O   GLY A 203 " =    2.533
peak=   -3.291 closest distance to " CE1 PHE A 208 " =    2.005
peak=   -3.285 closest distance to " O   HOH Z 385 " =    2.112
peak=   -3.283 closest distance to " O   HOH Z  65 " =    1.139
peak=   -3.274 closest distance to " CB  ALA A   9 " =    2.667
peak=   -3.273 closest distance to " CG  ASP A  50 " =    1.970
peak=   -3.269 closest distance to " N   GLN A 122 " =    1.485
peak=   -3.268 closest distance to " O   HOH Z 132 " =    0.942
peak=   -3.265 closest distance to " O   HOH Z 365 " =    1.455
peak=   -3.261 closest distance to " OD1 ASP A 200 " =    1.274
peak=   -3.260 closest distance to " C   HIS A 108 " =    1.184
peak=   -3.256 closest distance to " O   HOH Z 177 " =    1.610
peak=   -3.251 closest distance to " O   HOH Z 308 " =    1.685
peak=   -3.248 closest distance to " NE2 GLN A 278 " =    1.186
peak=   -3.246 closest distance to " O   HOH Z 171 " =    2.126
peak=   -3.239 closest distance to " O   HOH Z 152 " =    5.040
peak=   -3.236 closest distance to " N   THR A  52 " =    1.814
peak=   -3.235 closest distance to " O   HOH Z 184 " =    1.830
peak=   -3.232 closest distance to " CG  ASN A  45 " =    1.674
peak=   -3.228 closest distance to " O   THR A  18 " =    1.677
peak=   -3.228 closest distance to " N   ALA A 226 " =    2.060
peak=   -3.227 closest distance to " CD1 TRP A 179 " =    0.881
peak=   -3.218 closest distance to " O   HOH Z 222 " =    2.909
peak=   -3.211 closest distance to " N   SER A 276 " =    1.229
peak=   -3.208 closest distance to " CD1 ILE A 239 " =    2.072
peak=   -3.205 closest distance to " CA  ARG A  56 " =    1.399
peak=   -3.203 closest distance to " O   VAL A 197 " =    1.407
peak=   -3.199 closest distance to " NH1AARG A 275 " =    1.897
peak=   -3.198 closest distance to " O   SER A 135 " =    1.528
peak=   -3.197 closest distance to " N   GLY A  23 " =    2.107
peak=   -3.196 closest distance to " OH  TYR A 172 " =    1.715
peak=   -3.194 closest distance to " OH  TYR A 214 " =    1.074
peak=   -3.192 closest distance to " O   HOH Z 411 " =    3.619
peak=   -3.190 closest distance to " O   HOH Z 322 " =    0.743
peak=   -3.188 closest distance to " O   VAL A  67 " =    2.600
peak=   -3.186 closest distance to " OG  SER A  97 " =    2.196
peak=   -3.182 closest distance to " NH2 ARG A  66 " =    2.300
peak=   -3.176 closest distance to " O   SER A  12 " =    1.559
peak=   -3.173 closest distance to " ND2 ASN A 249 " =    2.029
peak=   -3.172 closest distance to " O   HOH Z 186 " =    0.977
peak=   -3.169 closest distance to " CE2 TYR A  30 " =    2.877
peak=   -3.169 closest distance to " O   HOH Z 119 " =    2.591
peak=   -3.169 closest distance to " CG2 VAL A 112 " =    2.489
peak=   -3.162 closest distance to " O   HOH Z 234 " =    4.231
peak=   -3.162 closest distance to " CB  ALA A 227 " =    2.364
peak=   -3.157 closest distance to " O   HOH Z 351 " =    1.297
peak=   -3.151 closest distance to " C   LEU A 222 " =    0.721
peak=   -3.146 closest distance to " O   GLN A  77 " =    1.735
peak=   -3.145 closest distance to " O   HOH Z 238 " =    1.287
peak=   -3.142 closest distance to " N   LYS A 166 " =    1.984
peak=   -3.137 closest distance to " CE  LYS A  76 " =    2.866
