# Date 2008-01-16 Time 02:37:33 PST -0800 (1200479853.26 s)
#phil __OFF__

Command line arguments: "../906.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11411
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 906

-------------------------------------------------------------------------------
  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, 46.93, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99103
Completeness in resolution range: 0.967549
Completeness with d_max=infinity: 0.964595

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0819
                             d_min =   1.9910

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, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99103
Completeness in resolution range: 0.967549
Completeness with d_max=infinity: 0.964595

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0824 -  4.2603 [2117/2143]  1907   210   9.9%
  bin  2:  4.2603 -  3.3942 [2048/2067]  1842   206  10.1%
  bin  3:  3.3942 -  2.9689 [2013/2032]  1809   204  10.1%
  bin  4:  2.9689 -  2.6991 [1997/2027]  1803   194   9.7%
  bin  5:  2.6991 -  2.5066 [1981/2000]  1784   197   9.9%
  bin  6:  2.5066 -  2.3594 [1972/1997]  1769   203  10.3%
  bin  7:  2.3594 -  2.2417 [1967/1995]  1769   198  10.1%
  bin  8:  2.2417 -  2.1444 [1955/1991]  1764   191   9.8%
  bin  9:  2.1444 -  2.0620 [1966/2008]  1771   195   9.9%
  bin 10:  2.0620 -  1.9910 [1573/1986]  1412   161  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_906/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 10
        2.42 -     3.04: 2200
        3.04 -     3.66: 4647
        3.66 -     4.28: 9013
        4.28 -     4.90: 12334
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.091 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.364 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28199 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_906/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_906/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 46.93 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4149   r_free= 0.4014   ksol= 0.00   Bsol= 0.00   scale= 0.830    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.201321                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7517 0.99   1383  154 0.3581 0.3389      6.5066        6.41|
|  2:  4.7517 -  3.7913 0.99   1333  146 0.3050 0.3135      6.5868      6.6316|
|  3:  3.7913 -  3.3179 0.99   1292  144 0.3521 0.3181      6.5103      6.5117|
|  4:  3.3179 -  3.0172 0.99   1291  147 0.3874 0.3446      6.4179      6.3179|
|  5:  3.0172 -  2.8024 0.99   1292  142 0.4273 0.4215      6.2842      6.3119|
|  6:  2.8024 -  2.6381 0.99   1281  143 0.4361 0.4664      6.2074      6.1987|
|  7:  2.6381 -  2.5066 0.99   1273  135 0.4721 0.4742      6.2042      6.1692|
|  8:  2.5066 -  2.3979 0.98   1265  150 0.4597 0.4275      6.1289      6.1042|
|  9:  2.3979 -  2.3060 0.98   1271  137 0.4555 0.4607       6.067      6.0381|
| 10:  2.3060 -  2.2267 0.99   1260  140 0.4710 0.4656      6.0736      6.0677|
| 11:  2.2267 -  2.1572 0.98   1257  136 0.4809 0.4249      6.0212      5.9632|
| 12:  2.1572 -  2.0957 0.97   1248  142 0.4586 0.4630      5.9425      5.9963|
| 13:  2.0957 -  2.0407 1.00   1256  140 0.5008 0.5137      5.8779      5.8601|
| 14:  2.0407 -  1.9910 0.71    928  103 0.4830 0.4476      5.8195      5.6909|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7517  1383   154  0.75  30.17   0.82     0.77      55416.49|
|  2:  4.7517 -  3.7913  1333   146  0.80  26.34   0.92     0.84      64474.74|
|  3:  3.7913 -  3.3179  1292   144  0.74  31.89   0.88     0.82      66199.59|
|  4:  3.3179 -  3.0172  1291   147  0.68  36.90   0.85     0.75      61079.77|
|  5:  3.0172 -  2.8024  1292   142  0.58  45.14   0.78     0.66      56750.36|
|  6:  2.8024 -  2.6381  1281   143  0.55  47.70   0.78     0.62      52346.67|
|  7:  2.6381 -  2.5066  1273   135  0.54  48.97   0.75     0.60      48867.63|
|  8:  2.5066 -  2.3979  1265   150  0.53  49.43   0.77     0.61      43934.17|
|  9:  2.3979 -  2.3060  1271   137  0.55  48.32   0.76     0.61      38323.58|
| 10:  2.3060 -  2.2267  1260   140  0.55  48.45   0.79     0.61      34357.50|
| 11:  2.2267 -  2.1572  1257   136  0.53  49.80   0.78     0.60      32536.73|
| 12:  2.1572 -  2.0957  1248   142  0.50  52.12   0.79     0.58      32938.01|
| 13:  2.0957 -  2.0407  1256   140  0.47  54.92   0.76     0.55      29365.19|
| 14:  2.0407 -  1.9910   928   103  0.52  50.44   0.74     0.56      22566.15|
|alpha:            min =        0.55 max =            0.84 mean =         0.66|
|beta:             min =    22566.15 max =        66199.59 mean =     46339.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.95 mean =        44.01|
|phase err.(test): min =        0.00 max =           89.89 mean =        44.12|
|-----------------------------------------------------------------------------|

============================== 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 = 6.987226              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 72.710   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.528605              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.540   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      679 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1506 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2622 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3915 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5028 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6576 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7689 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.896 |
| 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 |       1.627 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4241   r_free= 0.4109   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.208664                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4069   r_free= 0.3908   ksol= 0.34   Bsol= 20.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.18,8.08,8.01,0.00,0.00,0.00); trace/3= 8.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.197284                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.423626              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.902   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.543343              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.429   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4069      final r-factor (work) = 0.2942          |
| start r-factor (free) = 0.3908      final r-factor (free) = 0.3210          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 73.8735 = 6.42 * 0.50 * 6.2199 + 1.00 * 53.8964                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.4426 = 6.42 * 0.50 * 6.0194 + 1.00 * 0.1096                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2942      final r-factor (work) = 0.2220          |
