# Date 2008-01-16 Time 02:39:31 PST -0800 (1200479971.68 s)
#phil __OFF__

Command line arguments: "../923.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27609
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 923

-------------------------------------------------------------------------------
  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: (70.9525, 47.1647, 88.5498, 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: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.01212
Completeness in resolution range: 0.964643
Completeness with d_max=infinity: 0.961659

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   2.0121

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: (70.9525, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.01212
Completeness in resolution range: 0.964643
Completeness with d_max=infinity: 0.961659

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2043 -  4.3052 [2140/2164]  1922   218  10.2%
  bin  2:  4.3052 -  3.4301 [2041/2061]  1841   200   9.8%
  bin  3:  3.4301 -  3.0003 [2021/2040]  1818   203  10.0%
  bin  4:  3.0003 -  2.7277 [1994/2024]  1793   201  10.1%
  bin  5:  2.7277 -  2.5332 [2002/2021]  1803   199   9.9%
  bin  6:  2.5332 -  2.3844 [1986/2011]  1784   202  10.2%
  bin  7:  2.3844 -  2.2654 [1960/1988]  1767   193   9.8%
  bin  8:  2.2654 -  2.1671 [1964/2000]  1769   195   9.9%
  bin  9:  2.1671 -  2.0839 [1945/1987]  1753   192   9.9%
  bin 10:  2.0839 -  2.0121 [1536/2011]  1380   156  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_923/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:
        1.73 -     2.36: 11
        2.36 -     3.00: 1866
        3.00 -     3.63: 4483
        3.63 -     4.27: 8927
        4.27 -     4.90: 12473
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.729 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.827 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.827 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.989 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27755 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_923/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_923/model_refine_001.geo

CPU time processing inputs: 9.48


============================ 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 = 70.9525 47.16465 88.54975 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: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4750   r_free= 0.4680   ksol= 0.00   Bsol= 0.00   scale= 0.782    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.276205                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8017 0.99   1389  152 0.3921 0.3619       6.602      6.4907|
|  2:  4.8017 -  3.8314 0.99   1331  152 0.3891 0.4266      6.7778      6.9083|
|  3:  3.8314 -  3.3530 0.99   1298  143 0.4329 0.4163      6.6723       6.653|
|  4:  3.3530 -  3.0491 0.99   1306  144 0.4668 0.4078      6.5319      6.4312|
|  5:  3.0491 -  2.8321 0.99   1283  146 0.4983 0.4752      6.3734      6.4049|
|  6:  2.8321 -  2.6660 0.99   1289  141 0.4971 0.5670      6.2822      6.1935|
|  7:  2.6660 -  2.5332 0.99   1281  143 0.5164 0.5049      6.2375      6.1911|
|  8:  2.5332 -  2.4233 0.98   1276  137 0.5335 0.4483        6.19      6.1575|
|  9:  2.4233 -  2.3304 0.98   1261  144 0.5063 0.5900      6.1111      6.1821|
| 10:  2.3304 -  2.2502 1.00   1279  143 0.5232 0.4857      6.1215      6.0715|
| 11:  2.2502 -  2.1801 0.97   1248  137 0.5143 0.5099       6.027      6.0874|
| 12:  2.1801 -  2.1179 0.98   1256  142 0.5197 0.4973      5.9797      6.0255|
| 13:  2.1179 -  2.0623 0.99   1273  133 0.5273 0.5213      5.8846      5.8395|
| 14:  2.0623 -  2.0121 0.67    860  102 0.5283 0.5097      5.8658      5.7688|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.8017  1389   152  0.72  32.47   0.79     0.74      64246.12|
|  2:  4.8017 -  3.8314  1331   152  0.72  33.31   0.87     0.77      98619.04|
|  3:  3.8314 -  3.3530  1298   143  0.63  41.32   0.82     0.72     104320.45|
|  4:  3.3530 -  3.0491  1306   144  0.53  49.33   0.79     0.61      95081.72|
|  5:  3.0491 -  2.8321  1283   146  0.44  56.93   0.74     0.50      78965.29|
|  6:  2.8321 -  2.6660  1289   141  0.39  60.71   0.71     0.43      73117.57|
|  7:  2.6660 -  2.5332  1281   143  0.38  61.67   0.72     0.42      64665.22|
|  8:  2.5332 -  2.4233  1276   137  0.39  60.98   0.72     0.44      56417.94|
|  9:  2.4233 -  2.3304  1261   144  0.39  60.80   0.72     0.45      52444.51|
| 10:  2.3304 -  2.2502  1279   143  0.37  61.91   0.73     0.43      47826.55|
| 11:  2.2502 -  2.1801  1248   137  0.34  64.29   0.73     0.41      46987.46|
| 12:  2.1801 -  2.1179  1256   142  0.34  64.25   0.74     0.41      42193.39|
| 13:  2.1179 -  2.0623  1273   133  0.32  66.37   0.70     0.39      37581.92|
| 14:  2.0623 -  2.0121   860   102  0.32  66.14   0.71     0.34      31229.26|
|alpha:            min =        0.34 max =            0.77 mean =         0.51|
|beta:             min =    31229.26 max =       104320.45 mean =     64895.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.23|
|phase err.(test): min =        0.00 max =           89.97 mean =        55.50|
|-----------------------------------------------------------------------------|