peak=   -3.134 closest distance to " O   HOH Z 353 " =    2.146
peak=   -3.134 closest distance to " O   HOH Z 438 " =    1.088
peak=   -3.131 closest distance to " C   VAL A 174 " =    1.832
peak=   -3.130 closest distance to " O   HOH Z 426 " =    2.219
peak=   -3.127 closest distance to " O   HOH Z 124 " =    3.287
peak=   -3.125 closest distance to " CB  ASP A 132 " =    2.306
peak=   -3.125 closest distance to " CZ  ARG A 259 " =    0.806
peak=   -3.125 closest distance to " N   ALA A 248 " =    1.674
peak=   -3.123 closest distance to " CZ BARG A 275 " =    1.770
peak=   -3.122 closest distance to " O   HOH Z 394 " =    1.415
peak=   -3.121 closest distance to " C   GLN A 240 " =    2.325
peak=   -3.119 closest distance to " CE BMET A  47 " =    1.685
peak=   -3.115 closest distance to " O   HOH Z 410 " =    2.073
peak=   -3.114 closest distance to " O   HOH Z 281 " =    5.018
peak=   -3.113 closest distance to " O   HOH Z  93 " =    0.920
peak=   -3.112 closest distance to " O   SER A  22 " =    2.331
peak=   -3.108 closest distance to " O   HOH Z  11 " =    1.851
peak=   -3.104 closest distance to " CG  TYR A 172 " =    2.172
peak=   -3.103 closest distance to " O   HOH Z 367 " =    1.694
peak=   -3.097 closest distance to " O   HOH Z 295 " =    1.331
peak=   -3.096 closest distance to " CA  ARG A 139 " =    0.969
peak=   -3.091 closest distance to " O   HOH Z 423 " =    2.183
peak=   -3.084 closest distance to " N   VAL A 125 " =    0.885
peak=   -3.081 closest distance to " O   HOH Z 179 " =    2.270
peak=   -3.079 closest distance to " O   MET A  40 " =    2.819
peak=   -3.078 closest distance to " O   HOH Z 283 " =    1.732
peak=   -3.073 closest distance to " O   HOH Z 185 " =    2.214
peak=   -3.067 closest distance to " CA  GLY A  35 " =    1.899
peak=   -3.060 closest distance to " CA  GLY A 133 " =    1.948
peak=   -3.054 closest distance to " CD1 ILE A 199 " =    2.559
peak=   -3.053 closest distance to " CB  ARG A  79 " =    2.549
peak=   -3.048 closest distance to " CD2 LEU A   5 " =    1.020
peak=   -3.028 closest distance to " CG1 VAL A 197 " =    2.313
peak=   -3.016 closest distance to " O   HOH Z  97 " =    1.136
peak=   -3.008 closest distance to " CD2 LEU A 300 " =    2.894
peak=   -3.007 closest distance to " O   HOH Z 186 " =    0.745

================= 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    :  0.4909 0.4766   6.288853e+00   6.281320e+00
   1_bss:  0.4827 0.4688   6.109141e+00   6.123858e+00
   1_xyz:  0.4083 0.4328   6.191135e+00   6.227365e+00
   1_adp:  0.3684 0.4239   6.129744e+00   6.211079e+00
   1_occ:  0.3680 0.4242   6.128970e+00   6.210449e+00
   2_bss:  0.3666 0.4193   6.128509e+00   6.206977e+00
   2_xyz:  0.2652 0.3218   5.874513e+00   6.024916e+00
   2_adp:  0.2356 0.3026   5.789446e+00   5.966335e+00
   2_occ:  0.2355 0.3027   5.789264e+00   5.966356e+00
   3_bss:  0.2337 0.3001   5.788019e+00   5.963947e+00
   3_xyz:  0.1675 0.2200   5.492946e+00   5.703062e+00
   3_adp:  0.1505 0.2017   5.399275e+00   5.625949e+00
   3_occ:  0.1503 0.2010   5.397632e+00   5.623840e+00
   4_bss:  0.1499 0.2003   5.394991e+00   5.619801e+00
   4_xyz:  0.1329 0.1786   5.283702e+00   5.511149e+00
   4_adp:  0.1295 0.1742   5.258361e+00   5.484045e+00