| start r-factor (free) = 0.3210      final r-factor (free) = 0.2565          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2853 = 0.54 * 1.00 * 6.0194 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1650 = 0.54 * 1.00 * 5.8054 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    55.07   9.99     None  None   None       |
|    all(noH): 2823   0      0.00    55.07   9.99     None  None   None       |
|    Sol.    : 438    0      0.00    55.07   27.07    None  None   None       |
|    Mac.    : 2385   0      0.00    55.00   6.85     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 -   5.507: 1275   |   5:    27.533 -  33.040:  122        |
|      1:     5.507 -  11.013:  783   |   6:    33.040 -  38.547:   80        |
|      2:    11.013 -  16.520:  237   |   7:    38.547 -  44.053:   51        |
|      3:    16.520 -  22.027:  132   |   8:    44.053 -  49.560:   23        |
|      4:    22.027 -  27.533:  112   |   9:    49.560 -  55.066:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2220 r_free = 0.2565             target_work(ml) = 5.704         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2215 r_free = 0.2564             target_work(ml) = 5.702         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2215   r_free= 0.2564   ksol= 0.34   Bsol= 20.00   scale= 1.084   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.18,8.08,8.01,0.00,0.00,0.00); trace/3= 8.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.702440                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2163   r_free= 0.2500   ksol= 0.35   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.74,4.40,5.22,0.00,0.00,0.00); trace/3= 4.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.699951                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.646581              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.578   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.276533              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.492  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2163      final r-factor (work) = 0.1518          |
| start r-factor (free) = 0.2500      final r-factor (free) = 0.1916          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8098 = 2.65 * 0.50 * 5.8193 + 1.00 * 0.1092                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3868 = 2.65 * 0.50 * 5.5366 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1518      final r-factor (work) = 0.1395          |
| start r-factor (free) = 0.1916      final r-factor (free) = 0.1794          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5417 = 0.28 * 1.00 * 5.5366 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4886 = 0.28 * 1.00 * 5.3472 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    57.89   10.63    None  None   None       |
|    all(noH): 2823   0      0.00    57.89   10.63    None  None   None       |
|    Sol.    : 438    0      0.63    57.89   30.84    None  None   None       |
|    Mac.    : 2385   0      0.00    56.84   6.92     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 -   5.789: 1383   |   5:    28.946 -  34.735:   91        |
|      1:     5.789 -  11.578:  703   |   6:    34.735 -  40.524:  103        |
|      2:    11.578 -  17.367:  230   |   7:    40.524 -  46.313:   79        |
|      3:    17.367 -  23.157:  105   |   8:    46.313 -  52.102:   34        |
|      4:    23.157 -  28.946:   82   |   9:    52.102 -  57.891:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1395 r_free = 0.1794             target_work(ml) = 5.315         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1395 r_free = 0.1795             target_work(ml) = 5.315         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1395   r_free= 0.1795   ksol= 0.35   Bsol= 50.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.74,4.40,5.22,0.00,0.00,0.00); trace/3= 4.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.314763                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1391   r_free= 0.1789   ksol= 0.33   Bsol= 47.95   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.57,3.55,4.46,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.315362                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.508356              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.824  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.154046              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.693  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1391      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1789      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7731 = 2.51 * 0.50 * 5.3524 + 1.00 * 0.0602                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6451 = 2.51 * 0.50 * 5.2455 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.3089 = 2.15 * 1.00 * 5.2455 + 1.00 * 0.0099                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1588 = 2.15 * 1.00 * 5.1739 + 1.00 * 0.0141                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.24   11.54    None  None   None       |
|    all(noH): 2823   0      0.00    76.24   11.54    None  None   None       |
|    Sol.    : 438    0      0.36    76.24   34.80    None  None   None       |
|    Mac.    : 2385   0      0.00    76.24   7.26     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 -   7.624: 1670   |   5:    38.122 -  45.746:   76        |
|      1:     7.624 -  15.249:  554   |   6:    45.746 -  53.370:   83        |
|      2:    15.249 -  22.873:  164   |   7:    53.370 -  60.995:   45        |
|      3:    22.873 -  30.497:   97   |   8:    60.995 -  68.619:   16        |
|      4:    30.497 -  38.122:  108   |   9:    68.619 -  76.243:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1600             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1600             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1600   ksol= 0.33   Bsol= 47.95   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.57,3.55,4.46,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.169648                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1600   ksol= 0.33   Bsol= 47.95   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.47,3.52,4.39,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.169298                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.945762              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.717  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.164551              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.991  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0996 = 1.95 * 0.50 * 5.1734 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0821 = 1.95 * 0.50 * 5.1622 + 1.00 * 0.0598                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1149          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8635 = 0.16 * 1.00 * 5.1622 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8609 = 0.16 * 1.00 * 5.1684 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.65   11.20    None  None   None       |