============================== 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 = 13.869060             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.309   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.246545              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.395   (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:        4 |
| 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:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      673 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1478 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2561 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3833 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4975 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6495 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7550 |
|-----------------------------------------------------------------------------|
|-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 |       54.587 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.706 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    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 = 12.339)------------------------------------------|
|    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: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4801   r_free= 0.4676   ksol= 0.00   Bsol= 0.00   scale= 0.754    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.278587                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4663   r_free= 0.4538   ksol= 0.32   Bsol= 35.05   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.85,6.97,11.90,0.00,0.00,0.00); trace/3= 8.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.270331                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.395250             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.967   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.164256              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.360   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4663      final r-factor (work) = 0.3775          |
| start r-factor (free) = 0.4538      final r-factor (free) = 0.4091          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.4870 = 12.40 * 0.50 * 6.2765 + 1.00 * 54.5873                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.4089 = 12.40 * 0.50 * 6.1737 + 1.00 * 0.1465                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3775      final r-factor (work) = 0.3309          |
| start r-factor (free) = 0.4091      final r-factor (free) = 0.3834          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2023 = 1.16 * 1.00 * 6.1737 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0958 = 1.16 * 1.00 * 6.0802 + 1.00 * 0.0170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.46   13.13    None  None   None       |
|    all(noH): 2823   0      0.00    74.46   13.13    None  None   None       |
|    Sol.    : 438    0      0.00    74.46   27.64    None  None   None       |
|    Mac.    : 2385   0      0.00    73.61   10.46    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 -   7.446: 1151   |   5:    37.228 -  44.674:   63        |
|      1:     7.446 -  14.891:  770   |   6:    44.674 -  52.119:   45        |
|      2:    14.891 -  22.337:  383   |   7:    52.119 -  59.565:   37        |
|      3:    22.337 -  29.782:  235   |   8:    59.565 -  67.010:    8        |
|      4:    29.782 -  37.228:  123   |   9:    67.010 -  74.456:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3309 r_free = 0.3834             target_work(ml) = 6.053         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3306 r_free = 0.3845             target_work(ml) = 6.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3306   r_free= 0.3845   ksol= 0.32   Bsol= 35.05   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.85,6.97,11.90,0.00,0.00,0.00); trace/3= 8.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.052712                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3289   r_free= 0.3818   ksol= 0.31   Bsol= 43.73   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.03,4.33,8.53,0.00,0.00,0.00); trace/3= 5.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.054207                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.167401              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.070   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.483361              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.146  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3289      final r-factor (work) = 0.2474          |
| start r-factor (free) = 0.3818      final r-factor (free) = 0.3065          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.9142 = 7.17 * 0.50 * 6.0741 + 1.00 * 0.1465                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3572 = 7.17 * 0.50 * 5.9350 + 1.00 * 0.0881                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2474      final r-factor (work) = 0.2273          |
| start r-factor (free) = 0.3065      final r-factor (free) = 0.2867          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8863 = 0.48 * 1.00 * 5.9350 + 1.00 * 0.0175                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9190 = 0.48 * 1.00 * 5.7761 + 1.00 * 0.1271                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.90   13.03    None  None   None       |
|    all(noH): 2823   0      0.00    98.90   13.03    None  None   None       |
|    Sol.    : 438    0      0.00    74.22   30.90    None  None   None       |
|    Mac.    : 2385   0      0.00    98.90   9.75     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.890: 1537   |   5:    49.449 -  59.339:   45        |
|      1:     9.890 -  19.780:  683   |   6:    59.339 -  69.228:    9        |
|      2:    19.780 -  29.669:  301   |   7:    69.228 -  79.118:    5        |
|      3:    29.669 -  39.559:  150   |   8:    79.118 -  89.008:    1        |
|      4:    39.559 -  49.449:   91   |   9:    89.008 -  98.898:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2273 r_free = 0.2867             target_work(ml) = 5.749         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2270 r_free = 0.2865             target_work(ml) = 5.748         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2270   r_free= 0.2865   ksol= 0.31   Bsol= 43.73   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.03,4.33,8.53,0.00,0.00,0.00); trace/3= 5.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.748281                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2254   r_free= 0.2862   ksol= 0.31   Bsol= 61.03   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.56,3.08,5.52,0.00,0.00,0.00); trace/3= 3.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.749515                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.245237              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.518  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.560487              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.123   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2254      final r-factor (work) = 0.1720          |
| start r-factor (free) = 0.2862      final r-factor (free) = 0.2256          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2469 = 5.25 * 0.50 * 5.7799 + 1.00 * 0.0884                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.8736 = 5.25 * 0.50 * 5.6402 + 1.00 * 0.0815                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1720      final r-factor (work) = 0.1487          |
| start r-factor (free) = 0.2256      final r-factor (free) = 0.2014          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.5303 = 2.56 * 1.00 * 5.6402 + 1.00 * 0.0887                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.9545 = 2.56 * 1.00 * 5.4431 + 1.00 * 0.0174                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.69   13.91    None  None   None       |
|    all(noH): 2823   0      0.00    93.69   13.91    None  None   None       |
|    Sol.    : 438    0      0.50    93.69   40.01    None  None   None       |
|    Mac.    : 2385   0      0.00    84.76   9.11     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.370: 1611   |   5:    46.847 -  56.217:   96        |
|      1:     9.370 -  18.739:  629   |   6:    56.217 -  65.586:   59        |
|      2:    18.739 -  28.108:  169   |   7:    65.586 -  74.956:   33        |
|      3:    28.108 -  37.478:  104   |   8:    74.956 -  84.325:   11        |
|      4:    37.478 -  46.847:  106   |   9:    84.325 -  93.695:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1487 r_free = 0.2014             target_work(ml) = 5.388         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1485 r_free = 0.2013             target_work(ml) = 5.388         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1485   r_free= 0.2013   ksol= 0.31   Bsol= 61.03   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.56,3.08,5.52,0.00,0.00,0.00); trace/3= 3.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.387966                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1484   r_free= 0.2007   ksol= 0.33   Bsol= 73.12   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.05,2.38,4.32,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.386213                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.587711              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.512  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.689651              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.600  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1484      final r-factor (work) = 0.1288          |
| start r-factor (free) = 0.2007      final r-factor (free) = 0.1795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8531 = 3.59 * 0.50 * 5.4472 + 1.00 * 0.0815                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6464 = 3.59 * 0.50 * 5.3312 + 1.00 * 0.0831                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1288      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1795      final r-factor (free) = 0.1742          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6939 = 0.69 * 1.00 * 5.3312 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6453 = 0.69 * 1.00 * 5.2588 + 1.00 * 0.0185                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.32   13.44    None  None   None       |
