# Date 2008-01-16 Time 01:40:36 PST -0800 (1200476436.38 s)
#phil __OFF__

Command line arguments: "../521.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27054
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 521

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.4607, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.98157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9190
                             d_min =   1.9816

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.98157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9194 -  4.2396 [2102/2126]  1892   210  10.0%
  bin  2:  4.2396 -  3.3779 [2027/2047]  1823   204  10.1%
  bin  3:  3.3779 -  2.9547 [1993/2012]  1794   199  10.0%
  bin  4:  2.9547 -  2.6863 [1962/1992]  1765   197  10.0%
  bin  5:  2.6863 -  2.4947 [1977/1996]  1782   195   9.9%
  bin  6:  2.4947 -  2.3482 [1958/1983]  1758   200  10.2%
  bin  7:  2.3482 -  2.2310 [1940/1968]  1748   192   9.9%
  bin  8:  2.2310 -  2.1342 [1932/1968]  1739   193  10.0%
  bin  9:  2.1342 -  2.0522 [1917/1959]  1726   191  10.0%
  bin 10:  2.0522 -  1.9816 [1781/1974]  1603   178  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_521/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 22
        2.42 -     3.04: 2222
        3.04 -     3.66: 4733
        3.66 -     4.28: 9155
        4.28 -     4.90: 12431
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.092 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.218 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  2.218 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28558 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_521/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_521/model_refine_001.geo

CPU time processing inputs: 8.91


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.4607 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4355   r_free= 0.4216   ksol= 0.00   Bsol= 0.00   scale= 0.827    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.230718                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7283 0.99   1374  152 0.3659 0.3624      6.5194      6.5052|
|  2:  4.7283 -  3.7730 0.99   1303  146 0.3372 0.3216       6.662      6.6272|
|  3:  3.7730 -  3.3020 0.99   1287  144 0.3691 0.3504      6.5614      6.5902|
|  4:  3.3020 -  3.0028 0.99   1284  143 0.4114 0.3788      6.4654      6.3787|
|  5:  3.0028 -  2.7890 0.99   1267  138 0.4583 0.4713      6.3249      6.3493|
|  6:  2.7890 -  2.6255 0.99   1272  143 0.4592 0.5203      6.2454      6.2291|
|  7:  2.6255 -  2.4947 0.99   1269  139 0.4685 0.4221      6.2039      6.1508|
|  8:  2.4947 -  2.3865 0.98   1248  141 0.4875 0.4633      6.1715      6.1897|
|  9:  2.3865 -  2.2950 0.98   1256  138 0.4737 0.4926      6.0875      6.0846|
| 10:  2.2950 -  2.2161 1.00   1236  141 0.4956 0.4649       6.117       6.051|
| 11:  2.2161 -  2.1470 0.97   1255  135 0.4962 0.4102      6.0415       5.978|
| 12:  2.1470 -  2.0858 0.98   1245  140 0.4855 0.4860      5.9801       6.009|
| 13:  2.0858 -  2.0310 0.99   1243  136 0.5051 0.5006      5.8869      5.8695|
| 14:  2.0310 -  1.9816 0.86   1091  123 0.5219 0.4967      5.8473      5.7585|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7283  1374   152  0.71  32.97   0.81     0.75      65280.15|
|  2:  4.7283 -  3.7730  1303   146  0.77  29.21   0.91     0.83      77524.28|
|  3:  3.7730 -  3.3020  1287   144  0.70  35.17   0.89     0.80      79295.91|
|  4:  3.3020 -  3.0028  1284   143  0.64  40.59   0.84     0.72      72107.97|
|  5:  3.0028 -  2.7890  1267   138  0.53  49.32   0.78     0.61      64851.69|
|  6:  2.7890 -  2.6255  1272   143  0.50  51.98   0.76     0.56      60039.15|
|  7:  2.6255 -  2.4947  1269   139  0.48  53.73   0.76     0.54      55623.63|
|  8:  2.4947 -  2.3865  1248   141  0.48  53.43   0.77     0.56      49949.59|
|  9:  2.3865 -  2.2950  1256   138  0.52  50.82   0.75     0.58      41778.35|
| 10:  2.2950 -  2.2161  1236   141  0.54  49.44   0.78     0.60      36003.36|
| 11:  2.2161 -  2.1470  1255   135  0.53  50.16   0.78     0.62      33484.47|
| 12:  2.1470 -  2.0858  1245   140  0.48  54.05   0.80     0.57      34297.90|
| 13:  2.0858 -  2.0310  1243   136  0.41  59.47   0.76     0.48      32453.61|
| 14:  2.0310 -  1.9816  1091   123  0.37  62.62   0.74     0.40      28287.04|
|alpha:            min =        0.40 max =            0.83 mean =         0.62|
|beta:             min =    28287.04 max =        79295.91 mean =     52734.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.97 mean =        47.74|
|phase err.(test): min =        0.00 max =           89.97 mean =        47.79|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.742788              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.679   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.708170              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.234   (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:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      690 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1524 |
| 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:     3954 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5130 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6606 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7790 |
|-----------------------------------------------------------------------------|
|-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 |       53.352 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.800 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    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 = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4439   r_free= 0.4296   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.236038                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4272   r_free= 0.4128   ksol= 0.37   Bsol= 20.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.13,9.36,7.82,0.00,0.00,0.00); trace/3= 8.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.223978                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.189068              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.224   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.676166              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.047   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4272      final r-factor (work) = 0.3221          |
| start r-factor (free) = 0.4128      final r-factor (free) = 0.3432          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.7907 = 7.19 * 0.50 * 6.2424 + 1.00 * 53.3521                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.9739 = 7.19 * 0.50 * 6.0804 + 1.00 * 0.1178                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3221      final r-factor (work) = 0.2604          |
| start r-factor (free) = 0.3432      final r-factor (free) = 0.2962          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1260 = 0.68 * 1.00 * 6.0804 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0054 = 0.68 * 1.00 * 5.9056 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.33   10.94    None  None   None       |
|    all(noH): 2823   0      0.00    68.33   10.94    None  None   None       |
|    Sol.    : 438    0      0.00    61.13   27.31    None  None   None       |
|    Mac.    : 2385   0      0.00    68.33   7.93     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.833: 1357   |   5:    34.163 -  40.996:   97        |
|      1:     6.833 -  13.665:  746   |   6:    40.996 -  47.828:   37        |
|      2:    13.665 -  20.498:  248   |   7:    47.828 -  54.661:   18        |
|      3:    20.498 -  27.330:  190   |   8:    54.661 -  61.494:    7        |
|      4:    27.330 -  34.163:  122   |   9:    61.494 -  68.326:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2604 r_free = 0.2962             target_work(ml) = 5.844         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2596 r_free = 0.2956             target_work(ml) = 5.842         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2596   r_free= 0.2956   ksol= 0.37   Bsol= 20.00   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.13,9.36,7.82,0.00,0.00,0.00); trace/3= 8.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.842289                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2545   r_free= 0.2891   ksol= 0.34   Bsol= 33.69   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.83,5.06,4.96,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.839219                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.397661              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.421   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.368100              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.028  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2545      final r-factor (work) = 0.1781          |