|    all(noH): 2823   0      0.00    75.65   11.20    None  None   None       |
|    Sol.    : 438    0      0.90    71.92   33.23    None  None   None       |
|    Mac.    : 2385   0      0.00    75.65   7.15     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 -   7.565: 1708   |   5:    37.824 -  45.388:   76        |
|      1:     7.565 -  15.130:  540   |   6:    45.388 -  52.953:   73        |
|      2:    15.130 -  22.694:  156   |   7:    52.953 -  60.518:   40        |
|      3:    22.694 -  30.259:   98   |   8:    60.518 -  68.083:   13        |
|      4:    30.259 -  37.824:  110   |   9:    68.083 -  75.647:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1149 r_free = 0.1568             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1568             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1568   ksol= 0.33   Bsol= 47.95   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.47,3.52,4.39,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.157541                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1567   ksol= 0.33   Bsol= 47.95   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.47,3.52,4.39,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158793                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.004175              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.194  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.411631              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.057  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2397 = 2.00 * 0.50 * 5.1691 + 1.00 * 0.0598                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2222 = 2.00 * 0.50 * 5.1478 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1293 = 0.41 * 1.00 * 5.1478 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1264 = 0.41 * 1.00 * 5.1376 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.98   11.19    None  None   None       |
|    all(noH): 2823   0      0.00    75.98   11.19    None  None   None       |
|    Sol.    : 438    0      1.05    71.48   33.28    None  None   None       |
|    Mac.    : 2385   0      0.00    75.98   7.14     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.598: 1698   |   5:    37.988 -  45.586:   71        |
|      1:     7.598 -  15.195:  542   |   6:    45.586 -  53.184:   71        |
|      2:    15.195 -  22.793:  159   |   7:    53.184 -  60.781:   41        |
|      3:    22.793 -  30.391:  101   |   8:    60.781 -  68.379:   14        |
|      4:    30.391 -  37.988:  119   |   9:    68.379 -  75.977:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1113 r_free = 0.1563             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1563             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1563   ksol= 0.33   Bsol= 47.95   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.47,3.52,4.39,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142391                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7517 0.99   1383  154 0.1000 0.1332      5.3887      5.5282|
|  2:  4.7517 -  3.7913 0.99   1333  146 0.0881 0.1100      5.4512      5.6313|
|  3:  3.7913 -  3.3179 0.99   1292  144 0.1045 0.1532      5.4712      5.8667|
|  4:  3.3179 -  3.0172 0.99   1291  147 0.1196 0.1501       5.455      5.5765|
|  5:  3.0172 -  2.8024 0.99   1292  142 0.1315 0.1739       5.323      5.5562|
|  6:  2.8024 -  2.6381 0.99   1281  143 0.1180 0.1775      5.2009       5.428|
|  7:  2.6381 -  2.5066 0.99   1273  135 0.1253 0.1600      5.1662      5.3776|
|  8:  2.5066 -  2.3979 0.98   1265  150 0.1177 0.1758      5.0737      5.3627|
|  9:  2.3979 -  2.3060 0.98   1271  137 0.1177 0.1768      5.0486      5.3009|
| 10:  2.3060 -  2.2267 0.99   1260  140 0.1108 0.1659      4.9527       5.216|
| 11:  2.2267 -  2.1572 0.98   1257  136 0.1124 0.1695       4.939      5.2316|
| 12:  2.1572 -  2.0957 0.97   1248  142 0.1089 0.1663      4.8598      5.1768|
| 13:  2.0957 -  2.0407 1.00   1256  140 0.1150 0.1722       4.796      5.0829|
| 14:  2.0407 -  1.9910 0.71    928  103 0.1066 0.1754      4.6781      4.9086|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7517  1383   154  0.94   8.99   0.98     0.95       7092.67|
|  2:  4.7517 -  3.7913  1333   146  0.95   7.94   1.01     1.00       9052.85|
|  3:  3.7913 -  3.3179  1292   144  0.94  11.17   1.02     1.01      10350.37|
|  4:  3.3179 -  3.0172  1291   147  0.92  13.50   1.00     0.99      10311.44|
|  5:  3.0172 -  2.8024  1292   142  0.90  15.88   0.99     0.96       8180.14|
|  6:  2.8024 -  2.6381  1281   143  0.91  15.45   0.99     0.96       6988.93|
|  7:  2.6381 -  2.5066  1273   135  0.91  15.38   0.99     0.96       6108.17|
|  8:  2.5066 -  2.3979  1265   150  0.91  15.21   0.99     0.97       5355.19|
|  9:  2.3979 -  2.3060  1271   137  0.91  15.31   1.01     0.98       5097.56|
| 10:  2.3060 -  2.2267  1260   140  0.91  15.26   1.00     0.96       4256.90|
| 11:  2.2267 -  2.1572  1257   136  0.90  16.24   1.00     0.96       4320.78|
| 12:  2.1572 -  2.0957  1248   142  0.92  14.21   1.01     1.00       3744.98|
| 13:  2.0957 -  2.0407  1256   140  0.90  16.06   1.01     1.00       3373.22|
| 14:  2.0407 -  1.9910   928   103  0.91  14.93   0.99     0.95       2614.19|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2614.19 max =        10350.37 mean =      6309.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.89|
|phase err.(test): min =        0.00 max =           89.88 mean =        13.40|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1563   ksol= 0.33   Bsol= 51.63   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,-0.27,0.61,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142351                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1563   ksol= 0.33   Bsol= 51.63   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,-0.27,0.61,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142351                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7517 0.99   1383  154 0.1000 0.1331      5.3882      5.5275|
|  2:  4.7517 -  3.7913 0.99   1333  146 0.0880 0.1100       5.451      5.6314|
|  3:  3.7913 -  3.3179 0.99   1292  144 0.1045 0.1532      5.4712      5.8664|
|  4:  3.3179 -  3.0172 0.99   1291  147 0.1196 0.1501       5.455      5.5765|