|    all(noH): 2823   0      0.00    99.32   13.44    None  None   None       |
|    Sol.    : 438    0      0.58    99.32   39.29    None  None   None       |
|    Mac.    : 2385   0      0.00    83.28   8.69     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.932: 1762   |   5:    49.662 -  59.594:   83        |
|      1:     9.932 -  19.865:  530   |   6:    59.594 -  69.527:   51        |
|      2:    19.865 -  29.797:  150   |   7:    69.527 -  79.459:   18        |
|      3:    29.797 -  39.729:  125   |   8:    79.459 -  89.391:    8        |
|      4:    39.729 -  49.662:   92   |   9:    89.391 -  99.324:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1247 r_free = 0.1742             target_work(ml) = 5.241         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1246 r_free = 0.1740             target_work(ml) = 5.241         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1740   ksol= 0.33   Bsol= 73.12   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.05,2.38,4.32,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.240659                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1740   ksol= 0.33   Bsol= 73.12   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.13,2.36,4.11,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.240613                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.925323              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.653  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.166607              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.224   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1195          |
| start r-factor (free) = 0.1740      final r-factor (free) = 0.1695          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7743 = 2.93 * 0.50 * 5.2584 + 1.00 * 0.0831                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7228 = 2.93 * 0.50 * 5.2250 + 1.00 * 0.0804                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1195      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1695      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1120 = 1.17 * 1.00 * 5.2250 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0902 = 1.17 * 1.00 * 5.2074 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.84  13.24    None  None   None       |
|    all(noH): 2823   0      0.00    102.84  13.24    None  None   None       |
|    Sol.    : 438    0      0.83    102.84  38.83    None  None   None       |
|    Mac.    : 2385   0      0.00    86.34   8.55     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 -  10.284: 1825   |   5:    51.421 -  61.706:   79        |
|      1:    10.284 -  20.569:  489   |   6:    61.706 -  71.990:   34        |
|      2:    20.569 -  30.853:  147   |   7:    71.990 -  82.274:   19        |
|      3:    30.853 -  41.137:  123   |   8:    82.274 -  92.558:    7        |
|      4:    41.137 -  51.421:   97   |   9:    92.558 - 102.843:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1186 r_free = 0.1694             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1186 r_free = 0.1694             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1694   ksol= 0.33   Bsol= 73.12   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.13,2.36,4.11,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206583                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8017 0.99   1389  152 0.1016 0.1390       5.426      5.5808|
|  2:  4.8017 -  3.8314 0.99   1331  152 0.0854 0.1173      5.4596      5.6965|
|  3:  3.8314 -  3.3530 0.99   1298  143 0.1097 0.1513      5.5171       5.853|
|  4:  3.3530 -  3.0491 0.99   1306  144 0.1262 0.1834      5.4903      5.6937|
|  5:  3.0491 -  2.8321 0.99   1283  146 0.1434 0.1623      5.4014      5.5551|
|  6:  2.8321 -  2.6660 0.99   1289  141 0.1301 0.2396      5.2817      5.6303|
|  7:  2.6660 -  2.5332 0.99   1281  143 0.1383 0.1666       5.252      5.3825|
|  8:  2.5332 -  2.4233 0.98   1276  137 0.1285 0.1814      5.1604      5.4442|
|  9:  2.4233 -  2.3304 0.98   1261  144 0.1263 0.1909      5.1137      5.3647|
| 10:  2.3304 -  2.2502 1.00   1279  143 0.1213 0.1829      5.0276      5.2687|
| 11:  2.2502 -  2.1801 0.97   1248  137 0.1245 0.1867      5.0174      5.2958|
| 12:  2.1801 -  2.1179 0.98   1256  142 0.1203 0.1955      4.9482      5.3123|
| 13:  2.1179 -  2.0623 0.99   1273  133 0.1223 0.1797      4.8613      5.0927|
| 14:  2.0623 -  2.0121 0.67    860  102 0.1076 0.1753       4.724      4.9746|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.8017  1389   152  0.94   9.89   0.96     0.94       8334.36|
|  2:  4.8017 -  3.8314  1331   152  0.95   8.56   1.00     0.98       9973.88|
|  3:  3.8314 -  3.3530  1298   143  0.93  11.83   1.02     1.02      11379.78|
|  4:  3.3530 -  3.0491  1306   144  0.91  14.34   1.00     0.98      11144.15|
|  5:  3.0491 -  2.8321  1283   146  0.89  16.92   1.00     0.97       9552.61|
|  6:  2.8321 -  2.6660  1289   141  0.89  17.62   0.98     0.95       8300.56|
|  7:  2.6660 -  2.5332  1281   143  0.89  17.23   0.98     0.94       7335.07|
|  8:  2.5332 -  2.4233  1276   137  0.89  16.91   0.98     0.95       6388.59|
|  9:  2.4233 -  2.3304  1261   144  0.90  16.72   1.00     0.95       5989.89|
| 10:  2.3304 -  2.2502  1279   143  0.89  17.01   0.99     0.94       5021.71|
| 11:  2.2502 -  2.1801  1248   137  0.89  17.45   0.98     0.94       5068.25|
| 12:  2.1801 -  2.1179  1256   142  0.89  17.19   0.99     0.98       4648.98|
| 13:  2.1179 -  2.0623  1273   133  0.89  17.74   0.98     0.95       3942.63|
| 14:  2.0623 -  2.0121   860   102  0.91  15.17   0.95     0.92       2872.35|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2872.35 max =        11379.78 mean =      7277.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.26|
|phase err.(test): min =        0.00 max =           89.68 mean =        14.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1688   ksol= 0.33   Bsol= 71.25   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.69,-0.51,1.21,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.204572                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1688   ksol= 0.33   Bsol= 71.25   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.69,-0.51,1.21,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.204572                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8017 0.99   1389  152 0.1001 0.1356      5.4045      5.5528|
|  2:  4.8017 -  3.8314 0.99   1331  152 0.0854 0.1138      5.4526      5.6801|
|  3:  3.8314 -  3.3530 0.99   1298  143 0.1096 0.1514      5.5141      5.8543|
|  4:  3.3530 -  3.0491 0.99   1306  144 0.1264 0.1852       5.492      5.7003|
|  5:  3.0491 -  2.8321 0.99   1283  146 0.1435 0.1623      5.4038      5.5545|
|  6:  2.8321 -  2.6660 0.99   1289  141 0.1301 0.2395      5.2824      5.6304|
|  7:  2.6660 -  2.5332 0.99   1281  143 0.1383 0.1668      5.2528      5.3831|
|  8:  2.5332 -  2.4233 0.98   1276  137 0.1284 0.1817       5.161      5.4458|
|  9:  2.4233 -  2.3304 0.98   1261  144 0.1262 0.1910      5.1138      5.3655|
| 10:  2.3304 -  2.2502 1.00   1279  143 0.1213 0.1829      5.0276      5.2692|
| 11:  2.2502 -  2.1801 0.97   1248  137 0.1245 0.1866      5.0173      5.2954|
| 12:  2.1801 -  2.1179 0.98   1256  142 0.1203 0.1955      4.9478      5.3117|
| 13:  2.1179 -  2.0623 0.99   1273  133 0.1223 0.1800      4.8613      5.0933|
| 14:  2.0623 -  2.0121 0.67    860  102 0.1077 0.1753      4.7243      4.9743|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.8017  1389   152  0.94   9.79   0.96     0.94       7936.70|
|  2:  4.8017 -  3.8314  1331   152  0.95   8.35   1.00     0.98       9642.37|
|  3:  3.8314 -  3.3530  1298   143  0.93  11.68   1.02     1.02      11224.95|
|  4:  3.3530 -  3.0491  1306   144  0.91  14.38   1.00     0.98      11199.11|
|  5:  3.0491 -  2.8321  1283   146  0.89  16.96   1.00     0.98       9609.08|
|  6:  2.8321 -  2.6660  1289   141  0.89  17.64   0.98     0.95       8314.14|
|  7:  2.6660 -  2.5332  1281   143  0.89  17.24   0.98     0.94       7344.64|
|  8:  2.5332 -  2.4233  1276   137  0.89  16.93   0.98     0.96       6402.72|
|  9:  2.4233 -  2.3304  1261   144  0.90  16.74   1.00     0.96       6002.25|
| 10:  2.3304 -  2.2502  1279   143  0.89  17.00   0.99     0.94       5020.99|
| 11:  2.2502 -  2.1801  1248   137  0.89  17.44   0.98     0.94       5065.89|
| 12:  2.1801 -  2.1179  1256   142  0.89  17.18   1.00     0.98       4646.16|
| 13:  2.1179 -  2.0623  1273   133  0.89  17.74   0.98     0.95       3942.69|
| 14:  2.0623 -  2.0121   860   102  0.91  15.18   0.96     0.92       2873.68|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2873.68 max =        11224.95 mean =      7221.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.24|
|phase err.(test): min =        0.00 max =           89.93 mean =        14.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.92    105.77  16.17    None  None   None       |
|    all(noH): 2823   0      2.92    105.77  16.17    None  None   None       |
|    Sol.    : 438    0      3.76    105.77  41.75    None  None   None       |
|    Mac.    : 2385   0      2.92    89.26   11.47    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:     2.923 -  13.207: 1825   |   5:    54.344 -  64.628:   79        |
|      1:    13.207 -  23.491:  489   |   6:    64.628 -  74.913:   34        |
|      2:    23.491 -  33.776:  147   |   7:    74.913 -  85.197:   19        |
|      3:    33.776 -  44.060:  123   |   8:    85.197 -  95.481:    7        |
|      4:    44.060 -  54.344:   97   |   9:    95.481 - 105.765:    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)= 325         
Filter by distance & map next to the model:
   mapped sites are within: 0.322 - 5.916
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 325
   mapped sites are within: 0.724 - 5.916