| start r-factor (free) = 0.2891      final r-factor (free) = 0.2209          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2035 = 2.40 * 0.50 * 5.9110 + 1.00 * 0.1173                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8466 = 2.40 * 0.50 * 5.6644 + 1.00 * 0.0559                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1781      final r-factor (work) = 0.1616          |
| start r-factor (free) = 0.2209      final r-factor (free) = 0.2059          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0972 = 0.37 * 1.00 * 5.6644 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0264 = 0.37 * 1.00 * 5.4750 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.47   11.28    None  None   None       |
|    all(noH): 2823   0      0.00    71.47   11.28    None  None   None       |
|    Sol.    : 438    0      0.87    65.82   31.71    None  None   None       |
|    Mac.    : 2385   0      0.00    71.47   7.53     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.147: 1539   |   5:    35.737 -  42.884:  132        |
|      1:     7.147 -  14.295:  624   |   6:    42.884 -  50.031:   65        |
|      2:    14.295 -  21.442:  197   |   7:    50.031 -  57.179:   22        |
|      3:    21.442 -  28.589:  117   |   8:    57.179 -  64.326:    5        |
|      4:    28.589 -  35.737:  120   |   9:    64.326 -  71.473:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1616 r_free = 0.2059             target_work(ml) = 5.446         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1614 r_free = 0.2054             target_work(ml) = 5.445         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1614   r_free= 0.2054   ksol= 0.34   Bsol= 33.69   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.83,5.06,4.96,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.445336                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1610   r_free= 0.2048   ksol= 0.33   Bsol= 33.69   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,3.43,4.28,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.445006                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.687484              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.617  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.510424              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.967  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1610      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.2048      final r-factor (free) = 0.1668          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1598 = 3.69 * 0.50 * 5.4801 + 1.00 * 0.0559                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8898 = 3.69 * 0.50 * 5.3279 + 1.00 * 0.0665                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1237      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1668      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7304 = 0.51 * 1.00 * 5.3279 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6619 = 0.51 * 1.00 * 5.1924 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.36   11.59    None  None   None       |
|    all(noH): 2823   0      0.00    79.36   11.59    None  None   None       |
|    Sol.    : 438    0      0.96    70.41   33.96    None  None   None       |
|    Mac.    : 2385   0      0.00    79.36   7.48     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.936: 1694   |   5:    39.680 -  47.616:   99        |
|      1:     7.936 -  15.872:  546   |   6:    47.616 -  55.552:   71        |
|      2:    15.872 -  23.808:  158   |   7:    55.552 -  63.488:   25        |
|      3:    23.808 -  31.744:  111   |   8:    63.488 -  71.424:    6        |
|      4:    31.744 -  39.680:  111   |   9:    71.424 -  79.360:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1171 r_free = 0.1607             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1606             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1606   ksol= 0.33   Bsol= 33.69   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,3.43,4.28,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.169532                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1604   ksol= 0.32   Bsol= 33.69   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,3.10,4.16,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.169924                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.037565              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.679  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.191658              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.028  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1604      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3568 = 2.04 * 0.50 * 5.1930 + 1.00 * 0.0662                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3075 = 2.04 * 0.50 * 5.1539 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9992 = 0.19 * 1.00 * 5.1539 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9979 = 0.19 * 1.00 * 5.1438 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.41   11.42    None  None   None       |
|    all(noH): 2823   0      0.00    79.41   11.42    None  None   None       |
|    Sol.    : 438    0      1.52    69.82   33.30    None  None   None       |
|    Mac.    : 2385   0      0.00    79.41   7.40     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.941: 1716   |   5:    39.707 -  47.648:   97        |
|      1:     7.941 -  15.883:  542   |   6:    47.648 -  55.590:   66        |
|      2:    15.883 -  23.824:  148   |   7:    55.590 -  63.531:   21        |
|      3:    23.824 -  31.766:  119   |   8:    63.531 -  71.472:    5        |
|      4:    31.766 -  39.707:  107   |   9:    71.472 -  79.414:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1550             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1125 r_free = 0.1550             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1550   ksol= 0.32   Bsol= 33.69   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,3.10,4.16,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.135572                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1549   ksol= 0.32   Bsol= 37.23   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.75,2.97,4.14,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.135101                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.027056              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.096  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.887333              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.801   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2696 = 2.03 * 0.50 * 5.1432 + 1.00 * 0.0568                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2545 = 2.03 * 0.50 * 5.1249 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1102      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5586 = 0.89 * 1.00 * 5.1249 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5541 = 0.89 * 1.00 * 5.1131 + 1.00 * 0.0171                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.12   11.52    None  None   None       |
|    all(noH): 2823   0      0.00    84.12   11.52    None  None   None       |
|    Sol.    : 438    0      1.10    72.92   33.81    None  None   None       |
|    Mac.    : 2385   0      0.00    84.12   7.43     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 -   8.412: 1758   |   5:    42.058 -  50.469:   86        |
|      1:     8.412 -  16.823:  514   |   6:    50.469 -  58.881:   56        |
|      2:    16.823 -  25.235:  143   |   7:    58.881 -  67.292:   17        |
|      3:    25.235 -  33.646:  130   |   8:    67.292 -  75.704:    4        |