|  5:  3.0172 -  2.8024 0.99   1292  142 0.1316 0.1740      5.3231      5.5565|
|  6:  2.8024 -  2.6381 0.99   1281  143 0.1180 0.1774      5.2009       5.428|
|  7:  2.6381 -  2.5066 0.99   1273  135 0.1253 0.1599      5.1661      5.3772|
|  8:  2.5066 -  2.3979 0.98   1265  150 0.1177 0.1758      5.0737      5.3628|
|  9:  2.3979 -  2.3060 0.98   1271  137 0.1177 0.1768      5.0486      5.3009|
| 10:  2.3060 -  2.2267 0.99   1260  140 0.1108 0.1659      4.9527      5.2161|
| 11:  2.2267 -  2.1572 0.98   1257  136 0.1124 0.1695       4.939      5.2318|
| 12:  2.1572 -  2.0957 0.97   1248  142 0.1089 0.1662        4.86      5.1768|
| 13:  2.0957 -  2.0407 1.00   1256  140 0.1150 0.1723      4.7962      5.0833|
| 14:  2.0407 -  1.9910 0.71    928  103 0.1066 0.1754      4.6781      4.9087|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7517  1383   154  0.94   8.98   0.98     0.95       7083.25|
|  2:  4.7517 -  3.7913  1333   146  0.95   7.94   1.01     1.00       9045.78|
|  3:  3.7913 -  3.3179  1292   144  0.94  11.17   1.02     1.01      10348.50|
|  4:  3.3179 -  3.0172  1291   147  0.92  13.50   1.00     0.99      10312.90|
|  5:  3.0172 -  2.8024  1292   142  0.90  15.88   0.99     0.96       8181.44|
|  6:  2.8024 -  2.6381  1281   143  0.91  15.45   0.98     0.96       6989.78|
|  7:  2.6381 -  2.5066  1273   135  0.91  15.38   0.99     0.95       6107.22|
|  8:  2.5066 -  2.3979  1265   150  0.91  15.21   0.99     0.96       5355.03|
|  9:  2.3979 -  2.3060  1271   137  0.91  15.30   1.00     0.97       5096.66|
| 10:  2.3060 -  2.2267  1260   140  0.91  15.26   1.00     0.96       4257.67|
| 11:  2.2267 -  2.1572  1257   136  0.90  16.24   1.00     0.96       4321.17|
| 12:  2.1572 -  2.0957  1248   142  0.92  14.21   1.01     0.99       3746.38|
| 13:  2.0957 -  2.0407  1256   140  0.90  16.06   1.00     0.99       3374.09|
| 14:  2.0407 -  1.9910   928   103  0.91  14.93   0.98     0.94       2614.49|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2614.49 max =        10348.50 mean =      6308.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.89|
|phase err.(test): min =        0.00 max =           89.88 mean =        13.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.68    79.66   14.87    None  None   None       |
|    all(noH): 2823   0      3.68    79.66   14.87    None  None   None       |
|    Sol.    : 438    0      4.73    75.16   36.96    None  None   None       |
|    Mac.    : 2385   0      3.68    79.66   10.82    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:     3.680 -  11.277: 1698   |   5:    41.668 -  49.266:   71        |
|      1:    11.277 -  18.875:  542   |   6:    49.266 -  56.863:   71        |
|      2:    18.875 -  26.473:  159   |   7:    56.863 -  64.461:   41        |
|      3:    26.473 -  34.070:  101   |   8:    64.461 -  72.059:   14        |
|      4:    34.070 -  41.668:  119   |   9:    72.059 -  79.656:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 306         
Filter by distance & map next to the model:
   mapped sites are within: 0.364 - 4.722
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 306
   mapped sites are within: 0.728 - 4.722

peak=   10.785 closest distance to " CG2 VAL A 230 " =    1.397
peak=    7.005 closest distance to " CG2 VAL A 296 " =    1.124
peak=    6.312 closest distance to " NH2 ARG A  56 " =    2.253
peak=    6.226 closest distance to " CG  LEU A   5 " =    1.258
peak=    5.767 closest distance to " CD2 LEU A   5 " =    1.235
peak=    5.653 closest distance to " CG  LEU A 228 " =    1.181
peak=    5.644 closest distance to " CB  GLN A 223 " =    1.451
peak=    5.186 closest distance to " NE2 GLN A  11 " =    1.152
peak=    5.035 closest distance to " CB  SER A  63 " =    1.308
peak=    4.998 closest distance to " CB  GLN A 183 " =    1.253
peak=    4.962 closest distance to " CB  VAL A 296 " =    1.109
peak=    4.856 closest distance to " CB  VAL A 230 " =    1.212
peak=    4.847 closest distance to " CG  PRO A 213 " =    1.234
peak=    4.787 closest distance to " O   HOH Z 126 " =    2.019
peak=    4.772 closest distance to " O   HOH Z 232 " =    2.352
peak=    4.769 closest distance to " CB  ARG A 275 " =    0.839
peak=    4.696 closest distance to " C   PRO A 198 " =    1.531
peak=    4.633 closest distance to " O   HOH Z 272 " =    1.897
peak=    4.539 closest distance to " O   HOH Z 142 " =    1.645
peak=    4.508 closest distance to " O   HOH Z 427 " =    3.006
peak=    4.487 closest distance to " O   HOH Z 209 " =    2.283
peak=    4.478 closest distance to " O   HOH Z 369 " =    2.079
peak=    4.466 closest distance to " O   HOH Z 298 " =    1.780
peak=    4.464 closest distance to " CB  GLU A 152 " =    1.191
peak=    4.403 closest distance to " OD1 ASN A  69 " =    2.663
peak=    4.354 closest distance to " CD2 LEU A 228 " =    1.172
peak=    4.338 closest distance to " O   HOH Z 316 " =    3.117
peak=    4.307 closest distance to " CB  ASN A 148 " =    1.375
peak=    4.285 closest distance to " O   HOH Z  78 " =    1.780
peak=    4.251 closest distance to " CB  SER A   3 " =    1.320
peak=    4.227 closest distance to " O   HOH Z 368 " =    2.146
peak=    4.219 closest distance to " CG  PRO A 243 " =    1.115
peak=    4.216 closest distance to " O   HOH Z 236 " =    1.894
peak=    4.211 closest distance to " CB  TRP A 266 " =    0.935
peak=    4.184 closest distance to " CG  PRO A 198 " =    1.232
peak=    4.174 closest distance to " CB  VAL A 265 " =    1.308
peak=    4.170 closest distance to " O   HOH Z 158 " =    3.143
peak=    4.162 closest distance to " O   HOH Z  61 " =    1.656
peak=    4.151 closest distance to " O   HOH Z 303 " =    2.041
peak=    4.149 closest distance to " O   HOH Z  43 " =    1.968
peak=    4.148 closest distance to " CB  GLU A 128 " =    1.047
peak=    4.140 closest distance to " O   HOH Z  54 " =    2.439
peak=    4.121 closest distance to " O   SER A  87 " =    2.307
peak=    4.051 closest distance to " O   HOH Z 261 " =    2.054
peak=    4.044 closest distance to " ND2 ASN A 187 " =    1.473
peak=    4.037 closest distance to " CB  ARG A  79 " =    1.448
peak=    4.027 closest distance to " O   HOH Z 346 " =    1.622
peak=    4.025 closest distance to " O   HOH Z 403 " =    1.660
peak=    4.025 closest distance to " O   HOH Z 193 " =    1.845
peak=    4.023 closest distance to " O   HOH Z 423 " =    1.703
peak=    4.016 closest distance to " CA  TYR A  30 " =    0.948
peak=    3.963 closest distance to " CB  ASN A  39 " =    0.885
peak=    3.954 closest distance to " O   HOH Z  15 " =    2.133
peak=    3.954 closest distance to " CZ  PHE A 218 " =    1.087
peak=    3.952 closest distance to " O   HOH Z 425 " =    1.345
peak=    3.949 closest distance to " CB  GLU A 277 " =    3.597