peak=   10.608 closest distance to " CB  VAL A 230 " =    1.432
peak=    5.961 closest distance to " CG  LEU A   5 " =    1.190
peak=    5.474 closest distance to " CB  GLN A 223 " =    1.516
peak=    5.430 closest distance to " CG  LEU A 228 " =    1.204
peak=    5.164 closest distance to " NE2 GLN A  11 " =    1.109
peak=    5.108 closest distance to " CB  VAL A 296 " =    1.053
peak=    5.093 closest distance to " NH2 ARG A  56 " =    2.179
peak=    5.019 closest distance to " CG2 VAL A 296 " =    1.041
peak=    4.951 closest distance to " O   HOH Z 142 " =    1.864
peak=    4.914 closest distance to " CB  GLN A 183 " =    1.304
peak=    4.782 closest distance to " CD2 LEU A   5 " =    1.112
peak=    4.770 closest distance to " CZ  PHE A 218 " =    1.129
peak=    4.678 closest distance to " O   HOH Z 425 " =    1.524
peak=    4.563 closest distance to " CB  ARG A 190 " =    1.459
peak=    4.538 closest distance to " O   HOH Z 369 " =    2.186
peak=    4.476 closest distance to " CG  PRO A 243 " =    1.127
peak=    4.455 closest distance to " O   HOH Z 232 " =    2.248
peak=    4.429 closest distance to " CA  ALA A  51 " =    0.984
peak=    4.428 closest distance to " O   HOH Z 368 " =    2.378
peak=    4.393 closest distance to " CB  SER A  63 " =    1.243
peak=    4.366 closest distance to " O   HOH Z   9 " =    1.530
peak=    4.357 closest distance to " O   HOH Z 427 " =    3.114
peak=    4.352 closest distance to " O   HOH Z 126 " =    1.662
peak=    4.322 closest distance to " CG  MET A 185 " =    1.227
peak=    4.311 closest distance to " CB  ASN A 142 " =    1.120
peak=    4.294 closest distance to " O   SER A  87 " =    2.400
peak=    4.292 closest distance to " CZ3 TRP A 266 " =    1.163
peak=    4.284 closest distance to " O   HOH Z 248 " =    1.530
peak=    4.267 closest distance to " O   HOH Z 188 " =    3.023
peak=    4.251 closest distance to " O   HOH Z 265 " =    2.046
peak=    4.250 closest distance to " CG  PRO A 198 " =    1.311
peak=    4.241 closest distance to " CB  ASP A 124 " =    0.814
peak=    4.215 closest distance to " O   HOH Z 359 " =    1.793
peak=    4.214 closest distance to " CB  GLU A 277 " =    3.768
peak=    4.198 closest distance to " O   HOH Z 303 " =    2.137
peak=    4.168 closest distance to " O  BHOH Z 338 " =    2.268
peak=    4.144 closest distance to " CB  ASN A 148 " =    1.417
peak=    4.115 closest distance to " O   HOH Z 346 " =    1.593
peak=    4.109 closest distance to " CA  TYR A  30 " =    1.000
peak=    4.094 closest distance to " CD  LYS A 166 " =    1.388
peak=    4.091 closest distance to " O   HOH Z 290 " =    1.073
peak=    4.072 closest distance to " O   HOH Z 214 " =    1.228
peak=    4.048 closest distance to " NH1AARG A 145 " =    1.229
peak=    4.047 closest distance to " CB  ASP A 140 " =    0.996
peak=    4.045 closest distance to " CG  PRO A 213 " =    1.188
peak=    4.042 closest distance to " CB  ARG A 275 " =    0.990
peak=    4.018 closest distance to " ND2 ASN A 187 " =    1.524
peak=    4.012 closest distance to " CE  LYS A  76 " =    0.888
peak=    3.982 closest distance to " O   HOH Z 411 " =    3.868
peak=    3.961 closest distance to " O   HOH Z 313 " =    1.826
peak=    3.946 closest distance to " CD  ARG A 159 " =    0.737
peak=    3.937 closest distance to " O   HOH Z 207 " =    1.214
peak=    3.932 closest distance to " CB  VAL A 202 " =    1.593
peak=    3.906 closest distance to " CB  ARG A  79 " =    1.535
peak=    3.904 closest distance to " CB  VAL A 265 " =    1.279
peak=    3.903 closest distance to " O   HOH Z 227 " =    1.769
peak=    3.902 closest distance to " CB  GLU A 128 " =    0.997
peak=    3.898 closest distance to " CB  VAL A 230 " =    1.211
peak=    3.867 closest distance to " CA  ALA A 295 " =    1.154
peak=    3.863 closest distance to " O   HOH Z 298 " =    1.931
peak=    3.844 closest distance to " O   HOH Z  59 " =    2.242
peak=    3.842 closest distance to " CB  TRP A 266 " =    1.088
peak=    3.833 closest distance to " CB  LEU A  83 " =    0.795
peak=    3.828 closest distance to " O   PRO A 198 " =    1.552
peak=    3.822 closest distance to " O   HOH Z 214 " =    2.494
peak=    3.817 closest distance to " O   HOH Z 126 " =    1.995
peak=    3.817 closest distance to " CD2 LEU A 228 " =    1.223
peak=    3.817 closest distance to " O   HOH Z  76 " =    1.220
peak=    3.815 closest distance to " O   HOH Z 251 " =    1.563
peak=    3.803 closest distance to " CA  ARG A 195 " =    1.212
peak=    3.798 closest distance to " O   HOH Z  19 " =    2.245
peak=    3.783 closest distance to " O   HOH Z  43 " =    2.034
peak=    3.761 closest distance to " CG  LEU A 167 " =    1.199
peak=    3.757 closest distance to " CD  ARG A  66 " =    2.587
peak=    3.754 closest distance to " CG1 VAL A 296 " =    1.234
peak=    3.754 closest distance to " CG2 ILE A 234 " =    0.970
peak=    3.751 closest distance to " CZ  PHE A  38 " =    1.207
peak=    3.746 closest distance to " O   HOH Z 158 " =    3.114
peak=    3.736 closest distance to " O   HOH Z 261 " =    1.714
peak=    3.736 closest distance to " O   HOH Z 258 " =    1.988
peak=    3.736 closest distance to " O   HOH Z 422 " =    2.609
peak=    3.732 closest distance to " CG  ARG A 138 " =    1.275
peak=    3.732 closest distance to " O   HOH Z  78 " =    1.636
peak=    3.730 closest distance to " O   HOH Z  21 " =    1.759
peak=    3.730 closest distance to " CB  GLU A  46 " =    0.944
peak=    3.724 closest distance to " O   HOH Z 287 " =    1.926
peak=    3.720 closest distance to " CD  ARG A 269 " =    0.938
peak=    3.717 closest distance to " CB  PRO A  54 " =    0.804
peak=    3.716 closest distance to " CG  GLU A  37 " =    0.962
peak=    3.714 closest distance to " NE2 HIS A 207 " =    1.208
peak=    3.710 closest distance to " O   HOH Z  49 " =    1.107
peak=    3.709 closest distance to " CA  TYR A 116 " =    1.406
peak=    3.708 closest distance to " O   HOH Z 128 " =    1.054
peak=    3.690 closest distance to " O   HOH Z 193 " =    2.033
peak=    3.687 closest distance to " CB  ALA A   9 " =    1.680
peak=    3.686 closest distance to " CB AVAL A  41 " =    1.253
peak=    3.685 closest distance to " CB  TRP A 150 " =    1.336
peak=    3.679 closest distance to " O   ASP A 124 " =    1.175
peak=    3.679 closest distance to " O   HOH Z 406 " =    1.562
peak=    3.672 closest distance to " CA  ALA A 160 " =    1.042
peak=    3.671 closest distance to " CB  GLN A  89 " =    1.206
peak=    3.669 closest distance to " CA  ARG A  36 " =    1.166
peak=    3.661 closest distance to " O   HOH Z 280 " =    3.004
peak=    3.660 closest distance to " O   HOH Z 353 " =    2.563
peak=    3.655 closest distance to " CB  GLU A 152 " =    1.227
peak=    3.654 closest distance to " CD1 LEU A  96 " =    0.850
peak=    3.654 closest distance to " O   HOH Z  80 " =    1.802
peak=    3.638 closest distance to " CD ALYS A 290 " =    1.024
peak=    3.638 closest distance to " CB  LYS A 117 " =    1.213
peak=    3.636 closest distance to " N   ASN A  39 " =    1.260
peak=    3.630 closest distance to " N   PHE A 130 " =    1.271
peak=    3.628 closest distance to " CG AARG A 275 " =    1.359
peak=    3.622 closest distance to " NE2 GLN A  77 " =    3.420
peak=    3.620 closest distance to " O   HOH Z 234 " =    3.588
peak=    3.612 closest distance to " CG2 THR A 221 " =    1.141
peak=    3.610 closest distance to " CB  ASN A  39 " =    0.974
peak=    3.608 closest distance to " O   HOH Z 199 " =    1.606
peak=    3.607 closest distance to " O   HOH Z 365 " =    2.865
peak=    3.606 closest distance to " CA  VAL A 125 " =    1.178
peak=    3.603 closest distance to " CA  SER A  87 " =    0.952
peak=    3.594 closest distance to " CG2 VAL A 257 " =    0.850
peak=    3.588 closest distance to " O   HOH Z 261 " =    1.933
peak=    3.587 closest distance to " O   HOH Z 193 " =    1.638
peak=    3.586 closest distance to " O   HOH Z 213 " =    1.921
peak=    3.579 closest distance to " CD2 TRP A 179 " =    1.283
peak=    3.573 closest distance to " O   HOH Z  44 " =    2.787
peak=    3.562 closest distance to " N   ALA A 256 " =    1.212
peak=    3.557 closest distance to " CD1 ILE A 199 " =    0.975
peak=    3.545 closest distance to " O   HOH Z 272 " =    1.865
peak=    3.541 closest distance to " CD1 ILE A  33 " =    1.848
peak=    3.536 closest distance to " O   HOH Z 180 " =    2.161
peak=    3.536 closest distance to " CA  ALA A 100 " =    0.895
peak=    3.536 closest distance to " CG1 ILE A  49 " =    1.539
peak=    3.535 closest distance to " CG1 VAL A 153 " =    0.971
peak=    3.531 closest distance to " NH2AARG A 145 " =    1.137
peak=    3.530 closest distance to " O   ALA A 158 " =    1.354
peak=    3.529 closest distance to " CA  ALA A 291 " =    0.906
peak=    3.528 closest distance to " CG  PHE A 204 " =    0.913
peak=    3.523 closest distance to " OE2 GLU A  53 " =    2.019
peak=    3.519 closest distance to " CE3 TRP A 150 " =    1.106
peak=    3.514 closest distance to " OD1 ASN A  69 " =    2.597
peak=    3.508 closest distance to " O   HOH Z 368 " =    3.432
peak=    3.504 closest distance to " CD1 LEU A 300 " =    1.161
peak=    3.501 closest distance to " O   HOH Z  68 " =    2.083
peak=    3.497 closest distance to " CB  SER A 212 " =    1.302
peak=    3.494 closest distance to " O   ALA A 165 " =    1.437
peak=    3.493 closest distance to " O   HOH Z 316 " =    3.174
peak=    3.492 closest distance to " CA  GLY A 267 " =    0.775
peak=    3.482 closest distance to " O   HOH Z 203 " =    1.699
peak=    3.479 closest distance to " O  BHOH Z  74 " =    1.252
peak=    3.477 closest distance to " CA  ASN A 127 " =    1.109
peak=    3.475 closest distance to " CG  ARG A 269 " =    1.858
peak=    3.473 closest distance to " O   HOH Z 361 " =    3.765
peak=    3.471 closest distance to " O   HOH Z 184 " =    1.392
peak=    3.468 closest distance to " O   HOH Z 423 " =    1.751
peak=    3.459 closest distance to " CA  ASP A 162 " =    0.973
peak=    3.458 closest distance to " CB  SER A  62 " =    0.894
peak=    3.457 closest distance to " O   HOH Z 171 " =    3.977
peak=    3.457 closest distance to " O   HOH Z 438 " =    2.929
peak=    3.457 closest distance to " CB  PRO A  90 " =    1.242