|      4:    33.646 -  42.058:  112   |   9:    75.704 -  84.116:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1090 r_free = 0.1539             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1539             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1539   ksol= 0.32   Bsol= 37.23   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.75,2.97,4.14,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119000                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7283 0.99   1374  152 0.0983 0.1238      5.3636      5.4923|
|  2:  4.7283 -  3.7730 0.99   1303  146 0.0837 0.1114      5.4159      5.6147|
|  3:  3.7730 -  3.3020 0.99   1287  144 0.1046 0.1465      5.4656      5.8186|
|  4:  3.3020 -  3.0028 0.99   1284  143 0.1174 0.1569      5.4338      5.5857|
|  5:  3.0028 -  2.7890 0.99   1267  138 0.1254 0.1666      5.3069       5.527|
|  6:  2.7890 -  2.6255 0.99   1272  143 0.1160 0.1837      5.1843       5.462|
|  7:  2.6255 -  2.4947 0.99   1269  139 0.1237 0.1553      5.1468      5.3196|
|  8:  2.4947 -  2.3865 0.98   1248  141 0.1139 0.1742      5.0608      5.3731|
|  9:  2.3865 -  2.2950 0.98   1256  138 0.1134 0.1676      5.0174      5.2161|
| 10:  2.2950 -  2.2161 1.00   1236  141 0.1061 0.1753      4.9357      5.2471|
| 11:  2.2161 -  2.1470 0.97   1255  135 0.1111 0.1597      4.9236      5.2071|
| 12:  2.1470 -  2.0858 0.98   1245  140 0.1107 0.1751      4.8659      5.2552|
| 13:  2.0858 -  2.0310 0.99   1243  136 0.1089 0.1567      4.7821      5.0131|
| 14:  2.0310 -  1.9816 0.86   1091  123 0.0988 0.1756      4.6388      4.9356|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7283  1374   152  0.94   8.68   0.98     0.96       6694.10|
|  2:  4.7283 -  3.7730  1303   146  0.96   7.49   1.02     1.01       8525.34|
|  3:  3.7730 -  3.3020  1287   144  0.94  10.81   1.03     1.02       9937.39|
|  4:  3.3020 -  3.0028  1284   143  0.93  12.93   1.01     1.00       9900.23|
|  5:  3.0028 -  2.7890  1267   138  0.91  15.29   1.00     0.97       8088.24|
|  6:  2.7890 -  2.6255  1272   143  0.90  15.43   0.99     0.96       6766.42|
|  7:  2.6255 -  2.4947  1269   139  0.91  15.39   0.99     0.96       5971.30|
|  8:  2.4947 -  2.3865  1248   141  0.91  14.47   0.99     0.97       5080.06|
|  9:  2.3865 -  2.2950  1256   138  0.91  15.00   1.01     0.99       4899.04|
| 10:  2.2950 -  2.2161  1236   141  0.91  14.70   1.00     0.96       4145.85|
| 11:  2.2161 -  2.1470  1255   135  0.90  15.90   1.00     0.97       4291.21|
| 12:  2.1470 -  2.0858  1245   140  0.91  14.96   1.02     1.00       3813.69|
| 13:  2.0858 -  2.0310  1243   136  0.91  15.19   1.01     1.00       3265.02|
| 14:  2.0310 -  1.9816  1091   123  0.92  14.00   0.99     0.95       2445.95|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2445.95 max =         9937.39 mean =      6053.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.72 mean =        13.53|
|phase err.(test): min =        0.00 max =           87.90 mean =        13.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1539   ksol= 0.32   Bsol= 42.10   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.52,-0.33,0.86,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118849                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1539   ksol= 0.32   Bsol= 42.10   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.52,-0.33,0.86,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118849                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7283 0.99   1374  152 0.0984 0.1240      5.3638      5.4925|
|  2:  4.7283 -  3.7730 0.99   1303  146 0.0838 0.1116      5.4174      5.6161|
|  3:  3.7730 -  3.3020 0.99   1287  144 0.1047 0.1466      5.4663      5.8194|
|  4:  3.3020 -  3.0028 0.99   1284  143 0.1174 0.1568      5.4336      5.5851|
|  5:  3.0028 -  2.7890 0.99   1267  138 0.1254 0.1665      5.3062       5.526|
|  6:  2.7890 -  2.6255 0.99   1272  143 0.1158 0.1835      5.1835      5.4613|
|  7:  2.6255 -  2.4947 0.99   1269  139 0.1237 0.1554      5.1462      5.3193|
|  8:  2.4947 -  2.3865 0.98   1248  141 0.1138 0.1741      5.0604      5.3723|
|  9:  2.3865 -  2.2950 0.98   1256  138 0.1133 0.1677      5.0172      5.2162|
| 10:  2.2950 -  2.2161 1.00   1236  141 0.1061 0.1753      4.9355      5.2471|
| 11:  2.2161 -  2.1470 0.97   1255  135 0.1110 0.1596      4.9233      5.2068|
| 12:  2.1470 -  2.0858 0.98   1245  140 0.1107 0.1750      4.8656      5.2549|
| 13:  2.0858 -  2.0310 0.99   1243  136 0.1089 0.1566      4.7818      5.0129|
| 14:  2.0310 -  1.9816 0.86   1091  123 0.0988 0.1755      4.6382      4.9347|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7283  1374   152  0.94   8.69   0.98     0.96       6697.25|
|  2:  4.7283 -  3.7730  1303   146  0.96   7.51   1.02     1.01       8538.66|
|  3:  3.7730 -  3.3020  1287   144  0.94  10.82   1.03     1.02       9951.72|
|  4:  3.3020 -  3.0028  1284   143  0.93  12.92   1.01     1.00       9894.06|
|  5:  3.0028 -  2.7890  1267   138  0.91  15.28   1.00     0.97       8076.29|
|  6:  2.7890 -  2.6255  1272   143  0.90  15.41   0.99     0.96       6754.57|
|  7:  2.6255 -  2.4947  1269   139  0.91  15.38   0.99     0.96       5962.32|
|  8:  2.4947 -  2.3865  1248   141  0.91  14.46   1.00     0.98       5075.51|
|  9:  2.3865 -  2.2950  1256   138  0.91  15.00   1.01     0.99       4898.26|
| 10:  2.2950 -  2.2161  1236   141  0.91  14.70   1.01     0.97       4143.96|
| 11:  2.2161 -  2.1470  1255   135  0.90  15.89   1.01     0.97       4288.74|
| 12:  2.1470 -  2.0858  1245   140  0.91  14.95   1.02     1.01       3810.36|
| 13:  2.0858 -  2.0310  1243   136  0.91  15.18   1.01     1.01       3261.37|
| 14:  2.0310 -  1.9816  1091   123  0.92  13.99   0.99     0.96       2442.09|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2442.09 max =         9951.72 mean =      6051.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.56 mean =        13.53|
|phase err.(test): min =        0.00 max =           87.84 mean =        13.12|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.40    87.52   14.92    None  None   None       |
|    all(noH): 2823   0      3.40    87.52   14.92    None  None   None       |
|    Sol.    : 438    0      4.50    76.32   37.21    None  None   None       |
|    Mac.    : 2385   0      3.40    87.52   10.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.400 -  11.811: 1758   |   5:    45.457 -  53.869:   86        |
|      1:    11.811 -  20.223:  514   |   6:    53.869 -  62.280:   56        |
|      2:    20.223 -  28.634:  143   |   7:    62.280 -  70.692:   17        |
|      3:    28.634 -  37.046:  130   |   8:    70.692 -  79.104:    4        |
|      4:    37.046 -  45.457:  112   |   9:    79.104 -  87.515:    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)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.338 - 4.646
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 301
   mapped sites are within: 0.706 - 4.646

peak=   11.543 closest distance to " CB  VAL A 230 " =    1.441
peak=    8.372 closest distance to " CG2 VAL A 296 " =    1.214
peak=    6.388 closest distance to " CG  LEU A   5 " =    1.189
peak=    5.981 closest distance to " NE2 GLN A  11 " =    1.199
peak=    5.935 closest distance to " CD2 LEU A   5 " =    1.182
peak=    5.692 closest distance to " CG  PRO A  54 " =    1.274
peak=    5.544 closest distance to " O   HOH Z 144 " =    1.868
peak=    5.445 closest distance to " CG  LEU A 228 " =    1.117
peak=    5.345 closest distance to " NH2 ARG A  56 " =    2.093
peak=    5.135 closest distance to " CB  GLN A 183 " =    1.240
peak=    5.058 closest distance to " CB  GLN A 223 " =    1.499
peak=    4.992 closest distance to " CB  VAL A 296 " =    1.036
peak=    4.899 closest distance to " CB  ARG A 275 " =    0.921
peak=    4.876 closest distance to " O   HOH Z 427 " =    2.769
peak=    4.867 closest distance to " CB  PRO A  54 " =    0.967
peak=    4.830 closest distance to " O   HOH Z 209 " =    2.270
peak=    4.770 closest distance to " O   HOH Z 126 " =    1.896
peak=    4.745 closest distance to " CG  PRO A 213 " =    1.225
peak=    4.694 closest distance to " O   HOH Z 232 " =    2.382
peak=    4.678 closest distance to " CB  VAL A 230 " =    1.137
peak=    4.653 closest distance to " CB  SER A  63 " =    1.235