peak=    3.940 closest distance to " O   HOH Z 203 " =    1.743
peak=    3.931 closest distance to " CD  ARG A  66 " =    2.705
peak=    3.913 closest distance to " O   HOH Z  68 " =    2.217
peak=    3.905 closest distance to " CB  LEU A 228 " =    1.237
peak=    3.895 closest distance to " CB  ASN A 187 " =    1.287
peak=    3.894 closest distance to " O   HOH Z 234 " =    3.671
peak=    3.890 closest distance to " O   HOH Z  88 " =    3.206
peak=    3.881 closest distance to " O   HOH Z 280 " =    2.941
peak=    3.872 closest distance to " CB  ARG A 139 " =    0.938
peak=    3.861 closest distance to " O   HOH Z 189 " =    2.744
peak=    3.840 closest distance to " O   HOH Z 197 " =    3.187
peak=    3.840 closest distance to " NH2 ARG A 156 " =    1.104
peak=    3.838 closest distance to " CA  ALA A  51 " =    0.987
peak=    3.833 closest distance to " O   HOH Z 344 " =    2.993
peak=    3.832 closest distance to " CA  ASN A 215 " =    1.218
peak=    3.827 closest distance to " CB  ASP A 140 " =    0.862
peak=    3.821 closest distance to " CB  LEU A 143 " =    1.155
peak=    3.808 closest distance to " O   HOH Z 411 " =    3.773
peak=    3.807 closest distance to " CA  THR A 264 " =    0.772
peak=    3.804 closest distance to " O   HOH Z  63 " =    2.050
peak=    3.760 closest distance to " OD2 ASP A 286 " =    2.832
peak=    3.757 closest distance to " CB  PRO A  54 " =    0.762
peak=    3.757 closest distance to " CD  ARG A 159 " =    0.747
peak=    3.747 closest distance to " CG  LEU A 167 " =    1.200
peak=    3.743 closest distance to " O   MET A 105 " =    1.826
peak=    3.739 closest distance to " O   HOH Z 193 " =    2.009
peak=    3.727 closest distance to " CB  ALA A   9 " =    1.585
peak=    3.726 closest distance to " CG1BVAL A  72 " =    1.659
peak=    3.720 closest distance to " CB  ARG A 190 " =    1.623
peak=    3.712 closest distance to " O   HOH Z 248 " =    1.712
peak=    3.711 closest distance to " CZ  PHE A 192 " =    0.997
peak=    3.708 closest distance to " CB  SER A 216 " =    0.799
peak=    3.703 closest distance to " O   HOH Z  97 " =    2.009
peak=    3.700 closest distance to " O   HOH Z 263 " =    1.671
peak=    3.694 closest distance to " CB  VAL A 202 " =    1.574
peak=    3.685 closest distance to " O   HOH Z 402 " =    1.505
peak=    3.683 closest distance to " CD1 LEU A 300 " =    1.214
peak=    3.678 closest distance to " ND2 ASN A 249 " =    1.936
peak=    3.677 closest distance to " CD BLYS A 290 " =    1.048
peak=    3.665 closest distance to " CB  TRP A 179 " =    1.403
peak=    3.663 closest distance to " NH1AARG A 145 " =    1.097
peak=    3.647 closest distance to " CB  ALA A 291 " =    1.379
peak=    3.630 closest distance to " O   TRP A 274 " =    1.913
peak=    3.626 closest distance to " OG BSER A 164 " =    2.219
peak=    3.615 closest distance to " CG2 THR A 221 " =    1.153
peak=    3.611 closest distance to " CG2 VAL A 257 " =    0.898
peak=    3.610 closest distance to " CB  ASN A 142 " =    1.034
peak=    3.609 closest distance to " O   HOH Z 250 " =    1.355
peak=    3.607 closest distance to " O   HOH Z  97 " =    2.589
peak=    3.607 closest distance to " CD  LYS A 166 " =    1.303
peak=    3.606 closest distance to " CD  ARG A 269 " =    0.975
peak=    3.600 closest distance to " O   HOH Z 147 " =    1.707
peak=    3.596 closest distance to " O   HOH Z 128 " =    2.122
peak=    3.595 closest distance to " CA  ALA A 158 " =    1.194
peak=    3.595 closest distance to " N   VAL A 126 " =    1.329
peak=    3.594 closest distance to " CA  ALA A  21 " =    1.173
peak=    3.580 closest distance to " N   PHE A 130 " =    1.278
peak=    3.579 closest distance to " CB  SER A 212 " =    1.208
peak=    3.578 closest distance to " O   HOH Z 371 " =    3.050
peak=    3.576 closest distance to " CG  MET A 185 " =    1.209
peak=    3.567 closest distance to " CA  ARG A 195 " =    1.192
peak=    3.563 closest distance to " CB BVAL A  41 " =    1.141
peak=    3.561 closest distance to " O   HOH Z 145 " =    2.010
peak=    3.559 closest distance to " CA  SER A  87 " =    0.998
peak=    3.556 closest distance to " CD1 ILE A  33 " =    1.610
peak=    3.552 closest distance to " CG1 VAL A 153 " =    0.944
peak=    3.550 closest distance to " O   HOH Z 273 " =    2.639
peak=    3.549 closest distance to " CB  MET A  40 " =    0.818
peak=    3.549 closest distance to " O   HOH Z 214 " =    2.081
peak=    3.541 closest distance to " O   HOH Z 180 " =    2.115
peak=    3.541 closest distance to " O   HOH Z  40 " =    2.416
peak=    3.540 closest distance to " CB  HIS A 108 " =    0.790
peak=    3.522 closest distance to " CA  THR A 221 " =    0.932
peak=    3.513 closest distance to " N   ASN A  39 " =    1.153
peak=    3.508 closest distance to " O   HOH Z 128 " =    2.155
peak=    3.503 closest distance to " CG1 ILE A  49 " =    1.428
peak=    3.502 closest distance to " O   HOH Z  59 " =    2.113
peak=    3.500 closest distance to " CE1 TYR A 186 " =    1.358
peak=    3.494 closest distance to " O   HOH Z 227 " =    1.691
peak=    3.491 closest distance to " O   HOH Z 305 " =    3.544
peak=    3.487 closest distance to " CE  LYS A  76 " =    0.898
peak=    3.487 closest distance to " CG1 ILE A  33 " =    1.295
peak=    3.486 closest distance to " CG1 VAL A 296 " =    1.210
peak=    3.484 closest distance to " ND1 HIS A  81 " =    1.678
peak=    3.482 closest distance to " O   ALA A 158 " =    1.463
peak=    3.480 closest distance to " O   HOH Z 193 " =    1.711
peak=    3.478 closest distance to " CB  THR A 157 " =    1.131
peak=    3.474 closest distance to " O   HOH Z 290 " =    1.044
peak=    3.474 closest distance to " NZ  LYS A 117 " =    3.275
peak=    3.470 closest distance to " OG  SER A  22 " =    2.812
peak=    3.466 closest distance to " O   HOH Z  19 " =    2.451
peak=    3.460 closest distance to " O   HOH Z 245 " =    1.402
peak=    3.460 closest distance to " CB  ALA A 248 " =    1.438
peak=    3.458 closest distance to " CB  GLU A  46 " =    1.018
peak=    3.455 closest distance to " O   HOH Z 437 " =    1.852
peak=    3.454 closest distance to " O   HOH Z  21 " =    1.690
peak=    3.443 closest distance to " O   HOH Z 133 " =    1.648
peak=    3.441 closest distance to " CB  THR A  31 " =    1.688
peak=    3.440 closest distance to " O   HOH Z 132 " =    2.731
peak=    3.429 closest distance to " CA  LEU A 282 " =    1.069
peak=    3.422 closest distance to " CB  GLN A  88 " =    1.226
peak=    3.420 closest distance to " CG  GLN A  88 " =    1.047
peak=    3.419 closest distance to " O   ASP A 124 " =    1.040
peak=    3.416 closest distance to " CA  ALA A 291 " =    0.943
peak=    3.414 closest distance to " O   HOH Z 435 " =    1.992
peak=    3.402 closest distance to " CA  LYS A 117 " =    1.187