   4_occ:  0.1294 0.1739   5.257061e+00   5.482360e+00
   5_bss:  0.1293 0.1737   5.256907e+00   5.482252e+00
   5_xyz:  0.1188 0.1659   5.195440e+00   5.435501e+00
   5_adp:  0.1189 0.1644   5.191591e+00   5.428428e+00
   5_occ:  0.1187 0.1640   5.190487e+00   5.427146e+00
   5_bss:  0.1189 0.1639   5.190443e+00   5.428562e+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:  0.329   1.486   7.887   7.074   7.543   0.000   0.000   0.000
   1_xyz:  0.329   1.486   7.887   7.074   7.543   0.000   0.000   0.000
   1_adp:  0.329   1.486   7.887   7.074   7.543   0.000   0.000   0.000
   1_occ:  0.329   1.486   7.887   7.074   7.543   0.000   0.000   0.000
   2_bss:  0.339  36.695   4.611   3.816   5.171   0.000   0.000   0.000
   2_xyz:  0.339  36.695   4.611   3.816   5.171   0.000   0.000   0.000
   2_adp:  0.339  36.695   4.611   3.816   5.171   0.000   0.000   0.000
   2_occ:  0.339  36.695   4.611   3.816   5.171   0.000   0.000   0.000
   3_bss:  0.349  46.807   2.639   1.828   3.035   0.000   0.000   0.000
   3_xyz:  0.349  46.807   2.639   1.828   3.035   0.000   0.000   0.000
   3_adp:  0.349  46.807   2.639   1.828   3.035   0.000   0.000   0.000
   3_occ:  0.349  46.807   2.639   1.828   3.035   0.000   0.000   0.000
   4_bss:  0.332  45.388   1.768   1.054   1.936   0.000   0.000   0.000
   4_xyz:  0.332  45.388   1.768   1.054   1.936   0.000   0.000   0.000
   4_adp:  0.332  45.388   1.768   1.054   1.936   0.000   0.000   0.000
   4_occ:  0.332  45.388   1.768   1.054   1.936   0.000   0.000   0.000
   5_bss:  0.332  45.388   1.383   0.816   1.591   0.000   0.000   0.000
   5_xyz:  0.332  45.388   1.383   0.816   1.591   0.000   0.000   0.000
   5_adp:  0.332  45.388   1.383   0.816   1.591   0.000   0.000   0.000
   5_occ:  0.332  45.388   1.383   0.816   1.591   0.000   0.000   0.000
   5_bss:  0.323  43.976   0.114  -0.425   0.312  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.877 0.4084  0.4880    73468.282
   1_bss:  59.793 0.3945  0.5747    71289.332
   1_xyz:  51.037 0.5058  0.7250    56200.804
   1_adp:  48.199 0.5416  0.8359    52342.383
   1_occ:  48.273 0.5406  0.8333    52375.996
   2_bss:  47.888 0.5452  0.7637    51684.339
   2_xyz:  34.536 0.7054  0.9558    28477.306
   2_adp:  31.327 0.7425  0.9865    24569.781
   2_occ:  31.337 0.7424  0.9859    24572.770
   3_bss:  31.158 0.7442  0.9183    24345.119
   3_xyz:  21.677 0.8449  0.9968    12722.713
   3_adp:  19.386 0.8678  1.0086    10762.369
   3_occ:  19.330 0.8683  1.0088    10691.404
   4_bss:  19.217 0.8692  0.9760    10553.927
   4_xyz:  16.467 0.8943  0.9875     8169.819
   4_adp:  15.772 0.9007  0.9897     7761.821
   4_occ:  15.735 0.9010  0.9897     7722.406
   5_bss:  15.728 0.9011  0.9783     7718.262
   5_xyz:  14.851 0.9082  0.9822     7004.846
   5_adp:  14.624 0.9104  0.9837     6919.503
   5_occ:  14.597 0.9106  0.9838     6895.878
   5_bss:  14.611 0.9104  0.9780     6909.285
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3468e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3468e+01
   1_xyz:   1.715  0.013  0.108 18.545  0.007  4.109   1.4682e-01
   1_adp:   1.715  0.013  0.108 18.545  0.007  4.109   1.4682e-01
   1_occ:   1.715  0.013  0.108 18.545  0.007  4.109   1.4682e-01