peak=    4.626 closest distance to " O   HOH Z 193 " =    1.713
peak=    4.532 closest distance to " O   HOH Z  78 " =    1.838
peak=    4.491 closest distance to " C   PRO A 198 " =    1.501
peak=    4.478 closest distance to " O   HOH Z 203 " =    1.685
peak=    4.464 closest distance to " O   SER A  87 " =    2.362
peak=    4.440 closest distance to " CB  GLU A 152 " =    1.235
peak=    4.405 closest distance to " O   HOH Z 346 " =    1.587
peak=    4.404 closest distance to " O   HOH Z 272 " =    1.840
peak=    4.365 closest distance to " O   HOH Z 236 " =    1.986
peak=    4.347 closest distance to " CB  SER A   3 " =    1.308
peak=    4.337 closest distance to " O   HOH Z   9 " =    1.193
peak=    4.316 closest distance to " CD2 LEU A 228 " =    1.149
peak=    4.303 closest distance to " CB  VAL A 265 " =    1.333
peak=    4.301 closest distance to " OG ASER A 258 " =    3.058
peak=    4.297 closest distance to " CB  ARG A  79 " =    1.418
peak=    4.227 closest distance to " CB  ASN A 148 " =    1.378
peak=    4.211 closest distance to " OD1 ASN A  69 " =    2.634
peak=    4.208 closest distance to " O   HOH Z  61 " =    1.653
peak=    4.205 closest distance to " O   HOH Z 369 " =    2.144
peak=    4.202 closest distance to " ND2 ASN A 187 " =    1.483
peak=    4.195 closest distance to " CG  PRO A 243 " =    1.109
peak=    4.150 closest distance to " O   HOH Z 298 " =    1.733
peak=    4.142 closest distance to " O   HOH Z 303 " =    2.083
peak=    4.093 closest distance to " CG  PRO A 198 " =    1.185
peak=    4.074 closest distance to " CB  TRP A 266 " =    1.034
peak=    4.071 closest distance to " CG1BVAL A  72 " =    1.530
peak=    4.061 closest distance to " CB  TRP A 179 " =    1.308
peak=    4.048 closest distance to " CB BVAL A  41 " =    1.066
peak=    4.044 closest distance to " O   HOH Z 261 " =    2.277
peak=    4.038 closest distance to " CB  TYR A 169 " =    0.706
peak=    4.014 closest distance to " O   HOH Z 368 " =    2.047
peak=    4.011 closest distance to " O   HOH Z 403 " =    1.670
peak=    3.986 closest distance to " CA  TYR A  30 " =    0.967
peak=    3.978 closest distance to " OG BSER A 164 " =    2.122
peak=    3.970 closest distance to " CB  GLU A 128 " =    1.029
peak=    3.961 closest distance to " O   HOH Z 124 " =    1.343
peak=    3.950 closest distance to " N   PHE A 130 " =    1.270
peak=    3.949 closest distance to " O   HOH Z 411 " =    3.776
peak=    3.946 closest distance to " CB  ARG A 139 " =    0.963
peak=    3.938 closest distance to " O   HOH Z 234 " =    3.498
peak=    3.933 closest distance to " CG2 VAL A 257 " =    0.822
peak=    3.923 closest distance to " O   HOH Z 158 " =    3.146
peak=    3.913 closest distance to " O   HOH Z   9 " =    2.039
peak=    3.906 closest distance to " O   HOH Z  43 " =    2.007
peak=    3.893 closest distance to " O   HOH Z 371 " =    2.874
peak=    3.892 closest distance to " O   HOH Z  66 " =    2.235
peak=    3.882 closest distance to " O   HOH Z 189 " =    2.738
peak=    3.870 closest distance to " CA  ASN A 215 " =    1.131
peak=    3.869 closest distance to " CB  ASN A 187 " =    1.297
peak=    3.858 closest distance to " O   HOH Z 265 " =    2.448
peak=    3.853 closest distance to " CB  GLU A 277 " =    3.520
peak=    3.845 closest distance to " O   HOH Z 128 " =    2.011
peak=    3.832 closest distance to " O   HOH Z 193 " =    1.808
peak=    3.820 closest distance to " CB  ASN A  39 " =    0.912
peak=    3.820 closest distance to " O   HOH Z  97 " =    1.998
peak=    3.800 closest distance to " O   HOH Z 248 " =    1.593
peak=    3.783 closest distance to " O   HOH Z 263 " =    1.629
peak=    3.765 closest distance to " O   HOH Z 130 " =    2.175
peak=    3.764 closest distance to " O   HOH Z 425 " =    1.367
peak=    3.758 closest distance to " CB  SER A  26 " =    1.674
peak=    3.753 closest distance to " CB  VAL A 202 " =    1.605
peak=    3.752 closest distance to " O   HOH Z  44 " =    1.678
peak=    3.751 closest distance to " O   HOH Z 402 " =    1.403
peak=    3.741 closest distance to " O   HOH Z 392 " =    3.190
peak=    3.740 closest distance to " CG  ARG A  66 " =    2.786
peak=    3.731 closest distance to " O   HOH Z 389 " =    1.835
peak=    3.723 closest distance to " O   HOH Z 422 " =    2.549
peak=    3.715 closest distance to " CB  SER A 216 " =    0.790
peak=    3.706 closest distance to " CZ  PHE A 218 " =    1.123
peak=    3.703 closest distance to " O   HOH Z 280 " =    2.976
peak=    3.698 closest distance to " O   HOH Z 180 " =    2.145
peak=    3.695 closest distance to " O   HOH Z 145 " =    1.991
peak=    3.693 closest distance to " O   HOH Z 250 " =    1.341
peak=    3.692 closest distance to " CB  ASP A 140 " =    0.868
peak=    3.690 closest distance to " O   HOH Z  59 " =    1.832
peak=    3.684 closest distance to " CA  PHE A 283 " =    1.183
peak=    3.682 closest distance to " O   HOH Z 425 " =    2.123
peak=    3.681 closest distance to " CB  ASN A 148 " =    1.913
peak=    3.679 closest distance to " O   HOH Z 423 " =    2.666
peak=    3.676 closest distance to " CB  THR A 157 " =    1.112
peak=    3.671 closest distance to " O   HOH Z 147 " =    1.699
peak=    3.666 closest distance to " O   HOH Z  93 " =    2.520
peak=    3.653 closest distance to " O   HOH Z 322 " =    2.023
peak=    3.642 closest distance to " CA  ALA A 158 " =    1.247
peak=    3.641 closest distance to " O   HOH Z 273 " =    2.700
peak=    3.640 closest distance to " O   HOH Z 286 " =    2.388
peak=    3.634 closest distance to " O   HOH Z 423 " =    1.731
peak=    3.634 closest distance to " NZ  LYS A 117 " =    3.134
peak=    3.632 closest distance to " CG  LEU A 167 " =    1.185
peak=    3.631 closest distance to " O   HOH Z   1 " =    1.799
peak=    3.613 closest distance to " O   HOH Z  10 " =    1.772
peak=    3.609 closest distance to " O   HOH Z 145 " =    3.422
peak=    3.604 closest distance to " NH2AARG A 190 " =    1.895
peak=    3.603 closest distance to " O   HOH Z 214 " =    2.162
peak=    3.602 closest distance to " O   HOH Z 407 " =    2.368
peak=    3.600 closest distance to " O   HOH Z 193 " =    1.854
peak=    3.599 closest distance to " CB  ASN A 142 " =    1.031
peak=    3.599 closest distance to " CD2 TRP A 179 " =    1.393
peak=    3.596 closest distance to " CG1 ILE A  33 " =    1.300
peak=    3.592 closest distance to " CB  LEU A 143 " =    1.144
peak=    3.585 closest distance to " OD2 ASP A 286 " =    2.721
peak=    3.584 closest distance to " O   HOH Z 175 " =    2.019
peak=    3.582 closest distance to " NH2 ARG A 156 " =    1.087
peak=    3.566 closest distance to " CA  ALA A  21 " =    1.179
peak=    3.553 closest distance to " CB  ALA A   9 " =    1.579
peak=    3.553 closest distance to " O   HOH Z 419 " =    1.962
peak=    3.553 closest distance to " CD BLYS A 290 " =    1.212
peak=    3.550 closest distance to " CE  LYS A  76 " =    0.952
peak=    3.536 closest distance to " O   HOH Z 126 " =    1.518
peak=    3.535 closest distance to " O   HOH Z   1 " =    1.724
peak=    3.534 closest distance to " O   HOH Z  40 " =    1.941
peak=    3.529 closest distance to " CD1 LEU A 228 " =    2.016
peak=    3.528 closest distance to " O   HOH Z 368 " =    3.628
peak=    3.524 closest distance to " CD1 ILE A  33 " =    1.662
peak=    3.516 closest distance to " CB  SER A 212 " =    1.200
peak=    3.510 closest distance to " CB  ASN A 110 " =    1.122
peak=    3.508 closest distance to " O   HOH Z 380 " =    1.661
peak=    3.507 closest distance to " O   HOH Z   3 " =    1.920
peak=    3.506 closest distance to " O   HOH Z 222 " =    2.443
peak=    3.502 closest distance to " CE1 TYR A 186 " =    1.343
peak=    3.496 closest distance to " CB  ARG A 190 " =    1.607
peak=    3.491 closest distance to " O   HOH Z   2 " =    1.502
peak=    3.487 closest distance to " CD1 ILE A 106 " =    1.115
peak=    3.482 closest distance to " O   HOH Z  30 " =    1.386
peak=    3.482 closest distance to " O   HOH Z 148 " =    3.388
peak=    3.481 closest distance to " N   ARG A 156 " =    1.297
peak=    3.481 closest distance to " O   LYS A 290 " =    2.397
peak=    3.479 closest distance to " O   HOH Z 227 " =    2.184
peak=    3.478 closest distance to " CG BARG A 102 " =    1.824
peak=    3.477 closest distance to " O   HOH Z  61 " =    1.519
peak=    3.477 closest distance to " O   HOH Z 371 " =    1.657