peak=    3.392 closest distance to " CB  THR A  82 " =    1.374
peak=    3.386 closest distance to " O   HOH Z 112 " =    1.595
peak=    3.385 closest distance to " CA  ALA A 295 " =    1.036
peak=    3.381 closest distance to " CA  VAL A  41 " =    0.858
peak=    3.375 closest distance to " CD1 ILE A 106 " =    0.986
peak=    3.374 closest distance to " CG BARG A 275 " =    1.439
peak=    3.373 closest distance to " N   SER A 135 " =    1.365
peak=    3.368 closest distance to " CG  MET A 185 " =    1.063
peak=    3.364 closest distance to " ND1 HIS A  86 " =    1.668
peak=    3.362 closest distance to " N   ARG A 190 " =    1.054
peak=    3.362 closest distance to " O   HOH Z 291 " =    1.674
peak=    3.360 closest distance to " O   HOH Z 313 " =    1.763
peak=    3.357 closest distance to " O   HOH Z 286 " =    2.387
peak=    3.356 closest distance to " O   HOH Z 350 " =    1.654
peak=    3.353 closest distance to " CA  SER A 146 " =    1.747
peak=    3.351 closest distance to " CA  ARG A  36 " =    1.103
peak=    3.349 closest distance to " O   HOH Z 313 " =    1.791
peak=    3.348 closest distance to " O   HOH Z 329 " =    3.821
peak=    3.348 closest distance to " O   HOH Z 171 " =    2.384
peak=    3.345 closest distance to " O   HOH Z 407 " =    2.341
peak=    3.343 closest distance to " CB  TRP A 150 " =    1.452
peak=    3.343 closest distance to " O   HOH Z 189 " =    2.891
peak=    3.336 closest distance to " CA  LYS A 290 " =    1.288
peak=    3.335 closest distance to " CA  ALA A 233 " =    1.367
peak=    3.330 closest distance to " CB  GLN A 278 " =    0.876
peak=    3.329 closest distance to " O   HOH Z 345 " =    3.443
peak=    3.326 closest distance to " O   HOH Z  10 " =    1.782
peak=    3.325 closest distance to " CB  SER A 273 " =    0.867
peak=    3.324 closest distance to " O   HOH Z 299 " =    4.292
peak=    3.323 closest distance to " O   HOH Z 409 " =    3.166
peak=    3.322 closest distance to " CB  VAL A 268 " =    0.840
peak=    3.322 closest distance to " CG BARG A 102 " =    1.778
peak=    3.320 closest distance to " O   HOH Z 425 " =    2.020
peak=    3.317 closest distance to " CD2 TRP A 179 " =    1.357
peak=    3.314 closest distance to " CD1 LEU A 228 " =    1.929
peak=    3.314 closest distance to " O   HOH Z 368 " =    3.541
peak=    3.313 closest distance to " CD1 LEU A   5 " =    1.375
peak=    3.311 closest distance to " CG2 THR A 220 " =    0.913
peak=    3.311 closest distance to " O   HOH Z 353 " =    2.664
peak=    3.309 closest distance to " CD2 LEU A 255 " =    1.634
peak=    3.306 closest distance to " O   HOH Z   9 " =    1.977
peak=    3.304 closest distance to " O   HOH Z 175 " =    2.159
peak=    3.304 closest distance to " CB  ALA A  34 " =    0.876
peak=    3.302 closest distance to " CD  LYS A 119 " =    1.560
peak=    3.301 closest distance to " CA  ALA A 154 " =    1.003
peak=    3.299 closest distance to " O   HOH Z 417 " =    2.004
peak=    3.298 closest distance to " NH2 ARG A 219 " =    1.803
peak=    3.295 closest distance to " O   HOH Z 148 " =    3.273
peak=    3.293 closest distance to " O   HOH Z 227 " =    2.078
peak=    3.292 closest distance to " O   HOH Z 426 " =    1.578
peak=    3.292 closest distance to " CB  ASN A 224 " =    1.045
peak=    3.288 closest distance to " ND2 ASN A 110 " =    1.699
peak=    3.283 closest distance to " CA  GLY A 267 " =    0.767
peak=    3.274 closest distance to " NE2 HIS A 207 " =    1.388
peak=    3.272 closest distance to " O   HOH Z 359 " =    3.810
peak=    3.268 closest distance to " O   HOH Z 132 " =    3.174
peak=    3.266 closest distance to " O   HOH Z 172 " =    3.696
peak=    3.262 closest distance to " O   HOH Z  80 " =    1.594
peak=    3.258 closest distance to " CA  MET A  40 " =    1.113
peak=    3.256 closest distance to " OH  TYR A 214 " =    1.224
peak=    3.255 closest distance to " CG1 ILE A 151 " =    1.032
peak=    3.253 closest distance to " O   HOH Z 116 " =    1.744
peak=    3.252 closest distance to " O   HOH Z 295 " =    1.508
peak=    3.249 closest distance to " CA  VAL A 126 " =    0.861
peak=    3.249 closest distance to " N   ASN A 127 " =    1.236
peak=    3.248 closest distance to " OG BSER A 134 " =    2.819
peak=    3.247 closest distance to " CB  ILE A 120 " =    1.317
peak=    3.247 closest distance to " O   HOH Z 135 " =    1.858
peak=    3.242 closest distance to " CA  ASP A 162 " =    1.052
peak=    3.242 closest distance to " CB  ALA A 104 " =    0.728
peak=    3.240 closest distance to " CA  ASP A 140 " =    1.246
peak=    3.239 closest distance to " CB  PRO A 198 " =    1.025
peak=    3.237 closest distance to " C   ALA A 299 " =    0.966
peak=    3.236 closest distance to " O  BHOH Z 338 " =    2.406
peak=    3.234 closest distance to " CA  LYS A 181 " =    1.054
peak=    3.233 closest distance to " O   HOH Z 285 " =    3.018
peak=    3.231 closest distance to " CG2 ILE A  20 " =    1.467
peak=    3.226 closest distance to " CB  MET A  47 " =    1.091
peak=    3.226 closest distance to " O   HOH Z 366 " =    3.019
peak=    3.223 closest distance to " OG1 THR A 294 " =    1.729
peak=    3.222 closest distance to " O   HOH Z  48 " =    1.650
peak=    3.221 closest distance to " CB  ALA A 114 " =    1.330
peak=    3.220 closest distance to " O   HOH Z   1 " =    1.895
peak=    3.220 closest distance to " CB  GLN A 205 " =    1.093
peak=    3.215 closest distance to " CB  SER A  26 " =    1.656
peak=    3.215 closest distance to " CA  ILE A 106 " =    0.768
peak=    3.215 closest distance to " OG1 THR A 294 " =    2.393
peak=    3.211 closest distance to " O   HOH Z 166 " =    3.618
peak=    3.209 closest distance to " O   HOH Z 411 " =    1.794
peak=    3.205 closest distance to " CG  GLN A 278 " =    1.314
peak=    3.203 closest distance to " CB  ALA A 248 " =    1.069
peak=    3.200 closest distance to " O   HOH Z 133 " =    2.455
peak=    3.199 closest distance to " O   HOH Z 250 " =    1.340
peak=    3.197 closest distance to " O   HOH Z  62 " =    2.291
peak=    3.192 closest distance to " O   GLN A 278 " =    1.534
peak=    3.190 closest distance to " O   HOH Z 293 " =    1.781
peak=    3.190 closest distance to " O   HOH Z 187 " =    2.283
peak=    3.190 closest distance to " NH2BARG A 145 " =    2.072
peak=    3.189 closest distance to " O   HOH Z 383 " =    2.054
peak=    3.186 closest distance to " O   HOH Z 422 " =    2.681
peak=    3.186 closest distance to " N   ARG A 156 " =    1.342
peak=    3.183 closest distance to " CG2 ILE A 120 " =    1.286
peak=    3.176 closest distance to " CB  ILE A  20 " =    1.404
peak=    3.176 closest distance to " CB  ASN A 110 " =    1.166
peak=    3.176 closest distance to " N   ASP A 162 " =    1.313
peak=    3.175 closest distance to " CA  TYR A 116 " =    1.438
peak=    3.173 closest distance to " CA  MET A 105 " =    0.968