peak=    3.451 closest distance to " CB  ARG A 138 " =    0.975
peak=    3.449 closest distance to " O   MET A 105 " =    1.787
peak=    3.446 closest distance to " CA  TYR A  30 " =    1.074
peak=    3.441 closest distance to " O   HOH Z 371 " =    2.875
peak=    3.441 closest distance to " CD1 LEU A   5 " =    1.296
peak=    3.438 closest distance to " NZ  LYS A 117 " =    3.133
peak=    3.433 closest distance to " O   ASP A 200 " =    1.626
peak=    3.432 closest distance to " CB  ASP A 298 " =    1.174
peak=    3.430 closest distance to " CB  SER A 273 " =    0.915
peak=    3.429 closest distance to " ND2 ASN A 249 " =    1.881
peak=    3.428 closest distance to " O   HOH Z   4 " =    1.715
peak=    3.428 closest distance to " CG  MET A 185 " =    1.041
peak=    3.425 closest distance to " OE1 GLN A  55 " =    1.385
peak=    3.425 closest distance to " CB  ASN A 215 " =    1.231
peak=    3.423 closest distance to " CB  THR A  82 " =    1.306
peak=    3.421 closest distance to " OG BSER A 164 " =    2.305
peak=    3.412 closest distance to " CA  MET A 105 " =    1.069
peak=    3.406 closest distance to " O   HOH Z 313 " =    1.454
peak=    3.402 closest distance to " CD2 LEU A 255 " =    1.738
peak=    3.400 closest distance to " CA  LEU A 282 " =    1.184
peak=    3.399 closest distance to " O   HOH Z  63 " =    1.818
peak=    3.396 closest distance to " O   HOH Z 285 " =    2.033
peak=    3.394 closest distance to " ND1 HIS A  81 " =    1.755
peak=    3.394 closest distance to " ND2 ASN A 249 " =    0.865
peak=    3.393 closest distance to " NZ  LYS A  48 " =    1.246
peak=    3.382 closest distance to " CB  LEU A 143 " =    1.260
peak=    3.381 closest distance to " O   ASN A  74 " =    1.445
peak=    3.378 closest distance to " CB  THR A  52 " =    0.825
peak=    3.377 closest distance to " CA  ALA A 158 " =    1.228
peak=    3.375 closest distance to " CG  GLN A  58 " =    1.002
peak=    3.375 closest distance to " OG BSER A 134 " =    2.869
peak=    3.371 closest distance to " CB  THR A  31 " =    1.652
peak=    3.370 closest distance to " O   HOH Z 329 " =    4.219
peak=    3.367 closest distance to " CB  GLN A 205 " =    1.021
peak=    3.366 closest distance to " O   PHE A 192 " =    1.396
peak=    3.365 closest distance to " CG2 ILE A  20 " =    1.501
peak=    3.365 closest distance to " OG  SER A 245 " =    1.666
peak=    3.364 closest distance to " O   HOH Z  30 " =    1.305
peak=    3.363 closest distance to " CA  GLU A 152 " =    0.924
peak=    3.363 closest distance to " CE1 TYR A 186 " =    1.192
peak=    3.347 closest distance to " CB  TRP A 179 " =    1.397
peak=    3.346 closest distance to " CB  TYR A 116 " =    1.018
peak=    3.345 closest distance to " CH2 TRP A  70 " =    1.004
peak=    3.342 closest distance to " O   HOH Z 417 " =    3.161
peak=    3.341 closest distance to " CB  SER A   3 " =    1.448
peak=    3.337 closest distance to " O   HOH Z  61 " =    1.709
peak=    3.325 closest distance to " O   HOH Z  88 " =    3.571
peak=    3.323 closest distance to " OG  SER A  62 " =    2.943
peak=    3.322 closest distance to " CG AARG A 102 " =    1.123
peak=    3.314 closest distance to " CG1 ILE A 151 " =    1.110
peak=    3.312 closest distance to " O   HOH Z  40 " =    1.780
peak=    3.310 closest distance to " O   GLN A  88 " =    1.679
peak=    3.307 closest distance to " O   HOH Z 148 " =    3.369
peak=    3.305 closest distance to " CA  ARG A 139 " =    1.131
peak=    3.302 closest distance to " CB  PRO A 243 " =    1.612
peak=    3.298 closest distance to " CG  MET A 113 " =    1.814
peak=    3.297 closest distance to " CA  ALA A 129 " =    1.459
peak=    3.296 closest distance to " CD  ARG A 219 " =    1.084
peak=    3.293 closest distance to " O   HOH Z 368 " =    4.111
peak=    3.292 closest distance to " CA  ASP A 124 " =    0.772
peak=    3.292 closest distance to " O   HOH Z  97 " =    2.091
peak=    3.288 closest distance to " CB  GLN A  88 " =    1.250
peak=    3.288 closest distance to " OD2 ASP A  65 " =    2.834
peak=    3.285 closest distance to " O   HOH Z 391 " =    2.966
peak=    3.283 closest distance to " CB  ASN A 110 " =    1.162
peak=    3.282 closest distance to " O   HOH Z 172 " =    3.919
peak=    3.281 closest distance to " O   THR A 220 " =    1.228
peak=    3.277 closest distance to " O   HOH Z  78 " =    1.849
peak=    3.277 closest distance to " O   HOH Z  20 " =    1.460
peak=    3.276 closest distance to " O   HOH Z   3 " =    1.726
peak=    3.275 closest distance to " CB  GLU A  37 " =    0.940
peak=    3.275 closest distance to " NH2AARG A 275 " =    3.248
peak=    3.274 closest distance to " OG1 THR A 279 " =    1.498
peak=    3.274 closest distance to " CB  SER A 288 " =    1.422
peak=    3.273 closest distance to " O   HOH Z 211 " =    1.237
peak=    3.267 closest distance to " CD  GLU A 152 " =    0.863
peak=    3.267 closest distance to " CE  LYS A  48 " =    1.192
peak=    3.265 closest distance to " CB  MET A  40 " =    0.810
peak=    3.264 closest distance to " CB  ASN A 187 " =    1.145
peak=    3.263 closest distance to " CA  ASP A 140 " =    1.638
peak=    3.262 closest distance to " CB  LEU A 228 " =    1.247
peak=    3.259 closest distance to " O   THR A 251 " =    1.176
peak=    3.259 closest distance to " C   ALA A 299 " =    0.857
peak=    3.256 closest distance to " O   HOH Z 393 " =    3.098
peak=    3.256 closest distance to " O   HOH Z 148 " =    2.077
peak=    3.255 closest distance to " CB  ALA A 291 " =    1.079
peak=    3.254 closest distance to " CA  ASN A 215 " =    1.085
peak=    3.247 closest distance to " O   HOH Z 291 " =    1.511
peak=    3.246 closest distance to " CB  LEU A 300 " =    0.829
peak=    3.240 closest distance to " OH  TYR A 247 " =    1.134
peak=    3.237 closest distance to " CB  ALA A 242 " =    0.794
peak=    3.236 closest distance to " O   HOH Z 403 " =    1.607
peak=    3.235 closest distance to " CA  ALA A 184 " =    1.152
peak=    3.234 closest distance to " CG1BVAL A  72 " =    1.787
peak=    3.233 closest distance to " CB  ALA A 248 " =    1.158
peak=    3.229 closest distance to " O   HOH Z  88 " =    3.052
peak=    3.228 closest distance to " CA  ASP A 191 " =    1.282
peak=    3.225 closest distance to " NE  ARG A  79 " =    1.118
peak=    3.223 closest distance to " CB  TYR A 247 " =    1.013
peak=    3.220 closest distance to " CB  ALA A 104 " =    0.779
peak=    3.219 closest distance to " CB  VAL A 268 " =    0.861
peak=    3.217 closest distance to " O   GLU A   2 " =    1.640
peak=    3.217 closest distance to " O   HOH Z 133 " =    1.339
peak=    3.214 closest distance to " CB  VAL A 257 " =    0.792
peak=    3.212 closest distance to " O   HOH Z 420 " =    5.916
peak=    3.212 closest distance to " O   HOH Z 394 " =    3.861
peak=    3.212 closest distance to " O   HOH Z 263 " =    1.647
peak=    3.210 closest distance to " O   HOH Z 109 " =    2.870
peak=    3.210 closest distance to " O   HOH Z 299 " =    4.357
peak=    3.209 closest distance to " CZ3 TRP A 274 " =    4.585
peak=    3.209 closest distance to " O   HOH Z 133 " =    2.835
peak=    3.208 closest distance to " CG2 ILE A 151 " =    0.796
peak=    3.205 closest distance to " CZ  PHE A 192 " =    0.983
peak=    3.205 closest distance to " CB  ASP A 171 " =    1.169
peak=    3.204 closest distance to " CB  SER A 216 " =    0.893
peak=    3.197 closest distance to " O   HOH Z  44 " =    1.990
peak=    3.196 closest distance to " CA  ALA A 180 " =    1.357
peak=    3.195 closest distance to " N   CYS A 260 " =    0.724
peak=    3.192 closest distance to " OG  SER A  62 " =    2.906
peak=    3.190 closest distance to " O   HOH Z 383 " =    1.845
peak=    3.187 closest distance to " CB  ALA A 227 " =    1.058
peak=    3.186 closest distance to " CD  LYS A 119 " =    2.136
peak=    3.185 closest distance to " CA  ALA A 154 " =    1.075
peak=    3.183 closest distance to " O   THR A 182 " =    1.428
peak=    3.177 closest distance to " O   HOH Z 215 " =    2.926
peak=    3.177 closest distance to " O   HOH Z 116 " =    1.806
peak=    3.172 closest distance to " O   HOH Z 340 " =    2.135
peak=    3.171 closest distance to " CG  ARG A 159 " =    0.940
peak=    3.170 closest distance to " O   HOH Z 327 " =    2.261
peak=    3.170 closest distance to " O   HOH Z  10 " =    1.816
peak=    3.163 closest distance to " CB  ALA A   1 " =    4.914
peak=    3.162 closest distance to " O   HOH Z 128 " =    1.999
peak=    3.153 closest distance to " CB  ASN A 285 " =    1.044
peak=    3.153 closest distance to " CZ3 TRP A  85 " =    1.145
peak=    3.152 closest distance to " CA  LEU A  83 " =    1.201
peak=    3.151 closest distance to " CA  ILE A 106 " =    0.791
peak=    3.149 closest distance to " CG2AVAL A 121 " =    2.366
peak=    3.149 closest distance to " O   CYS A 168 " =    1.224
peak=    3.141 closest distance to " O   PRO A 213 " =    1.511
peak=    3.140 closest distance to " OG  SER A  22 " =    2.864
peak=    3.138 closest distance to " CB  SER A 210 " =    0.810
peak=    3.135 closest distance to " CA  ALA A  21 " =    1.135
peak=    3.134 closest distance to " O   PHE A  61 " =    1.377
peak=    3.133 closest distance to " O   HOH Z 171 " =    3.869
peak=    3.122 closest distance to " CG BARG A 102 " =    1.910
peak=    3.122 closest distance to " CB  LEU A  96 " =    1.304
peak=    3.121 closest distance to " OD1 ASN A 217 " =    1.561
peak=    3.120 closest distance to " CG1 ILE A  33 " =    1.232
peak=    3.119 closest distance to " O   HOH Z 305 " =    3.579
peak=    3.117 closest distance to " N   ARG A  66 " =    1.491
peak=    3.107 closest distance to " O   HOH Z 128 " =    0.968
peak=    3.103 closest distance to " CB  ALA A  43 " =    0.855
peak=    3.098 closest distance to " CA  GLN A  94 " =    0.762
peak=    3.079 closest distance to " CD  LYS A  76 " =    1.964
peak=    3.053 closest distance to " O   HOH Z 183 " =    1.269
peak=    3.045 closest distance to " N   ALA A   7 " =    1.243
peak=    3.034 closest distance to " N   ASP A 162 " =    1.236
peak=    3.021 closest distance to " O   HOH Z 238 " =    3.634
peak=    3.015 closest distance to " O   HOH Z   3 " =    1.962