peak=    3.473 closest distance to " N   ASN A  39 " =    1.223
peak=    3.468 closest distance to " O   HOH Z 305 " =    3.542
peak=    3.463 closest distance to " O   HOH Z 344 " =    2.986
peak=    3.462 closest distance to " CB  THR A  82 " =    1.325
peak=    3.458 closest distance to " CA  ARG A  36 " =    1.000
peak=    3.455 closest distance to " CA  ASP A 162 " =    1.048
peak=    3.453 closest distance to " O   GLN A 278 " =    1.327
peak=    3.453 closest distance to " O   HOH Z 227 " =    1.739
peak=    3.452 closest distance to " CB  HIS A 108 " =    0.824
peak=    3.451 closest distance to " CB  ILE A  20 " =    1.483
peak=    3.440 closest distance to " CA  ALA A  51 " =    0.973
peak=    3.437 closest distance to " CB  ALA A 291 " =    1.447
peak=    3.424 closest distance to " CG  GLN A  88 " =    1.049
peak=    3.418 closest distance to " O   HOH Z  88 " =    3.021
peak=    3.417 closest distance to " NH2BARG A 145 " =    2.003
peak=    3.411 closest distance to " O   HOH Z 245 " =    1.348
peak=    3.409 closest distance to " CB  LYS A 117 " =    1.203
peak=    3.404 closest distance to " O   HOH Z 299 " =    4.206
peak=    3.403 closest distance to " CA  VAL A  41 " =    0.801
peak=    3.394 closest distance to " O   HOH Z 261 " =    1.493
peak=    3.393 closest distance to " O   ASP A 124 " =    1.070
peak=    3.393 closest distance to " O   HOH Z 132 " =    2.347
peak=    3.392 closest distance to " O   HOH Z 426 " =    1.602
peak=    3.391 closest distance to " CG1 ILE A  49 " =    1.363
peak=    3.387 closest distance to " O   HOH Z 329 " =    3.851
peak=    3.385 closest distance to " CG  MET A 185 " =    1.198
peak=    3.384 closest distance to " O   HOH Z  54 " =    1.605
peak=    3.382 closest distance to " CA  LYS A 117 " =    1.225
peak=    3.382 closest distance to " CB  GLN A  88 " =    1.242
peak=    3.379 closest distance to " O   HOH Z 424 " =    1.494
peak=    3.379 closest distance to " CA  SER A 146 " =    1.760
peak=    3.375 closest distance to " CA  LYS A 290 " =    1.229
peak=    3.369 closest distance to " CA  THR A 264 " =    0.784
peak=    3.363 closest distance to " O   HOH Z 128 " =    2.177
peak=    3.362 closest distance to " CB  THR A  31 " =    1.617
peak=    3.362 closest distance to " CB  SER A 273 " =    0.836
peak=    3.359 closest distance to " O   TRP A 274 " =    1.863
peak=    3.355 closest distance to " O   HOH Z 353 " =    2.532
peak=    3.345 closest distance to " CA  ALA A 299 " =    0.984
peak=    3.341 closest distance to " O  BHOH Z 338 " =    2.419
peak=    3.339 closest distance to " CD1 LEU A 300 " =    1.339
peak=    3.339 closest distance to " CA  ALA A 291 " =    0.919
peak=    3.337 closest distance to " CB  GLN A 205 " =    1.209
peak=    3.335 closest distance to " CG2 THR A 221 " =    1.257
peak=    3.334 closest distance to " CB  LEU A 255 " =    0.747
peak=    3.328 closest distance to " CG2 ILE A 120 " =    1.204
peak=    3.326 closest distance to " CG2 ILE A  20 " =    1.499
peak=    3.326 closest distance to " O   HOH Z 437 " =    1.958
peak=    3.325 closest distance to " CG1 VAL A 153 " =    0.936
peak=    3.322 closest distance to " O   HOH Z 234 " =    1.882
peak=    3.320 closest distance to " CG  GLN A  77 " =    2.343
peak=    3.318 closest distance to " CA  VAL A 126 " =    0.915
peak=    3.317 closest distance to " OE1 GLU A   2 " =    2.073
peak=    3.317 closest distance to " CB  ALA A 248 " =    1.326
peak=    3.316 closest distance to " O   HOH Z 291 " =    1.509
peak=    3.303 closest distance to " O   HOH Z 366 " =    2.820
peak=    3.299 closest distance to " CB  MET A  40 " =    0.888
peak=    3.298 closest distance to " CG  LYS A 119 " =    1.110
peak=    3.297 closest distance to " ND1 HIS A  86 " =    1.715
peak=    3.285 closest distance to " O   HOH Z 374 " =    2.535
peak=    3.284 closest distance to " CD  ARG A 159 " =    0.708
peak=    3.283 closest distance to " O   HOH Z   1 " =    4.646
peak=    3.277 closest distance to " O   HOH Z 359 " =    3.567
peak=    3.276 closest distance to " O   HOH Z 290 " =    1.021
peak=    3.274 closest distance to " O   HOH Z 112 " =    1.632
peak=    3.272 closest distance to " O   HOH Z 128 " =    1.929
peak=    3.270 closest distance to " ND2 ASN A 110 " =    1.770
peak=    3.270 closest distance to " O   HOH Z 251 " =    1.651
peak=    3.266 closest distance to " O   HOH Z 213 " =    2.127
peak=    3.264 closest distance to " CD  LYS A 119 " =    1.420
peak=    3.261 closest distance to " O   HOH Z  21 " =    1.699
peak=    3.261 closest distance to " CB  ALA A  34 " =    0.990
peak=    3.249 closest distance to " O   MET A 105 " =    1.827
peak=    3.244 closest distance to " CG  GLU A 277 " =    2.039
peak=    3.240 closest distance to " O   HOH Z 345 " =    3.309
peak=    3.239 closest distance to " CA  ALA A 233 " =    1.098
peak=    3.239 closest distance to " CB  GLN A 278 " =    0.888
peak=    3.237 closest distance to " O   HOH Z 417 " =    3.370
peak=    3.233 closest distance to " O   HOH Z 435 " =    2.020
peak=    3.231 closest distance to " NH1AARG A 145 " =    1.054
peak=    3.230 closest distance to " O   HOH Z  85 " =    1.301
peak=    3.220 closest distance to " CB  TRP A 150 " =    1.443
peak=    3.218 closest distance to " CB  LYS A 290 " =    1.082
peak=    3.217 closest distance to " O   HOH Z 368 " =    2.695
peak=    3.217 closest distance to " OE2 GLU A  53 " =    1.970
peak=    3.215 closest distance to " O   HOH Z 172 " =    3.425
peak=    3.214 closest distance to " CD  LYS A 166 " =    1.324
peak=    3.213 closest distance to " OG  SER A  62 " =    2.884
peak=    3.212 closest distance to " CB  ASN A 224 " =    1.035
peak=    3.210 closest distance to " O   GLN A  58 " =    1.469
peak=    3.209 closest distance to " CD  GLN A 194 " =    1.330
peak=    3.205 closest distance to " CA  GLN A 194 " =    1.286
peak=    3.200 closest distance to " CG AARG A 275 " =    1.118
peak=    3.198 closest distance to " NZ  LYS A  76 " =    1.426
peak=    3.197 closest distance to " O   HOH Z  80 " =    2.316
peak=    3.196 closest distance to " O   HOH Z  88 " =    2.536
peak=    3.193 closest distance to " CD2 LEU A 297 " =    0.965
peak=    3.191 closest distance to " O   HOH Z  85 " =    2.140
peak=    3.186 closest distance to " CD2 LEU A 255 " =    1.501
peak=    3.185 closest distance to " CB  SER A  62 " =    1.307
peak=    3.185 closest distance to " O   HOH Z 432 " =    1.503
peak=    3.184 closest distance to " N   SER A 135 " =    1.252
peak=    3.183 closest distance to " CB  VAL A 268 " =    0.841
peak=    3.182 closest distance to " O   HOH Z 341 " =    2.306
peak=    3.179 closest distance to " CE  LYS A  48 " =    1.131
peak=    3.175 closest distance to " O   HOH Z 303 " =    1.738
peak=    3.174 closest distance to " O   HOH Z 433 " =    1.775
peak=    3.171 closest distance to " CB  TYR A  30 " =    1.622
peak=    3.170 closest distance to " CZ2 TRP A 179 " =    1.626
peak=    3.164 closest distance to " O   HOH Z 154 " =    2.163
peak=    3.161 closest distance to " OG BSER A 134 " =    3.161
peak=    3.156 closest distance to " CG2 THR A 294 " =    1.659
peak=    3.155 closest distance to " CD2 HIS A  81 " =    0.959
peak=    3.155 closest distance to " CG1 ILE A 151 " =    0.994
peak=    3.134 closest distance to " N   VAL A 126 " =    1.268
peak=    3.133 closest distance to " O   HOH Z 109 " =    2.511
peak=    3.133 closest distance to " O   HOH Z 336 " =    1.896
peak=    3.131 closest distance to " OG  SER A  22 " =    2.780
peak=    3.130 closest distance to " CG1 ILE A 120 " =    1.148
peak=    3.129 closest distance to " O   HOH Z 279 " =    2.215
peak=    3.128 closest distance to " CG  LEU A 281 " =    1.000
peak=    3.128 closest distance to " CG  MET A 113 " =    1.100
peak=    3.116 closest distance to " O   HOH Z 271 " =    1.990
peak=    3.114 closest distance to " CA  SER A  87 " =    0.994
peak=    3.108 closest distance to " O   ALA A   1 " =    1.742
peak=    3.106 closest distance to " CG  GLN A  89 " =    1.473
peak=    3.106 closest distance to " O   HOH Z 423 " =    1.518
peak=    3.101 closest distance to " O   HOH Z 189 " =    2.646
peak=    3.101 closest distance to " CA  MET A 105 " =    0.939
peak=    3.097 closest distance to " N   ASP A 162 " =    1.267
peak=    3.093 closest distance to " CG  LYS A  76 " =    0.962