   2_bss:   1.715  0.013  0.108 18.545  0.007  4.109   1.4682e-01
   2_xyz:   1.228  0.010  0.089 17.053  0.006  4.106   9.6821e-02
   2_adp:   1.228  0.010  0.089 17.053  0.006  4.106   9.6821e-02
   2_occ:   1.228  0.010  0.089 17.053  0.006  4.106   9.6821e-02
   3_bss:   1.228  0.010  0.089 17.053  0.006  4.106   9.6821e-02
   3_xyz:   1.074  0.007  0.077 16.057  0.004  4.124   6.9795e-02
   3_adp:   1.074  0.007  0.077 16.057  0.004  4.124   6.9795e-02
   3_occ:   1.074  0.007  0.077 16.057  0.004  4.124   6.9795e-02
   4_bss:   1.074  0.007  0.077 16.057  0.004  4.124   6.9795e-02
   4_xyz:   0.934  0.005  0.071 15.545  0.003  4.117   5.6272e-02
   4_adp:   0.934  0.005  0.071 15.545  0.003  4.117   5.6272e-02
   4_occ:   0.934  0.005  0.071 15.545  0.003  4.117   5.6272e-02
   5_bss:   0.934  0.005  0.071 15.545  0.003  4.117   5.6272e-02
   5_xyz:   1.077  0.007  0.081 15.981  0.004  4.122   6.8312e-02
   5_adp:   1.077  0.007  0.081 15.981  0.004  4.122   6.8312e-02
   5_occ:   1.077  0.007  0.081 15.981  0.004  4.122   6.8312e-02
   5_bss:   1.077  0.007  0.081 15.981  0.004  4.122   6.8312e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9313e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9313e+00
   1_xyz:  14.121  0.171  0.465 84.995  0.046  2.188   1.0176e-01
   1_adp:  14.121  0.171  0.465 84.995  0.046  2.188   1.0176e-01
   1_occ:  14.121  0.171  0.465 84.995  0.046  2.188   1.0176e-01
   2_bss:  14.121  0.171  0.465 84.995  0.046  2.188   1.0176e-01
   2_xyz:   7.911  0.060  0.285 83.846  0.049  2.106   6.9413e-02
   2_adp:   7.911  0.060  0.285 83.846  0.049  2.106   6.9413e-02
   2_occ:   7.911  0.060  0.285 83.846  0.049  2.106   6.9413e-02
   3_bss:   7.911  0.060  0.285 83.846  0.049  2.106   6.9413e-02
   3_xyz:   8.792  0.053  0.371 84.316  0.026  2.334   5.4140e-02
   3_adp:   8.792  0.053  0.371 84.316  0.026  2.334   5.4140e-02
   3_occ:   8.792  0.053  0.371 84.316  0.026  2.334   5.4140e-02
   4_bss:   8.792  0.053  0.371 84.316  0.026  2.334   5.4140e-02
   4_xyz:   7.827  0.048  0.341 82.278  0.036  2.306   3.4704e-02
   4_adp:   7.827  0.048  0.341 82.278  0.036  2.306   3.4704e-02
   4_occ:   7.827  0.048  0.341 82.278  0.036  2.306   3.4704e-02
   5_bss:   7.827  0.048  0.341 82.278  0.036  2.306   3.4704e-02
   5_xyz:   8.465  0.061  0.476 86.459  0.022  2.214   4.1938e-02
   5_adp:   8.465  0.061  0.476 86.459  0.022  2.214   4.1938e-02
   5_occ:   8.465  0.061  0.476 86.459  0.022  2.214   4.1938e-02
   5_bss:   8.465  0.061  0.476 86.459  0.022  2.214   4.1938e-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:  99.35   0.00  13.89  99.35   0.00  11.71  79.65   0.00  25.78
   1_occ:  99.35   0.00  13.89  99.35   0.00  11.71  79.65   0.00  25.78
   2_bss:  99.35   0.00  13.89  99.35   0.00  11.71  79.65   0.00  25.78
   2_xyz:  99.35   0.00  13.89  99.35   0.00  11.71  79.65   0.00  25.78
   2_adp:  91.66   0.00  13.80  91.66   0.00  10.08  78.63   1.11  34.04
   2_occ:  91.66   0.00  13.80  91.66   0.00  10.08  78.63   1.11  34.04
   3_bss:  91.66   0.00  13.80  91.66   0.00  10.08  78.63   1.11  34.04
   3_xyz:  91.66   0.00  13.80  91.66   0.00  10.08  78.63   1.11  34.04
   3_adp:  91.38   0.00  14.29  91.38   0.00   9.76  83.71   2.50  38.95