peak=    3.170 closest distance to " O   HOH Z 423 " =    2.902
peak=    3.169 closest distance to " O   HOH Z 141 " =    1.609
peak=    3.169 closest distance to " OG  SER A 206 " =    1.175
peak=    3.169 closest distance to " O   HOH Z  14 " =    2.295
peak=    3.168 closest distance to " O   HOH Z 213 " =    2.067
peak=    3.165 closest distance to " CB  ALA A 242 " =    0.808
peak=    3.160 closest distance to " CA  ASP A 191 " =    0.770
peak=    3.155 closest distance to " O   HOH Z  61 " =    1.601
peak=    3.153 closest distance to " CB  LYS A 117 " =    1.167
peak=    3.153 closest distance to " O   ALA A   1 " =    1.574
peak=    3.149 closest distance to " O   HOH Z 419 " =    1.766
peak=    3.143 closest distance to " CG2 VAL A 197 " =    1.032
peak=    3.141 closest distance to " N   GLN A 278 " =    1.091
peak=    3.133 closest distance to " O   HOH Z 201 " =    3.176
peak=    3.133 closest distance to " O   HOH Z 294 " =    1.562
peak=    3.123 closest distance to " NH2AARG A 275 " =    3.667
peak=    3.114 closest distance to " O   HOH Z 329 " =    2.730
peak=    3.106 closest distance to " O   HOH Z 271 " =    2.456
peak=    3.105 closest distance to " CB  LEU A 255 " =    0.813
peak=    3.091 closest distance to " CB  ALA A   1 " =    4.722
peak=    3.087 closest distance to " O   HOH Z  40 " =    1.523
peak=    3.083 closest distance to " CA  ASN A 176 " =    1.039
peak=    3.076 closest distance to " O   HOH Z  49 " =    2.683
peak=    3.064 closest distance to " O   GLY A  75 " =    1.410
peak=    3.060 closest distance to " CB  SER A 245 " =    3.224
peak=    3.058 closest distance to " CB  ALA A 100 " =    1.205
peak=    3.052 closest distance to " NZ  LYS A  76 " =    1.372
peak=    3.050 closest distance to " CD2 LEU A   5 " =    0.760
peak=    3.044 closest distance to " O   SER A 164 " =    1.174
peak=    3.027 closest distance to " O   HOH Z 392 " =    1.958

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.502 - 5.452
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 209
   mapped sites are within: 0.773 - 5.452

peak=   -5.673 closest distance to " CG2 VAL A 230 " =    0.773
peak=   -4.664 closest distance to " CD  ARG A 156 " =    2.025
peak=   -4.340 closest distance to " SG  CYS A 254 " =    3.296
peak=   -4.311 closest distance to " CB  PRO A 243 " =    2.633
peak=   -4.275 closest distance to " O   HOH Z 266 " =    4.977
peak=   -4.052 closest distance to " O   ILE A 109 " =    2.587
peak=   -4.027 closest distance to " CG  ASP A 231 " =    0.782
peak=   -4.021 closest distance to " CG2 VAL A 296 " =    1.252
peak=   -4.018 closest distance to " O   HOH Z 290 " =    1.199
peak=   -4.015 closest distance to " CG  GLN A 223 " =    2.011
peak=   -4.013 closest distance to " CG2BVAL A  41 " =    2.597
peak=   -3.957 closest distance to " O   HOH Z 351 " =    1.519
peak=   -3.927 closest distance to " OG BSER A 134 " =    1.192
peak=   -3.907 closest distance to " CE2 TYR A  30 " =    2.827
peak=   -3.907 closest distance to " O   HOH Z  11 " =    1.952
peak=   -3.901 closest distance to " C   HIS A 108 " =    1.196
peak=   -3.865 closest distance to " NH2AARG A 275 " =    5.267
peak=   -3.840 closest distance to " O   HOH Z 231 " =    1.832
peak=   -3.831 closest distance to " CD2 LEU A 300 " =    2.772
peak=   -3.827 closest distance to " CD  GLN A  58 " =    1.032
peak=   -3.798 closest distance to " N   ALA A 226 " =    2.091
peak=   -3.789 closest distance to " O   PRO A 163 " =    2.124
peak=   -3.780 closest distance to " CG1 VAL A 112 " =    2.611
peak=   -3.754 closest distance to " O   HOH Z 185 " =    2.345
peak=   -3.749 closest distance to " O   HOH Z 118 " =    3.150
peak=   -3.731 closest distance to " CZ3 TRP A 179 " =    1.198
peak=   -3.719 closest distance to " O   VAL A  67 " =    2.720
peak=   -3.718 closest distance to " CB  ALA A  43 " =    2.458
peak=   -3.715 closest distance to " O   HOH Z  52 " =    1.475
peak=   -3.713 closest distance to " O   HOH Z 435 " =    2.794
peak=   -3.692 closest distance to " N   GLN A  58 " =    1.703
peak=   -3.679 closest distance to " O   HOH Z 389 " =    1.923
peak=   -3.668 closest distance to " CG  LEU A 101 " =    2.495
peak=   -3.666 closest distance to " OD1 ASN A 187 " =    1.665
peak=   -3.666 closest distance to " CD1 LEU A 228 " =    2.313
peak=   -3.662 closest distance to " CB  PRO A 163 " =    2.561
peak=   -3.660 closest distance to " CG1 VAL A 112 " =    2.964
peak=   -3.659 closest distance to " CB  ALA A 248 " =    2.083
peak=   -3.653 closest distance to " CB  PHE A 192 " =    1.918
peak=   -3.650 closest distance to " O   HOH Z 394 " =    1.517
peak=   -3.637 closest distance to " ND2 ASN A  45 " =    1.086
peak=   -3.635 closest distance to " O   VAL A 189 " =    2.637
peak=   -3.630 closest distance to " CE  MET A 105 " =    2.188
peak=   -3.629 closest distance to " O   PRO A 198 " =    1.208
peak=   -3.628 closest distance to " CG1 VAL A 250 " =    2.748
peak=   -3.628 closest distance to " C   ALA A 158 " =    1.331
peak=   -3.627 closest distance to " O   HOH Z 196 " =    2.177
peak=   -3.608 closest distance to " NH2 ARG A  79 " =    1.964
peak=   -3.606 closest distance to " CB  PRO A 280 " =    2.138
peak=   -3.598 closest distance to " N   ASP A 171 " =    2.366
peak=   -3.598 closest distance to " CG1 VAL A 296 " =    1.344
peak=   -3.597 closest distance to " OXT GLY A 302 " =    2.936
peak=   -3.582 closest distance to " O   HOH Z 166 " =    2.000
peak=   -3.580 closest distance to " OG  SER A  97 " =    2.216
peak=   -3.570 closest distance to " CG  PHE A 283 " =    2.792
peak=   -3.559 closest distance to " OD1 ASN A 148 " =    1.479
peak=   -3.556 closest distance to " N   THR A 157 " =    1.438
peak=   -3.550 closest distance to " CA  ASP A 298 " =    1.046
peak=   -3.548 closest distance to " O   HOH Z 426 " =    1.668
peak=   -3.530 closest distance to " OG  SER A  87 " =    1.423
peak=   -3.528 closest distance to " CD1 LEU A 101 " =    2.449
peak=   -3.523 closest distance to " CG2 ILE A 263 " =    2.400
peak=   -3.520 closest distance to " CD  LYS A 289 " =    2.562
peak=   -3.513 closest distance to " O   HOH Z  60 " =    2.046
peak=   -3.510 closest distance to " O   HOH Z 211 " =    1.590
peak=   -3.504 closest distance to " CD  ARG A 139 " =    1.614
peak=   -3.504 closest distance to " CB  ALA A 291 " =    2.233
peak=   -3.502 closest distance to " O   HOH Z  13 " =    1.386
peak=   -3.496 closest distance to " O   HOH Z 103 " =    1.833
peak=   -3.484 closest distance to " O   HOH Z  19 " =    2.457
peak=   -3.483 closest distance to " O   HOH Z  38 " =    1.628
peak=   -3.482 closest distance to " O   HOH Z 102 " =    1.679
peak=   -3.481 closest distance to " CG  TRP A 266 " =    1.853
peak=   -3.481 closest distance to " NZ  LYS A 119 " =    3.490