peak=    3.092 closest distance to " OG  SER A 206 " =    1.256
peak=    3.091 closest distance to " O   HOH Z 383 " =    1.749
peak=    3.090 closest distance to " OG  SER A  62 " =    2.843
peak=    3.088 closest distance to " O   HOH Z 421 " =    1.829
peak=    3.074 closest distance to " ND1 HIS A  81 " =    1.674
peak=    3.072 closest distance to " O   HOH Z 357 " =    1.832
peak=    3.072 closest distance to " CD1 LEU A 261 " =    1.163
peak=    3.072 closest distance to " O   HOH Z 409 " =    3.158
peak=    3.071 closest distance to " O   HOH Z 218 " =    2.302
peak=    3.059 closest distance to " CD2 TYR A  30 " =    1.011
peak=    3.055 closest distance to " N   ASN A 127 " =    1.274
peak=    3.053 closest distance to " O   HOH Z 133 " =    1.447
peak=    3.052 closest distance to " O   HOH Z 116 " =    1.648
peak=    3.046 closest distance to " CA  ARG A 102 " =    1.128
peak=    3.038 closest distance to " O   HOH Z  43 " =    2.779
peak=    3.033 closest distance to " O   HOH Z 367 " =    3.607

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.749 - 5.431
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 207
   mapped sites are within: 0.749 - 5.431

peak=   -5.002 closest distance to " CG2 VAL A 230 " =    0.782
peak=   -4.641 closest distance to " CD  ARG A 156 " =    2.025
peak=   -4.631 closest distance to " OG BSER A 134 " =    1.152
peak=   -4.439 closest distance to " O   HOH Z 266 " =    4.891
peak=   -4.437 closest distance to " CB  PRO A 243 " =    2.650
peak=   -4.425 closest distance to " SG  CYS A 254 " =    3.280
peak=   -4.235 closest distance to " CG  GLN A 223 " =    1.946
peak=   -4.220 closest distance to " C   HIS A 108 " =    1.185
peak=   -4.200 closest distance to " CG2 VAL A 296 " =    1.424
peak=   -4.198 closest distance to " CB  ALA A 248 " =    2.075
peak=   -4.197 closest distance to " O   HOH Z 435 " =    2.840
peak=   -4.007 closest distance to " CB  PHE A 192 " =    1.900
peak=   -4.003 closest distance to " CE  MET A 105 " =    2.284
peak=   -3.999 closest distance to " CA  VAL A  67 " =    2.703
peak=   -3.951 closest distance to " CE2 PHE A 218 " =    2.575
peak=   -3.950 closest distance to " O   HOH Z 290 " =    1.120
peak=   -3.901 closest distance to " CA  ASN A 110 " =    2.575
peak=   -3.891 closest distance to " CG2 THR A   4 " =    1.891
peak=   -3.887 closest distance to " CD  GLN A  58 " =    1.128
peak=   -3.874 closest distance to " O   VAL A  67 " =    2.630
peak=   -3.866 closest distance to " CG  ASP A 231 " =    0.791
peak=   -3.866 closest distance to " CE2 TYR A  30 " =    2.811
peak=   -3.841 closest distance to " OG  SER A   3 " =    1.671
peak=   -3.819 closest distance to " O   HOH Z 211 " =    1.564
peak=   -3.816 closest distance to " O   PRO A 198 " =    1.233
peak=   -3.785 closest distance to " CG1 VAL A 112 " =    2.731
peak=   -3.777 closest distance to " O   HOH Z 351 " =    1.568
peak=   -3.764 closest distance to " O   HOH Z 231 " =    2.079
peak=   -3.758 closest distance to " N   GLN A  58 " =    1.819
peak=   -3.750 closest distance to " CB  PRO A 280 " =    2.056
peak=   -3.738 closest distance to " N   THR A 157 " =    1.414
peak=   -3.736 closest distance to " NH2 ARG A  79 " =    1.916
peak=   -3.716 closest distance to " O   HOH Z 114 " =    2.965
peak=   -3.713 closest distance to " O   PRO A 163 " =    2.039
peak=   -3.706 closest distance to " ND2 ASN A  45 " =    1.513
peak=   -3.701 closest distance to " O   HOH Z 389 " =    1.918
peak=   -3.693 closest distance to " CB  ALA A 291 " =    2.384
peak=   -3.690 closest distance to " CB  PRO A 163 " =    2.489
peak=   -3.685 closest distance to " O   HOH Z 102 " =    1.623
peak=   -3.684 closest distance to " CZ  PHE A  59 " =    1.451
peak=   -3.668 closest distance to " O   SER A  22 " =    2.256
peak=   -3.661 closest distance to " ND2 ASN A 187 " =    1.539
peak=   -3.641 closest distance to " O   HOH Z  47 " =    1.619
peak=   -3.641 closest distance to " O   HOH Z 166 " =    2.152
peak=   -3.620 closest distance to " N   ALA A 226 " =    1.995
peak=   -3.616 closest distance to " CZ  TYR A 169 " =    1.656
peak=   -3.605 closest distance to " O   HOH Z 185 " =    2.225
peak=   -3.605 closest distance to " OXT GLY A 302 " =    2.926
peak=   -3.604 closest distance to " CZ3 TRP A 179 " =    1.214
peak=   -3.604 closest distance to " O   ALA A 161 " =    1.641
peak=   -3.591 closest distance to " CA  GLY A  98 " =    1.849
peak=   -3.583 closest distance to " O   PRO A 198 " =    1.314
peak=   -3.578 closest distance to " CG2 VAL A 296 " =    1.824
peak=   -3.571 closest distance to " N   PHE A  59 " =    2.155
peak=   -3.569 closest distance to " CB  ALA A 248 " =    2.326
peak=   -3.568 closest distance to " NE2 GLN A  88 " =    1.968
peak=   -3.547 closest distance to " ND2 ASN A  45 " =    1.104
peak=   -3.547 closest distance to " CB  TYR A  15 " =    2.174
peak=   -3.545 closest distance to " CB  ASP A 132 " =    2.328
peak=   -3.545 closest distance to " CD2 LEU A 300 " =    2.827
peak=   -3.528 closest distance to " O   HOH Z 407 " =    3.025
peak=   -3.525 closest distance to " OG  SER A  87 " =    1.320
peak=   -3.523 closest distance to " CG  TRP A 266 " =    1.874
peak=   -3.521 closest distance to " O   HOH Z  60 " =    2.136
peak=   -3.517 closest distance to " O   HOH Z  56 " =    2.472
peak=   -3.517 closest distance to " N   HIS A 115 " =    2.070
peak=   -3.516 closest distance to " O   HOH Z 166 " =    1.473
peak=   -3.507 closest distance to " O   HOH Z 191 " =    5.431
peak=   -3.504 closest distance to " CE BMET A  47 " =    1.709
peak=   -3.502 closest distance to " CB  ALA A 244 " =    2.067
peak=   -3.501 closest distance to " O   HOH Z 103 " =    1.703
peak=   -3.495 closest distance to " CG  PHE A 283 " =    2.609
peak=   -3.492 closest distance to " O   HOH Z 313 " =    1.655
peak=   -3.489 closest distance to " CD  LYS A 289 " =    2.476
peak=   -3.484 closest distance to " O   HOH Z 394 " =    1.480
peak=   -3.483 closest distance to " CA  GLY A 241 " =    2.248
peak=   -3.481 closest distance to " N   THR A 235 " =    1.317
peak=   -3.479 closest distance to " OD2 ASP A 171 " =    2.254
peak=   -3.470 closest distance to " C   MET A 188 " =    1.439
peak=   -3.469 closest distance to " CG2 THR A 178 " =    2.211
peak=   -3.462 closest distance to " O   HOH Z  43 " =    1.897
peak=   -3.460 closest distance to " CG1 VAL A 230 " =    1.865
peak=   -3.458 closest distance to " NH2AARG A 275 " =    5.117
peak=   -3.455 closest distance to " O   HOH Z 423 " =    1.125
peak=   -3.453 closest distance to " ND2 ASN A 249 " =    2.407
peak=   -3.449 closest distance to " O   HOH Z 198 " =    2.069
peak=   -3.449 closest distance to " O   HOH Z   9 " =    1.448
peak=   -3.448 closest distance to " CD1 LEU A 228 " =    2.052
peak=   -3.447 closest distance to " O   VAL A 189 " =    2.553
peak=   -3.427 closest distance to " OG1 THR A 178 " =    1.193
peak=   -3.426 closest distance to " O   HOH Z 385 " =    2.011
peak=   -3.425 closest distance to " N   ALA A  43 " =    2.501
peak=   -3.421 closest distance to " N   SER A 276 " =    1.259
peak=   -3.414 closest distance to " CB  ASP A 132 " =    2.307
peak=   -3.403 closest distance to " CD2 LEU A 237 " =    2.740
peak=   -3.399 closest distance to " CG1 VAL A 112 " =    2.645
peak=   -3.397 closest distance to " CD1 LEU A 101 " =    2.329
peak=   -3.395 closest distance to " CB  ASN A  39 " =    2.269
peak=   -3.393 closest distance to " CG  LEU A 228 " =    1.056
peak=   -3.391 closest distance to " CD1 PHE A  59 " =    1.977
peak=   -3.391 closest distance to " CB  ALA A  43 " =    2.346
peak=   -3.391 closest distance to " N   ALA A 248 " =    1.554
peak=   -3.386 closest distance to " O   HOH Z 423 " =    2.139
peak=   -3.385 closest distance to " C   LEU A 143 " =    1.007
peak=   -3.380 closest distance to " O   HOH Z 140 " =    1.557
peak=   -3.375 closest distance to " OD2 ASP A 191 " =    1.359
peak=   -3.370 closest distance to " O   HOH Z 309 " =    2.504
peak=   -3.366 closest distance to " CA  GLY A 203 " =    2.282
peak=   -3.366 closest distance to " NZ  LYS A 119 " =    3.408
peak=   -3.361 closest distance to " O   HOH Z 134 " =    2.923
peak=   -3.358 closest distance to " CA  GLY A 133 " =    1.974
peak=   -3.355 closest distance to " O   ALA A   8 " =    1.901