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.678 - 5.646
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 216
   mapped sites are within: 0.722 - 5.646

peak=   -4.863 closest distance to " CG2 VAL A 230 " =    0.779
peak=   -4.606 closest distance to " CD  ARG A  14 " =    3.279
peak=   -4.492 closest distance to " CB  PRO A 243 " =    2.756
peak=   -4.372 closest distance to " CD  GLN A  58 " =    0.978
peak=   -4.359 closest distance to " CD  ARG A 156 " =    2.125
peak=   -4.249 closest distance to " CG1 VAL A 112 " =    2.659
peak=   -4.219 closest distance to " O   HOH Z 193 " =    1.226
peak=   -4.120 closest distance to " OE1 GLN A 223 " =    2.323
peak=   -4.116 closest distance to " O   HOH Z 196 " =    2.272
peak=   -4.076 closest distance to " CA  ASP A 298 " =    1.082
peak=   -4.058 closest distance to " O   VAL A  67 " =    2.722
peak=   -4.051 closest distance to " CG1 VAL A 296 " =    1.202
peak=   -4.035 closest distance to " O   HOH Z 411 " =    5.511
peak=   -4.007 closest distance to " O   HOH Z 166 " =    1.868
peak=   -4.004 closest distance to " CG1 VAL A 250 " =    2.751
peak=   -3.991 closest distance to " O   HOH Z  73 " =    2.506
peak=   -3.974 closest distance to " CZ2 TRP A  92 " =    2.837
peak=   -3.929 closest distance to " CA  GLY A 241 " =    2.356
peak=   -3.908 closest distance to " O   SER A 271 " =    2.195
peak=   -3.891 closest distance to " OG BSER A 134 " =    1.434
peak=   -3.861 closest distance to " CB  VAL A 230 " =    1.124
peak=   -3.816 closest distance to " O   ILE A 109 " =    2.549
peak=   -3.814 closest distance to " CE3 TRP A  70 " =    1.809
peak=   -3.812 closest distance to " OE1 GLN A  88 " =    1.016
peak=   -3.808 closest distance to " C   HIS A 108 " =    1.220
peak=   -3.807 closest distance to " OG  SER A  97 " =    2.356
peak=   -3.799 closest distance to " CE2 TYR A  30 " =    2.629
peak=   -3.790 closest distance to " O   HOH Z 110 " =    1.160
peak=   -3.784 closest distance to " CE3 TRP A 150 " =    2.250
peak=   -3.780 closest distance to " CG2 VAL A 296 " =    1.146
peak=   -3.777 closest distance to " O   HOH Z 231 " =    2.136
peak=   -3.761 closest distance to " O   HOH Z 133 " =    1.088
peak=   -3.759 closest distance to " CD1 LEU A 101 " =    2.476
peak=   -3.754 closest distance to " O   VAL A  67 " =    2.791
peak=   -3.736 closest distance to " CB  HIS A  86 " =    1.162
peak=   -3.716 closest distance to " O   HOH Z  10 " =    1.558
peak=   -3.711 closest distance to " CG1 VAL A 112 " =    2.815
peak=   -3.711 closest distance to " O   MET A  40 " =    2.856
peak=   -3.701 closest distance to " CG2 VAL A 202 " =    2.799
peak=   -3.694 closest distance to " CD2 TYR A 293 " =    1.965
peak=   -3.689 closest distance to " C   ALA A 158 " =    1.312
peak=   -3.682 closest distance to " O   HOH Z 394 " =    1.583
peak=   -3.681 closest distance to " O   HOH Z 238 " =    0.999
peak=   -3.658 closest distance to " O   HOH Z 351 " =    1.619
peak=   -3.648 closest distance to " N   ALA A 226 " =    2.129
peak=   -3.646 closest distance to " O   PRO A 198 " =    1.267
peak=   -3.646 closest distance to " CG  ARG A 269 " =    2.316
peak=   -3.644 closest distance to " OD1 ASN A 148 " =    1.396
peak=   -3.627 closest distance to " CE2 TRP A  70 " =    2.294
peak=   -3.617 closest distance to " C   LEU A 143 " =    1.146
peak=   -3.608 closest distance to " O   HOH Z 198 " =    2.199
peak=   -3.606 closest distance to " O   ALA A 227 " =    1.445
peak=   -3.606 closest distance to " O   HOH Z  38 " =    1.876
peak=   -3.600 closest distance to " O   HOH Z 251 " =    4.958
peak=   -3.592 closest distance to " CG2 THR A 178 " =    2.399
peak=   -3.586 closest distance to " CG1 VAL A 125 " =    1.835
peak=   -3.582 closest distance to " CD2 PHE A  61 " =    2.061
peak=   -3.580 closest distance to " O   PRO A 163 " =    2.243
peak=   -3.570 closest distance to " O   GLY A  17 " =    1.261
peak=   -3.562 closest distance to " O   ASP A  27 " =    1.978
peak=   -3.558 closest distance to " O   VAL A 189 " =    2.700
peak=   -3.558 closest distance to " O   HOH Z 176 " =    0.722
peak=   -3.557 closest distance to " O   HOH Z  52 " =    1.636
peak=   -3.553 closest distance to " N   THR A  52 " =    1.603
peak=   -3.552 closest distance to " O   HOH Z 216 " =    1.086
peak=   -3.549 closest distance to " CA  GLY A 241 " =    3.233
peak=   -3.546 closest distance to " OG  SER A  62 " =    4.360
peak=   -3.544 closest distance to " O   HOH Z 359 " =    2.871
peak=   -3.544 closest distance to " CH2 TRP A 179 " =    1.212
peak=   -3.536 closest distance to " CD  GLN A 223 " =    1.434
peak=   -3.534 closest distance to " O   HOH Z  93 " =    2.178
peak=   -3.529 closest distance to " C   ARG A  79 " =    2.685
peak=   -3.524 closest distance to " CD1 ILE A 151 " =    2.480
peak=   -3.516 closest distance to " O   TYR A 186 " =    1.873
peak=   -3.510 closest distance to " O   HOH Z 103 " =    1.830
peak=   -3.506 closest distance to " O   HOH Z 149 " =    2.136
peak=   -3.505 closest distance to " CZ  PHE A  38 " =    2.587
peak=   -3.498 closest distance to " CG2 ILE A 263 " =    2.429
peak=   -3.497 closest distance to " O   HOH Z 275 " =    1.602
peak=   -3.489 closest distance to " O   HOH Z 426 " =    1.694
peak=   -3.485 closest distance to " ND2 ASN A  45 " =    2.198
peak=   -3.475 closest distance to " CB  PHE A 192 " =    1.935
peak=   -3.473 closest distance to " O   HOH Z  68 " =    1.402
peak=   -3.472 closest distance to " CG  GLU A 277 " =    1.254
peak=   -3.463 closest distance to " O   HOH Z 407 " =    3.008
peak=   -3.462 closest distance to " O   HOH Z 185 " =    2.433
peak=   -3.461 closest distance to " NE2 GLN A 194 " =    1.936
peak=   -3.460 closest distance to " O   HOH Z 377 " =    1.979
peak=   -3.450 closest distance to " CB  TRP A  85 " =    2.704
peak=   -3.448 closest distance to " CE BMET A  47 " =    1.564
peak=   -3.448 closest distance to " N   ALA A  43 " =    2.678
peak=   -3.441 closest distance to " CA  GLY A 203 " =    2.550
peak=   -3.432 closest distance to " O   HOH Z 111 " =    1.626
peak=   -3.428 closest distance to " O   SER A 210 " =    1.767
peak=   -3.426 closest distance to " CG2 VAL A 189 " =    2.053
peak=   -3.417 closest distance to " O   HOH Z 290 " =    1.301
peak=   -3.417 closest distance to " CG  PRO A 198 " =    2.026
peak=   -3.412 closest distance to " CA  GLY A 133 " =    2.291
peak=   -3.412 closest distance to " O   HOH Z 236 " =    1.456
peak=   -3.396 closest distance to " CB  ALA A 248 " =    2.160
peak=   -3.390 closest distance to " C   MET A 188 " =    1.475
peak=   -3.390 closest distance to " CB  ALA A 248 " =    2.312
peak=   -3.380 closest distance to " CB  ALA A  43 " =    2.677
peak=   -3.375 closest distance to " CE2 PHE A  61 " =    2.644
peak=   -3.375 closest distance to " CA  GLY A  98 " =    2.086
peak=   -3.365 closest distance to " CD1 TRP A 274 " =    0.991