   3_occ:  91.38   0.00  14.29  91.38   0.00   9.76  83.71   2.50  38.95
   4_bss:  91.38   0.00  14.29  91.38   0.00   9.76  83.71   2.50  38.95
   4_xyz:  91.38   0.00  14.29  91.38   0.00   9.76  83.71   2.50  38.95
   4_adp:  91.67   0.00  14.02  91.67   0.00   9.64  82.94   3.57  37.82
   4_occ:  91.67   0.00  14.02  91.67   0.00   9.64  82.94   3.57  37.82
   5_bss:  91.67   0.00  14.02  91.67   0.00   9.64  82.94   3.57  37.82
   5_xyz:  91.67   0.00  14.02  91.67   0.00   9.64  82.94   3.57  37.82
   5_adp:  89.50   0.00  13.58  89.50   0.00   9.54  81.22   3.71  35.60
   5_occ:  89.50   0.00  13.58  89.50   0.00   9.54  81.22   3.71  35.60
   5_bss:  90.61   1.11  14.69  90.61   1.11  10.65  82.33   4.82  36.71
------------------------------------------------------------------------
 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:    1.256    0.023    0.411
   1_adp:    1.256    0.023    0.411
   1_occ:    1.256    0.023    0.411
   2_bss:    1.256    0.023    0.411
   2_xyz:    1.532    0.052    0.624
   2_adp:    1.532    0.052    0.624
   2_occ:    1.532    0.052    0.624
   3_bss:    1.532    0.052    0.624
   3_xyz:    1.679    0.009    0.718
   3_adp:    1.679    0.009    0.718
   3_occ:    1.679    0.009    0.718
   4_bss:    1.679    0.009    0.718
   4_xyz:    1.953    0.048    0.748
   4_adp:    1.953    0.048    0.748
   4_occ:    1.953    0.048    0.748
   5_bss:    1.953    0.048    0.748
   5_xyz:    2.060    0.062    0.769
   5_adp:    2.060    0.062    0.769
   5_occ:    2.060    0.062    0.769
   5_bss:    2.060    0.062    0.769
------------------------------------------------------------------------

CPU time actual refinement: 331.69


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1123/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_1123/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1123/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1123/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1123/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.54 
  Macro-tasks:
    bulk solvent and scale       = 40.03  
    individual site refinement   = 133.25 
    weights calculation          = 32.42  
    collect and process          = 6.37   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 212.19 
  Micro-tasks:
    mask                            = 2.41   
    f_calc                          = 104.31 
    alpha_beta                      = 8.07   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 111.98 
    fmodel                         = 7.01   
    r_factors                      = 0.20   
    phase_errors                   = 10.44  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 245.82 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.763 micro seconds
Total CPU time: 5.76 minutes
from_scatterers_fft:    618 calls, 104.02 s
gradients_fft:          562 calls,  99.85 s

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

# Date 2008-01-16 Time 03:14:46 PST -0800 (1200482086.69 s)
Start R-work = 0.4909, R-free = 0.4766 (no bulk solvent and anisotropic scale)
Final R-work = 0.1357, R-free = 0.1814 (no bulk solvent and anisotropic scale)

Start R-work = 0.4827, R-free = 0.4688
Final R-work = 0.1189, R-free = 0.1639