peak=   -3.353 closest distance to " CD  ARG A 139 " =    1.604
peak=   -3.343 closest distance to " OG BSER A 134 " =    1.634
peak=   -3.337 closest distance to " C   ALA A 158 " =    1.288
peak=   -3.327 closest distance to " O   GLY A  80 " =    2.499
peak=   -3.323 closest distance to " CG2 VAL A 202 " =    2.627
peak=   -3.320 closest distance to " O   HOH Z 350 " =    1.957
peak=   -3.313 closest distance to " O   HOH Z 359 " =    3.315
peak=   -3.303 closest distance to " OD1 ASN A 148 " =    1.478
peak=   -3.303 closest distance to " CB  ASN A  69 " =    1.139
peak=   -3.302 closest distance to " N   ASN A  60 " =    1.364
peak=   -3.300 closest distance to " OG  SER A  97 " =    2.147
peak=   -3.299 closest distance to " NH1 ARG A  36 " =    2.036
peak=   -3.293 closest distance to " O   HOH Z  13 " =    1.574
peak=   -3.293 closest distance to " O   HOH Z 313 " =    1.105
peak=   -3.291 closest distance to " CD1 LEU A 101 " =    2.800
peak=   -3.290 closest distance to " O   HOH Z 198 " =    1.489
peak=   -3.287 closest distance to " N   MET A 188 " =    1.792
peak=   -3.284 closest distance to " CA  ASP A 298 " =    1.079
peak=   -3.282 closest distance to " O   HOH Z 139 " =    3.053
peak=   -3.278 closest distance to " O   PHE A 218 " =    1.659
peak=   -3.276 closest distance to " O   HOH Z 256 " =    1.229
peak=   -3.271 closest distance to " O   HOH Z 210 " =    1.122
peak=   -3.268 closest distance to " N   GLN A  77 " =    1.644
peak=   -3.263 closest distance to " O   HOH Z 165 " =    1.998
peak=   -3.261 closest distance to " O   ALA A  51 " =    1.307
peak=   -3.256 closest distance to " O   HOH Z 281 " =    3.212
peak=   -3.253 closest distance to " O   HOH Z  90 " =    2.562
peak=   -3.244 closest distance to " O   HOH Z 388 " =    2.183
peak=   -3.239 closest distance to " OG  SER A  62 " =    1.571
peak=   -3.236 closest distance to " CA  GLY A 241 " =    3.039
peak=   -3.235 closest distance to " O   HOH Z 369 " =    2.047
peak=   -3.234 closest distance to " O   HOH Z 339 " =    1.870
peak=   -3.231 closest distance to " CG1 VAL A 250 " =    2.710
peak=   -3.226 closest distance to " OH  TYR A 214 " =    1.194
peak=   -3.224 closest distance to " CG  LYS A 193 " =    2.421
peak=   -3.224 closest distance to " CD1 ILE A 239 " =    2.552
peak=   -3.223 closest distance to " O   HOH Z 131 " =    4.013
peak=   -3.222 closest distance to " CG  GLU A 277 " =    1.210
peak=   -3.222 closest distance to " O   HOH Z 111 " =    4.693
peak=   -3.217 closest distance to " CE3 TRP A 150 " =    1.973
peak=   -3.217 closest distance to " CD1 TYR A 247 " =    2.671
peak=   -3.216 closest distance to " C   GLN A 205 " =    1.899
peak=   -3.215 closest distance to " O   MET A  40 " =    2.697
peak=   -3.215 closest distance to " O   ILE A 106 " =    2.132
peak=   -3.214 closest distance to " O   HOH Z 281 " =    2.812
peak=   -3.209 closest distance to " OG  SER A 206 " =    1.661
peak=   -3.208 closest distance to " CB  ALA A   7 " =    2.136
peak=   -3.207 closest distance to " O   HOH Z 345 " =    1.958
peak=   -3.205 closest distance to " O   TYR A  30 " =    2.877
peak=   -3.203 closest distance to " O   HOH Z 111 " =    2.495
peak=   -3.201 closest distance to " OD1 ASP A 191 " =    1.419
peak=   -3.199 closest distance to " CD2 TYR A 293 " =    2.030
peak=   -3.198 closest distance to " O   LYS A 117 " =    1.697
peak=   -3.197 closest distance to " O   SER A 210 " =    1.987
peak=   -3.195 closest distance to " O   GLY A  75 " =    1.936
peak=   -3.191 closest distance to " CG  GLU A 152 " =    1.552
peak=   -3.190 closest distance to " N   VAL A  72 " =    1.598
peak=   -3.181 closest distance to " CB  ALA A 291 " =    2.185
peak=   -3.180 closest distance to " CZ2 TRP A 274 " =    0.860
peak=   -3.179 closest distance to " O   HOH Z 295 " =    1.603
peak=   -3.178 closest distance to " C   ASP A 231 " =    2.432
peak=   -3.178 closest distance to " CD2 PHE A 225 " =    1.030
peak=   -3.175 closest distance to " NE2 GLN A 278 " =    1.895
peak=   -3.171 closest distance to " CG1 VAL A 296 " =    1.387
peak=   -3.169 closest distance to " C   LEU A 222 " =    0.749
peak=   -3.158 closest distance to " CD2 LEU A   5 " =    1.152
peak=   -3.157 closest distance to " CG1 VAL A 197 " =    2.207
peak=   -3.152 closest distance to " O   HOH Z  52 " =    1.509
peak=   -3.150 closest distance to " CB  VAL A 296 " =    1.252
peak=   -3.147 closest distance to " CG  GLN A 278 " =    2.070
peak=   -3.139 closest distance to " O   HOH Z  38 " =    1.856
peak=   -3.122 closest distance to " OD1 ASN A 301 " =    1.996
peak=   -3.120 closest distance to " OE2 GLU A 152 " =    1.198
peak=   -3.120 closest distance to " O   GLN A 240 " =    1.800
peak=   -3.111 closest distance to " O   GLU A  44 " =    1.666
peak=   -3.110 closest distance to " O   TRP A  70 " =    1.453
peak=   -3.106 closest distance to " CG  PRO A 163 " =    2.550
peak=   -3.102 closest distance to " CE BMET A  47 " =    1.276
peak=   -3.098 closest distance to " O   HOH Z 389 " =    1.461
peak=   -3.097 closest distance to " O   HOH Z 377 " =    0.998
peak=   -3.094 closest distance to " O   HOH Z  77 " =    1.744
peak=   -3.094 closest distance to " OG ASER A 216 " =    1.004
peak=   -3.093 closest distance to " O   HOH Z 234 " =    3.911
peak=   -3.086 closest distance to " CA  GLY A 133 " =    2.231
peak=   -3.082 closest distance to " O   HOH Z 353 " =    2.044
peak=   -3.081 closest distance to " OXT GLY A 302 " =    3.522
peak=   -3.078 closest distance to " NH2BARG A 275 " =    1.649
peak=   -3.077 closest distance to " O   HOH Z 134 " =    3.578
peak=   -3.071 closest distance to " O   HOH Z 175 " =    4.323
peak=   -3.069 closest distance to " CG  ARG A 269 " =    2.296
peak=   -3.068 closest distance to " CD1 ILE A 199 " =    2.434
peak=   -3.055 closest distance to " CE  LYS A  76 " =    2.865
peak=   -3.050 closest distance to " O   HOH Z 250 " =    1.391
peak=   -3.023 closest distance to " SG ACYS A 201 " =    1.924

================= 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    :  0.4355 0.4216   6.230718e+00   6.207194e+00
   1_bss:  0.4272 0.4128   6.223978e+00   6.193206e+00
   1_xyz:  0.3221 0.3432   6.024314e+00   6.061893e+00
   1_adp:  0.2604 0.2962   5.844104e+00   5.946193e+00
   1_occ:  0.2596 0.2956   5.842289e+00   5.946398e+00
   2_bss:  0.2545 0.2891   5.839219e+00   5.939115e+00
   2_xyz:  0.1781 0.2209   5.528100e+00   5.695924e+00
   2_adp:  0.1616 0.2059   5.446416e+00   5.635951e+00
   2_occ:  0.1614 0.2054   5.445336e+00   5.634565e+00
   3_bss:  0.1610 0.2048   5.445006e+00   5.633172e+00
   3_xyz:  0.1237 0.1668   5.216934e+00   5.444517e+00
   3_adp:  0.1171 0.1607   5.169697e+00   5.403866e+00
   3_occ:  0.1170 0.1606   5.169532e+00   5.403793e+00
   4_bss:  0.1174 0.1604   5.169924e+00   5.402127e+00
   4_xyz:  0.1124 0.1568   5.142213e+00   5.384384e+00
   4_adp:  0.1125 0.1550   5.135942e+00   5.372504e+00
   4_occ:  0.1125 0.1550   5.135572e+00   5.372080e+00
   5_bss:  0.1124 0.1549   5.135101e+00   5.371691e+00
   5_xyz:  0.1102 0.1530   5.119562e+00   5.361638e+00
   5_adp:  0.1090 0.1539   5.119433e+00   5.370141e+00
   5_occ:  0.1089 0.1539   5.119000e+00   5.369695e+00
   5_bss:  0.1088 0.1539   5.118849e+00   5.369541e+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:  0.371  20.001   7.132   9.359   7.824   0.000   0.000   0.000
   1_xyz:  0.371  20.001   7.132   9.359   7.824   0.000   0.000   0.000
   1_adp:  0.371  20.001   7.132   9.359   7.824   0.000   0.000   0.000
   1_occ:  0.371  20.001   7.132   9.359   7.824   0.000   0.000   0.000
   2_bss:  0.343  33.694   3.834   5.057   4.961   0.000   0.000   0.000
   2_xyz:  0.343  33.694   3.834   5.057   4.961   0.000   0.000   0.000
   2_adp:  0.343  33.694   3.834   5.057   4.961   0.000   0.000   0.000
   2_occ:  0.343  33.694   3.834   5.057   4.961   0.000   0.000   0.000
   3_bss:  0.327  33.694   2.981   3.428   4.277   0.000   0.000   0.000
   3_xyz:  0.327  33.694   2.981   3.428   4.277   0.000   0.000   0.000
   3_adp:  0.327  33.694   2.981   3.428   4.277   0.000   0.000   0.000
   3_occ:  0.327  33.694   2.981   3.428   4.277   0.000   0.000   0.000
   4_bss:  0.317  33.694   2.797   3.098   4.165   0.000   0.000   0.000
   4_xyz:  0.317  33.694   2.797   3.098   4.165   0.000   0.000   0.000