peak=   -3.365 closest distance to " O   HOH Z 102 " =    1.653
peak=   -3.362 closest distance to " CD2 HIS A 207 " =    2.192
peak=   -3.351 closest distance to " O   HOH Z 177 " =    1.912
peak=   -3.350 closest distance to " CG  LEU A   5 " =    1.595
peak=   -3.345 closest distance to " CG  PRO A 163 " =    2.219
peak=   -3.343 closest distance to " O   HOH Z 435 " =    2.797
peak=   -3.342 closest distance to " O   HOH Z 434 " =    1.689
peak=   -3.337 closest distance to " OXT GLY A 302 " =    3.130
peak=   -3.330 closest distance to " ND2 ASN A 249 " =    2.458
peak=   -3.328 closest distance to " CG  GLN A  11 " =    1.700
peak=   -3.327 closest distance to " O   HOH Z 128 " =    2.614
peak=   -3.324 closest distance to " CD1 TYR A 247 " =    2.366
peak=   -3.322 closest distance to " CD  LYS A 289 " =    2.425
peak=   -3.321 closest distance to " CD1 ILE A  33 " =    2.567
peak=   -3.311 closest distance to " O   HOH Z 285 " =    2.139
peak=   -3.302 closest distance to " O   HOH Z 252 " =    3.701
peak=   -3.297 closest distance to " CG  GLU A  53 " =    1.701
peak=   -3.297 closest distance to " O   HOH Z  11 " =    1.814
peak=   -3.295 closest distance to " O   HOH Z 100 " =    1.225
peak=   -3.295 closest distance to " O   GLN A 240 " =    2.525
peak=   -3.295 closest distance to " CD1 LEU A   5 " =    2.522
peak=   -3.292 closest distance to " CG1 VAL A 112 " =    2.751
peak=   -3.292 closest distance to " CG2BVAL A  41 " =    1.834
peak=   -3.291 closest distance to " CD2 PHE A 225 " =    1.138
peak=   -3.289 closest distance to " CD2 LEU A 237 " =    2.808
peak=   -3.288 closest distance to " O   HOH Z 191 " =    5.646
peak=   -3.288 closest distance to " O   HOH Z 295 " =    1.675
peak=   -3.287 closest distance to " O   HOH Z 265 " =    2.517
peak=   -3.277 closest distance to " O   VAL A 189 " =    1.805
peak=   -3.277 closest distance to " N   PHE A  59 " =    2.014
peak=   -3.272 closest distance to " O   GLY A 211 " =    1.406
peak=   -3.270 closest distance to " O   HOH Z 131 " =    4.004
peak=   -3.268 closest distance to " NH2AARG A 275 " =    5.333
peak=   -3.266 closest distance to " O   PHE A 218 " =    1.531
peak=   -3.263 closest distance to " OD1 ASP A 171 " =    1.620
peak=   -3.254 closest distance to " CE  LYS A  76 " =    2.644
peak=   -3.254 closest distance to " CD  PRO A 243 " =    1.936
peak=   -3.253 closest distance to " O   HOH Z 431 " =    2.005
peak=   -3.253 closest distance to " CE3 TRP A 274 " =    2.530
peak=   -3.250 closest distance to " CG1 VAL A  67 " =    2.875
peak=   -3.250 closest distance to " ND2 ASN A  45 " =    1.226
peak=   -3.250 closest distance to " O   HOH Z 100 " =    1.070
peak=   -3.247 closest distance to " O   HOH Z 348 " =    2.217
peak=   -3.231 closest distance to " O   HOH Z 145 " =    1.083
peak=   -3.231 closest distance to " OD2 ASP A 171 " =    1.827
peak=   -3.228 closest distance to " O   HOH Z  19 " =    2.201
peak=   -3.228 closest distance to " CD2 LEU A 167 " =    1.874
peak=   -3.224 closest distance to " OG  SER A  87 " =    1.568
peak=   -3.222 closest distance to " O   HOH Z 140 " =    1.609
peak=   -3.222 closest distance to " CD1 LEU A 228 " =    2.372
peak=   -3.217 closest distance to " O   HOH Z   9 " =    1.657
peak=   -3.217 closest distance to " CB  HIS A  81 " =    1.018
peak=   -3.210 closest distance to " CG  PRO A 243 " =    1.660
peak=   -3.210 closest distance to " CG1BVAL A  72 " =    2.606
peak=   -3.210 closest distance to " O   HOH Z 411 " =    1.676
peak=   -3.209 closest distance to " O   HOH Z  17 " =    1.581
peak=   -3.208 closest distance to " OG  SER A 141 " =    1.786
peak=   -3.206 closest distance to " O   HOH Z 231 " =    1.534
peak=   -3.205 closest distance to " OG BSER A 210 " =    1.638
peak=   -3.190 closest distance to " CG  ARG A 259 " =    2.426
peak=   -3.190 closest distance to " CG  TRP A 266 " =    1.792
peak=   -3.189 closest distance to " O   HOH Z 259 " =    3.982
peak=   -3.189 closest distance to " NE2 GLN A 103 " =    1.722
peak=   -3.189 closest distance to " CB  PHE A  16 " =    2.422
peak=   -3.185 closest distance to " CE1 TYR A 247 " =    2.689
peak=   -3.185 closest distance to " CG  GLN A 103 " =    2.469
peak=   -3.184 closest distance to " CG  ASP A 231 " =    0.918
peak=   -3.182 closest distance to " O   HOH Z 105 " =    3.374
peak=   -3.181 closest distance to " O   HOH Z 393 " =    1.273
peak=   -3.181 closest distance to " CD  PRO A 213 " =    2.163
peak=   -3.166 closest distance to " ND2 ASN A  69 " =    1.957
peak=   -3.164 closest distance to " CZ  TYR A 169 " =    1.817
peak=   -3.161 closest distance to " O   HOH Z 136 " =    2.616
peak=   -3.156 closest distance to " OH  TYR A 214 " =    1.234
peak=   -3.153 closest distance to " O   HOH Z  17 " =    1.531
peak=   -3.153 closest distance to " O   HOH Z 292 " =    1.712
peak=   -3.152 closest distance to " N   LYS A 166 " =    1.906
peak=   -3.144 closest distance to " N   SER A 276 " =    1.490
peak=   -3.143 closest distance to " OD2 ASP A  27 " =    1.708
peak=   -3.142 closest distance to " CB  TYR A  15 " =    2.246
peak=   -3.141 closest distance to " O   HOH Z 234 " =    4.362
peak=   -3.140 closest distance to " CD1 ILE A 199 " =    2.498
peak=   -3.139 closest distance to " O   HOH Z  43 " =    1.633
peak=   -3.139 closest distance to " OH  TYR A 247 " =    1.840
peak=   -3.139 closest distance to " OG BSER A 134 " =    1.966
peak=   -3.137 closest distance to " NE2 GLN A 240 " =    1.617
peak=   -3.135 closest distance to " O   HOH Z 244 " =    1.526
peak=   -3.132 closest distance to " NH2 ARG A  79 " =    1.526
peak=   -3.124 closest distance to " CB  PRO A 163 " =    2.453
peak=   -3.123 closest distance to " CB  PRO A 163 " =    2.485
peak=   -3.116 closest distance to " N   ALA A 248 " =    1.846
peak=   -3.113 closest distance to " O   HOH Z 353 " =    2.072
peak=   -3.112 closest distance to " O   HOH Z  78 " =    1.980
peak=   -3.111 closest distance to " O   HOH Z 357 " =    2.222
peak=   -3.109 closest distance to " O   ALA A 180 " =    1.493
peak=   -3.106 closest distance to " O   ALA A  10 " =    1.767
peak=   -3.106 closest distance to " OG  SER A  63 " =    1.100
peak=   -3.105 closest distance to " O   HOH Z 350 " =    1.939
peak=   -3.104 closest distance to " CE  MET A 105 " =    2.546
peak=   -3.099 closest distance to " CA  SER A 135 " =    1.217
peak=   -3.098 closest distance to " N   ASP A 171 " =    2.413
peak=   -3.087 closest distance to " O   HOH Z   6 " =    1.617
peak=   -3.086 closest distance to " CD  GLN A  88 " =    0.878
peak=   -3.084 closest distance to " O   HOH Z 341 " =    1.061
peak=   -3.080 closest distance to " OD1 ASN A 173 " =    1.386
peak=   -3.080 closest distance to " O   HOH Z 189 " =    2.423
peak=   -3.075 closest distance to " C   PHE A  59 " =    1.309
peak=   -3.044 closest distance to " CA  GLY A 241 " =    2.908
peak=   -3.024 closest distance to " N   ALA A 248 " =    2.447