   4_adp:  0.317  33.694   2.797   3.098   4.165   0.000   0.000   0.000
   4_occ:  0.317  33.694   2.797   3.098   4.165   0.000   0.000   0.000
   5_bss:  0.322  37.226   2.746   2.969   4.144   0.000   0.000   0.000
   5_xyz:  0.322  37.226   2.746   2.969   4.144   0.000   0.000   0.000
   5_adp:  0.322  37.226   2.746   2.969   4.144   0.000   0.000   0.000
   5_occ:  0.322  37.226   2.746   2.969   4.144   0.000   0.000   0.000
   5_bss:  0.322  42.104  -0.524  -0.332   0.856   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.743 0.5502  0.6195    52736.047
   1_bss:  47.827 0.5467  0.7830    50024.350
   1_xyz:  36.754 0.6805  0.9521    32232.899
   1_adp:  29.409 0.7655  1.0548    22782.607
   1_occ:  29.396 0.7656  1.0533    22674.676
   2_bss:  29.045 0.7691  0.9311    22140.122
   2_xyz:  21.145 0.8504  0.9972    12066.327
   2_adp:  19.360 0.8683  1.0072    10646.364
   2_occ:  19.318 0.8687  1.0074    10599.767
   3_bss:  19.273 0.8690  0.9695    10554.701
   3_xyz:  15.310 0.9035  0.9905     7070.595
   3_adp:  14.382 0.9115  0.9926     6535.454
   3_occ:  14.379 0.9115  0.9925     6528.353
   4_bss:  14.351 0.9117  0.9845     6504.568
   4_xyz:  13.805 0.9167  0.9852     6218.892
   4_adp:  13.501 0.9193  0.9855     6088.135
   4_occ:  13.495 0.9193  0.9854     6079.803
   5_bss:  13.481 0.9194  0.9833     6076.471
   5_xyz:  13.326 0.9204  0.9839     5970.866
   5_adp:  13.495 0.9192  0.9801     6057.073
   5_occ:  13.490 0.9193  0.9800     6053.162
   5_bss:  13.485 0.9193  0.9842     6051.213
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3352e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3352e+01
   1_xyz:   1.525  0.011  0.100 17.843  0.006  4.118   1.1784e-01
   1_adp:   1.525  0.011  0.100 17.843  0.006  4.118   1.1784e-01
   1_occ:   1.525  0.011  0.100 17.843  0.006  4.118   1.1784e-01
   2_bss:   1.525  0.011  0.100 17.843  0.006  4.118   1.1784e-01
   2_xyz:   0.921  0.006  0.068 15.661  0.004  4.116   5.5937e-02
   2_adp:   0.921  0.006  0.068 15.661  0.004  4.116   5.5937e-02
   2_occ:   0.921  0.006  0.068 15.661  0.004  4.116   5.5937e-02
   3_bss:   0.921  0.006  0.068 15.661  0.004  4.116   5.5937e-02
   3_xyz:   1.079  0.007  0.082 15.834  0.004  4.119   6.6513e-02
   3_adp:   1.079  0.007  0.082 15.834  0.004  4.119   6.6513e-02
   3_occ:   1.079  0.007  0.082 15.834  0.004  4.119   6.6513e-02
   4_bss:   1.079  0.007  0.082 15.834  0.004  4.119   6.6513e-02
   4_xyz:   0.949  0.006  0.077 15.547  0.004  4.111   5.6843e-02
   4_adp:   0.949  0.006  0.077 15.547  0.004  4.111   5.6843e-02
   4_occ:   0.949  0.006  0.077 15.547  0.004  4.111   5.6843e-02
   5_bss:   0.949  0.006  0.077 15.547  0.004  4.111   5.6843e-02
   5_xyz:   0.996  0.006  0.080 15.454  0.004  4.117   6.0235e-02
   5_adp:   0.996  0.006  0.080 15.454  0.004  4.117   6.0235e-02
   5_occ:   0.996  0.006  0.080 15.454  0.004  4.117   6.0235e-02
   5_bss:   0.996  0.006  0.080 15.454  0.004  4.117   6.0235e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9167e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9167e+00
   1_xyz:  12.831  0.144  0.419 88.798  0.034  2.295   8.6384e-02
   1_adp:  12.831  0.144  0.419 88.798  0.034  2.295   8.6384e-02
   1_occ:  12.831  0.144  0.419 88.798  0.034  2.295   8.6384e-02
   2_bss:  12.831  0.144  0.419 88.798  0.034  2.295   8.6384e-02
   2_xyz:   5.492  0.053  0.255 88.392  0.039  2.330   4.0701e-02
   2_adp:   5.492  0.053  0.255 88.392  0.039  2.330   4.0701e-02
   2_occ:   5.492  0.053  0.255 88.392  0.039  2.330   4.0701e-02
   3_bss:   5.492  0.053  0.255 88.392  0.039  2.330   4.0701e-02
   3_xyz:   7.748  0.060  0.499 84.167  0.031  2.260   5.0200e-02
   3_adp:   7.748  0.060  0.499 84.167  0.031  2.260   5.0200e-02
   3_occ:   7.748  0.060  0.499 84.167  0.031  2.260   5.0200e-02
   4_bss:   7.748  0.060  0.499 84.167  0.031  2.260   5.0200e-02
   4_xyz:   6.146  0.035  0.477 83.801  0.037  2.350   3.7885e-02
   4_adp:   6.146  0.035  0.477 83.801  0.037  2.350   3.7885e-02
   4_occ:   6.146  0.035  0.477 83.801  0.037  2.350   3.7885e-02
   5_bss:   6.146  0.035  0.477 83.801  0.037  2.350   3.7885e-02
   5_xyz:   6.187  0.042  0.522 83.811  0.035  2.279   4.1663e-02
   5_adp:   6.187  0.042  0.522 83.811  0.035  2.279   4.1663e-02
   5_occ:   6.187  0.042  0.522 83.811  0.035  2.279   4.1663e-02
   5_bss:   6.187  0.042  0.522 83.811  0.035  2.279   4.1663e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  68.33   0.00  10.94  68.33   0.00   7.93  61.13   0.00  27.31
   1_occ:  68.33   0.00  10.94  68.33   0.00   7.93  61.13   0.00  27.31
   2_bss:  68.33   0.00  10.94  68.33   0.00   7.93  61.13   0.00  27.31
   2_xyz:  68.33   0.00  10.94  68.33   0.00   7.93  61.13   0.00  27.31
   2_adp:  71.47   0.00  11.28  71.47   0.00   7.53  65.82   0.87  31.71
   2_occ:  71.47   0.00  11.28  71.47   0.00   7.53  65.82   0.87  31.71
   3_bss:  71.47   0.00  11.28  71.47   0.00   7.53  65.82   0.87  31.71
   3_xyz:  71.47   0.00  11.28  71.47   0.00   7.53  65.82   0.87  31.71
   3_adp:  79.36   0.00  11.59  79.36   0.00   7.48  70.41   0.96  33.96
   3_occ:  79.36   0.00  11.59  79.36   0.00   7.48  70.41   0.96  33.96
   4_bss:  79.36   0.00  11.59  79.36   0.00   7.48  70.41   0.96  33.96
   4_xyz:  79.36   0.00  11.59  79.36   0.00   7.48  70.41   0.96  33.96
   4_adp:  79.41   0.00  11.42  79.41   0.00   7.40  69.82   1.52  33.30
   4_occ:  79.41   0.00  11.42  79.41   0.00   7.40  69.82   1.52  33.30
   5_bss:  79.41   0.00  11.42  79.41   0.00   7.40  69.82   1.52  33.30
   5_xyz:  79.41   0.00  11.42  79.41   0.00   7.40  69.82   1.52  33.30
   5_adp:  84.12   0.00  11.52  84.12   0.00   7.43  72.92   1.10  33.81
   5_occ:  84.12   0.00  11.52  84.12   0.00   7.43  72.92   1.10  33.81
   5_bss:  87.52   3.40  14.92  87.52   3.40  10.83  76.32   4.50  37.21
------------------------------------------------------------------------
 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:    1.181    0.012    0.402
   1_adp:    1.181    0.012    0.402
   1_occ:    1.181    0.012    0.402
   2_bss:    1.181    0.012    0.402
   2_xyz:    1.410    0.033    0.505
   2_adp:    1.410    0.033    0.505
   2_occ:    1.410    0.033    0.505
   3_bss:    1.410    0.033    0.505
   3_xyz:    1.436    0.037    0.552
   3_adp:    1.436    0.037    0.552
   3_occ:    1.436    0.037    0.552
   4_bss:    1.436    0.037    0.552
   4_xyz:    1.556    0.044    0.565
   4_adp:    1.556    0.044    0.565
   4_occ:    1.556    0.044    0.565
   5_bss:    1.556    0.044    0.565
   5_xyz:    1.577    0.048    0.574
   5_adp:    1.577    0.048    0.574
   5_occ:    1.577    0.048    0.574
   5_bss:    1.577    0.048    0.574
------------------------------------------------------------------------

CPU time actual refinement: 334.96


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_521/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_521/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_521/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_521/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_521/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.83 
  Macro-tasks:
    bulk solvent and scale       = 45.04  
    individual site refinement   = 134.88 
    weights calculation          = 33.08  
    collect and process          = 6.64   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 219.74 
  Micro-tasks:
    mask                            = 1.65   
    f_calc                          = 102.84 
    alpha_beta                      = 8.31   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 108.76 
    fmodel                         = 7.70   
    r_factors                      = 0.19   
    phase_errors                   = 11.79  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 242.70 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.681 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    657 calls, 102.32 s
gradients_fft:          602 calls,  97.14 s

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

# Date 2008-01-16 Time 01:46:25 PST -0800 (1200476785.29 s)
Start R-work = 0.4355, R-free = 0.4216 (no bulk solvent and anisotropic scale)
Final R-work = 0.1266, R-free = 0.1710 (no bulk solvent and anisotropic scale)

Start R-work = 0.4272, R-free = 0.4128
Final R-work = 0.1088, R-free = 0.1539