================= 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    :  0.4750 0.4680   6.276205e+00   6.260614e+00
   1_bss:  0.4663 0.4538   6.270331e+00   6.249096e+00
   1_xyz:  0.3775 0.4091   6.146713e+00   6.181665e+00
   1_adp:  0.3309 0.3834   6.053207e+00   6.141868e+00
   1_occ:  0.3306 0.3845   6.052712e+00   6.143605e+00
   2_bss:  0.3289 0.3818   6.054207e+00   6.143386e+00
   2_xyz:  0.2474 0.3065   5.815204e+00   5.967015e+00
   2_adp:  0.2273 0.2867   5.748548e+00   5.915987e+00
   2_occ:  0.2270 0.2865   5.748281e+00   5.916640e+00
   3_bss:  0.2254 0.2862   5.749515e+00   5.917520e+00
   3_xyz:  0.1720 0.2256   5.508208e+00   5.712674e+00
   3_adp:  0.1487 0.2014   5.387781e+00   5.617139e+00
   3_occ:  0.1485 0.2013   5.387966e+00   5.618129e+00
   4_bss:  0.1484 0.2007   5.386213e+00   5.614902e+00
   4_xyz:  0.1288 0.1795   5.271401e+00   5.511517e+00
   4_adp:  0.1247 0.1742   5.241185e+00   5.478932e+00
   4_occ:  0.1246 0.1740   5.240659e+00   5.478507e+00
   5_bss:  0.1245 0.1740   5.240613e+00   5.478583e+00
   5_xyz:  0.1195 0.1695   5.211792e+00   5.455534e+00
   5_adp:  0.1186 0.1694   5.207006e+00   5.453176e+00
   5_occ:  0.1186 0.1694   5.206583e+00   5.452793e+00
   5_bss:  0.1184 0.1688   5.204572e+00   5.450100e+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:  0.323  35.048   6.854   6.973  11.902   0.000   0.000   0.000
   1_xyz:  0.323  35.048   6.854   6.973  11.902   0.000   0.000   0.000
   1_adp:  0.323  35.048   6.854   6.973  11.902   0.000   0.000   0.000
   1_occ:  0.323  35.048   6.854   6.973  11.902   0.000   0.000   0.000
   2_bss:  0.306  43.727   4.034   4.327   8.528   0.000   0.000   0.000
   2_xyz:  0.306  43.727   4.034   4.327   8.528   0.000   0.000   0.000
   2_adp:  0.306  43.727   4.034   4.327   8.528   0.000   0.000   0.000
   2_occ:  0.306  43.727   4.034   4.327   8.528   0.000   0.000   0.000
   3_bss:  0.314  61.032   2.563   3.079   5.521   0.000   0.000   0.000
   3_xyz:  0.314  61.032   2.563   3.079   5.521   0.000   0.000   0.000
   3_adp:  0.314  61.032   2.563   3.079   5.521   0.000   0.000   0.000
   3_occ:  0.314  61.032   2.563   3.079   5.521   0.000   0.000   0.000
   4_bss:  0.329  73.123   2.053   2.378   4.316   0.000   0.000   0.000
   4_xyz:  0.329  73.123   2.053   2.378   4.316   0.000   0.000   0.000
   4_adp:  0.329  73.123   2.053   2.378   4.316   0.000   0.000   0.000
   4_occ:  0.329  73.123   2.053   2.378   4.316   0.000   0.000   0.000
   5_bss:  0.330  73.123   2.134   2.360   4.114   0.000   0.000   0.000
   5_xyz:  0.330  73.123   2.134   2.360   4.114   0.000   0.000   0.000
   5_adp:  0.330  73.123   2.134   2.360   4.114   0.000   0.000   0.000
   5_occ:  0.330  73.123   2.134   2.360   4.114   0.000   0.000   0.000
   5_bss:  0.325  71.250  -0.694  -0.512   1.206  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.260 0.4545  0.5115    64898.235
   1_bss:  53.602 0.4754  0.6920    62646.431
   1_xyz:  46.295 0.5655  0.7986    47330.003
   1_adp:  41.958 0.6191  0.9026    41163.976
   1_occ:  42.022 0.6184  0.9012    41316.434
   2_bss:  41.913 0.6196  0.8150    41162.187
   2_xyz:  31.560 0.7399  0.9543    24624.617
   2_adp:  28.847 0.7707  0.9866    21517.778
   2_occ:  28.926 0.7697  0.9853    21555.873
   3_bss:  28.874 0.7705  0.9219    21618.056
   3_xyz:  21.837 0.8435  0.9773    12892.986
   3_adp:  19.172 0.8695  0.9829    10410.491
   3_occ:  19.190 0.8693  0.9827    10419.983
   4_bss:  19.087 0.8702  0.9556    10316.314
   4_xyz:  16.658 0.8924  0.9672     8188.427
   4_adp:  15.870 0.8996  0.9636     7698.503
   4_occ:  15.864 0.8996  0.9637     7688.812
   5_bss:  15.862 0.8996  0.9623     7691.194
   5_xyz:  15.279 0.9050  0.9652     7320.317
   5_adp:  15.203 0.9057  0.9590     7285.786
   5_occ:  15.195 0.9058  0.9590     7277.885
   5_bss:  15.171 0.9059  0.9607     7221.547
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4587e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4587e+01
   1_xyz:   1.725  0.014  0.109 18.328  0.007  4.112   1.4647e-01
   1_adp:   1.725  0.014  0.109 18.328  0.007  4.112   1.4647e-01
   1_occ:   1.725  0.014  0.109 18.328  0.007  4.112   1.4647e-01
   2_bss:   1.725  0.014  0.109 18.328  0.007  4.112   1.4647e-01
   2_xyz:   1.242  0.009  0.084 16.781  0.005  4.135   8.8107e-02
   2_adp:   1.242  0.009  0.084 16.781  0.005  4.135   8.8107e-02
   2_occ:   1.242  0.009  0.084 16.781  0.005  4.135   8.8107e-02
   3_bss:   1.242  0.009  0.084 16.781  0.005  4.135   8.8107e-02
   3_xyz:   1.181  0.010  0.088 16.557  0.004  4.139   8.1502e-02
   3_adp:   1.181  0.010  0.088 16.557  0.004  4.139   8.1502e-02
   3_occ:   1.181  0.010  0.088 16.557  0.004  4.139   8.1502e-02
   4_bss:   1.181  0.010  0.088 16.557  0.004  4.139   8.1502e-02
   4_xyz:   1.149  0.011  0.090 15.988  0.004  4.117   8.3073e-02
   4_adp:   1.149  0.011  0.090 15.988  0.004  4.117   8.3073e-02
   4_occ:   1.149  0.011  0.090 15.988  0.004  4.117   8.3073e-02
   5_bss:   1.149  0.011  0.090 15.988  0.004  4.117   8.3073e-02
   5_xyz:   1.140  0.011  0.090 15.746  0.004  4.122   8.0388e-02
   5_adp:   1.140  0.011  0.090 15.746  0.004  4.122   8.0388e-02
   5_occ:   1.140  0.011  0.090 15.746  0.004  4.122   8.0388e-02
   5_bss:   1.140  0.011  0.090 15.746  0.004  4.122   8.0388e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0774e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0774e+00
   1_xyz:  14.514  0.165  0.441 87.328  0.035  2.202   1.0965e-01
   1_adp:  14.514  0.165  0.441 87.328  0.035  2.202   1.0965e-01
   1_occ:  14.514  0.165  0.441 87.328  0.035  2.202   1.0965e-01
   2_bss:  14.514  0.165  0.441 87.328  0.035  2.202   1.0965e-01
   2_xyz:   7.562  0.075  0.286 89.320  0.036  2.147   5.7923e-02
   2_adp:   7.562  0.075  0.286 89.320  0.036  2.147   5.7923e-02
   2_occ:   7.562  0.075  0.286 89.320  0.036  2.147   5.7923e-02
   3_bss:   7.562  0.075  0.286 89.320  0.036  2.147   5.7923e-02
   3_xyz:   9.559  0.067  0.328 85.726  0.040  2.313   6.5752e-02
   3_adp:   9.559  0.067  0.328 85.726  0.040  2.313   6.5752e-02
   3_occ:   9.559  0.067  0.328 85.726  0.040  2.313   6.5752e-02
   4_bss:   9.559  0.067  0.328 85.726  0.040  2.313   6.5752e-02
   4_xyz:   7.456  0.068  0.431 85.130  0.043  2.394   6.5969e-02
   4_adp:   7.456  0.068  0.431 85.130  0.043  2.394   6.5969e-02
   4_occ:   7.456  0.068  0.431 85.130  0.043  2.394   6.5969e-02
   5_bss:   7.456  0.068  0.431 85.130  0.043  2.394   6.5969e-02
   5_xyz:   7.610  0.056  0.496 81.771  0.040  2.281   5.0937e-02
   5_adp:   7.610  0.056  0.496 81.771  0.040  2.281   5.0937e-02
   5_occ:   7.610  0.056  0.496 81.771  0.040  2.281   5.0937e-02
   5_bss:   7.610  0.056  0.496 81.771  0.040  2.281   5.0937e-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:  74.46   0.00  13.13  73.61   0.00  10.46  74.46   0.00  27.64
   1_occ:  74.46   0.00  13.13  73.61   0.00  10.46  74.46   0.00  27.64
   2_bss:  74.46   0.00  13.13  73.61   0.00  10.46  74.46   0.00  27.64
   2_xyz:  74.46   0.00  13.13  73.61   0.00  10.46  74.46   0.00  27.64
   2_adp:  98.90   0.00  13.03  98.90   0.00   9.75  74.22   0.00  30.90
   2_occ:  98.90   0.00  13.03  98.90   0.00   9.75  74.22   0.00  30.90
   3_bss:  98.90   0.00  13.03  98.90   0.00   9.75  74.22   0.00  30.90
   3_xyz:  98.90   0.00  13.03  98.90   0.00   9.75  74.22   0.00  30.90
   3_adp:  93.69   0.00  13.91  84.76   0.00   9.11  93.69   0.50  40.01
   3_occ:  93.69   0.00  13.91  84.76   0.00   9.11  93.69   0.50  40.01
   4_bss:  93.69   0.00  13.91  84.76   0.00   9.11  93.69   0.50  40.01
   4_xyz:  93.69   0.00  13.91  84.76   0.00   9.11  93.69   0.50  40.01
   4_adp:  99.32   0.00  13.44  83.28   0.00   8.69  99.32   0.58  39.29
   4_occ:  99.32   0.00  13.44  83.28   0.00   8.69  99.32   0.58  39.29
   5_bss:  99.32   0.00  13.44  83.28   0.00   8.69  99.32   0.58  39.29
   5_xyz:  99.32   0.00  13.44  83.28   0.00   8.69  99.32   0.58  39.29
   5_adp: 102.84   0.00  13.24  86.34   0.00   8.55 102.84   0.83  38.83
   5_occ: 102.84   0.00  13.24  86.34   0.00   8.55 102.84   0.83  38.83
   5_bss: 105.77   2.92  16.17  89.26   2.92  11.47 105.77   3.76  41.75
------------------------------------------------------------------------
 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:    1.271    0.025    0.415
   1_adp:    1.271    0.025    0.415
   1_occ:    1.271    0.025    0.415
   2_bss:    1.271    0.025    0.415
   2_xyz:    1.853    0.025    0.582
   2_adp:    1.853    0.025    0.582
   2_occ:    1.853    0.025    0.582
   3_bss:    1.853    0.025    0.582
   3_xyz:    1.802    0.034    0.662
   3_adp:    1.802    0.034    0.662
   3_occ:    1.802    0.034    0.662
   4_bss:    1.802    0.034    0.662
   4_xyz:    1.977    0.041    0.699
   4_adp:    1.977    0.041    0.699
   4_occ:    1.977    0.041    0.699
   5_bss:    1.977    0.041    0.699
   5_xyz:    2.007    0.067    0.711
   5_adp:    2.007    0.067    0.711
   5_occ:    2.007    0.067    0.711
   5_bss:    2.007    0.067    0.711
------------------------------------------------------------------------

CPU time actual refinement: 333.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_923/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_923/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_923/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_923/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_923/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.36 
  Macro-tasks:
    bulk solvent and scale       = 35.13  
    individual site refinement   = 139.46 
    weights calculation          = 31.78  
    collect and process          = 6.46   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 212.95 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 105.29 
    alpha_beta                      = 8.56   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 116.42 
    fmodel                         = 6.56   
    r_factors                      = 0.12   
    phase_errors                   = 10.38  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 251.22 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.689 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    662 calls, 104.96 s
gradients_fft:          606 calls, 102.88 s

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

# Date 2008-01-16 Time 02:45:17 PST -0800 (1200480317.37 s)
Start R-work = 0.4750, R-free = 0.4680 (no bulk solvent and anisotropic scale)
Final R-work = 0.1350, R-free = 0.1836 (no bulk solvent and anisotropic scale)

Start R-work = 0.4663, R-free = 0.4538
Final R-work = 0.1184, R-free = 0.1688