peak=   -3.448 closest distance to " NH1 ARG A 195 " =    2.557
peak=   -3.448 closest distance to " OD2 ASP A  50 " =    2.340
peak=   -3.448 closest distance to " O   HOH Z  47 " =    1.658
peak=   -3.446 closest distance to " O   HOH Z  73 " =    2.209
peak=   -3.444 closest distance to " OG BSER A 134 " =    1.762
peak=   -3.437 closest distance to " O   HOH Z 407 " =    3.127
peak=   -3.437 closest distance to " N   ALA A  43 " =    2.476
peak=   -3.437 closest distance to " O   HOH Z 417 " =    2.862
peak=   -3.435 closest distance to " CB  ALA A 248 " =    2.411
peak=   -3.434 closest distance to " CA  GLY A 241 " =    3.053
peak=   -3.428 closest distance to " CE3 TRP A 150 " =    2.079
peak=   -3.426 closest distance to " O   HOH Z 241 " =    1.272
peak=   -3.419 closest distance to " ND2 ASN A 187 " =    1.661
peak=   -3.416 closest distance to " CE2 PHE A 218 " =    2.568
peak=   -3.402 closest distance to " C   ASN A 187 " =    1.844
peak=   -3.398 closest distance to " O   HOH Z  44 " =    2.162
peak=   -3.394 closest distance to " CG  LEU A 228 " =    0.933
peak=   -3.384 closest distance to " O   GLY A  80 " =    2.538
peak=   -3.381 closest distance to " O   HOH Z 372 " =    2.377
peak=   -3.377 closest distance to " O   HOH Z 166 " =    1.503
peak=   -3.375 closest distance to " CB  ALA A 291 " =    2.156
peak=   -3.373 closest distance to " N   THR A 235 " =    1.344
peak=   -3.368 closest distance to " O   HOH Z  43 " =    1.729
peak=   -3.367 closest distance to " CD1 LEU A 101 " =    2.612
peak=   -3.365 closest distance to " CD1 ILE A 239 " =    2.113
peak=   -3.361 closest distance to " CG  MET A 105 " =    0.939
peak=   -3.360 closest distance to " C   ASN A 285 " =    2.469
peak=   -3.358 closest distance to " O   HOH Z 165 " =    1.856
peak=   -3.358 closest distance to " CB  ASN A  69 " =    1.157
peak=   -3.353 closest distance to " OG  SER A  26 " =    1.173
peak=   -3.352 closest distance to " NE2 GLN A  88 " =    2.077
peak=   -3.348 closest distance to " O   HOH Z 222 " =    1.455
peak=   -3.343 closest distance to " CB  ASP A 132 " =    2.288
peak=   -3.342 closest distance to " O   HOH Z 198 " =    1.426
peak=   -3.342 closest distance to " O   HOH Z 350 " =    1.544
peak=   -3.341 closest distance to " ND2 ASN A  60 " =    1.443
peak=   -3.341 closest distance to " CD1 PHE A  59 " =    1.897
peak=   -3.341 closest distance to " CE BMET A  47 " =    1.794
peak=   -3.338 closest distance to " CG  ARG A 269 " =    2.409
peak=   -3.338 closest distance to " O   GLY A 196 " =    1.107
peak=   -3.337 closest distance to " O   HOH Z 310 " =    1.919
peak=   -3.334 closest distance to " O   HOH Z 436 " =    1.614
peak=   -3.329 closest distance to " OG  SER A  62 " =    1.687
peak=   -3.328 closest distance to " CD2 LEU A 167 " =    1.786
peak=   -3.320 closest distance to " O   HOH Z 353 " =    2.060
peak=   -3.319 closest distance to " C   MET A 188 " =    1.397
peak=   -3.318 closest distance to " O   PRO A 198 " =    1.320
peak=   -3.305 closest distance to " CG1 VAL A 230 " =    1.899
peak=   -3.305 closest distance to " O   HOH Z 275 " =    1.515
peak=   -3.304 closest distance to " O   HOH Z 134 " =    2.679
peak=   -3.302 closest distance to " C   LEU A 222 " =    0.822
peak=   -3.283 closest distance to " O   HOH Z 311 " =    3.746
peak=   -3.280 closest distance to " C   LEU A 143 " =    1.095
peak=   -3.269 closest distance to " O   HOH Z 191 " =    5.452
peak=   -3.266 closest distance to " CD1 ILE A 199 " =    2.565
peak=   -3.264 closest distance to " O   GLY A  17 " =    1.332
peak=   -3.262 closest distance to " N   SER A 212 " =    1.907
peak=   -3.261 closest distance to " OG  SER A 206 " =    1.711
peak=   -3.261 closest distance to " CB  ASN A  39 " =    2.173
peak=   -3.257 closest distance to " O   HOH Z 244 " =    2.025
peak=   -3.256 closest distance to " O   HOH Z  98 " =    2.089
peak=   -3.255 closest distance to " O   LEU A 167 " =    1.461
peak=   -3.253 closest distance to " O   SER A 271 " =    2.220
peak=   -3.251 closest distance to " O   GLY A 211 " =    1.337
peak=   -3.251 closest distance to " N   PHE A  59 " =    2.099
peak=   -3.249 closest distance to " O   HOH Z 388 " =    2.160
peak=   -3.247 closest distance to " O   HOH Z 111 " =    2.310
peak=   -3.239 closest distance to " CZ  TYR A 169 " =    1.641
peak=   -3.239 closest distance to " O   HOH Z 140 " =    1.712
peak=   -3.238 closest distance to " N   ALA A 248 " =    2.555
peak=   -3.238 closest distance to " CB  ASP A 132 " =    2.319
peak=   -3.237 closest distance to " O   HOH Z 359 " =    3.177
peak=   -3.236 closest distance to " CZ  PHE A  59 " =    1.554
peak=   -3.235 closest distance to " C   ASP A 231 " =    2.557
peak=   -3.235 closest distance to " O   HOH Z 234 " =    4.177
peak=   -3.233 closest distance to " C   GLY A 229 " =    1.189
peak=   -3.233 closest distance to " CG  GLU A 277 " =    1.169
peak=   -3.232 closest distance to " N   SER A 276 " =    1.332
peak=   -3.231 closest distance to " O   HOH Z 348 " =    1.837
peak=   -3.225 closest distance to " ND2 ASN A  60 " =    1.798
peak=   -3.223 closest distance to " SG BCYS A 201 " =    1.972
peak=   -3.220 closest distance to " OH  TYR A 214 " =    1.209
peak=   -3.220 closest distance to " O   HOH Z 174 " =    2.524
peak=   -3.220 closest distance to " CB  TYR A  15 " =    2.217
peak=   -3.216 closest distance to " CD  GLN A  88 " =    0.867
peak=   -3.209 closest distance to " CA  GLY A 203 " =    2.353
peak=   -3.207 closest distance to " O   SER A  22 " =    2.226
peak=   -3.205 closest distance to " CE1 TYR A 169 " =    2.405
peak=   -3.203 closest distance to " CA  GLY A 133 " =    2.240
peak=   -3.202 closest distance to " CD2 TYR A 293 " =    2.090
peak=   -3.201 closest distance to " CA  GLY A 241 " =    2.307
peak=   -3.199 closest distance to " OXT GLY A 302 " =    3.467
peak=   -3.198 closest distance to " CD2 LEU A 237 " =    2.746
peak=   -3.198 closest distance to " OG1 THR A 178 " =    1.282
peak=   -3.197 closest distance to " CD1 LEU A 297 " =    2.381
peak=   -3.195 closest distance to " NE2 GLN A 103 " =    1.752
peak=   -3.192 closest distance to " C   GLN A 205 " =    2.011
peak=   -3.189 closest distance to " OG ASER A 134 " =    1.485
peak=   -3.186 closest distance to " CG1 VAL A 197 " =    2.261
peak=   -3.182 closest distance to " O   HOH Z 281 " =    2.643
peak=   -3.181 closest distance to " OE1 GLN A  88 " =    1.144
peak=   -3.180 closest distance to " ND2 ASN A 249 " =    2.439
peak=   -3.168 closest distance to " O   HOH Z  10 " =    1.498
peak=   -3.163 closest distance to " NE2 GLN A 278 " =    2.017
peak=   -3.161 closest distance to " O   HOH Z 123 " =    2.396
peak=   -3.158 closest distance to " O   HOH Z 252 " =    4.082
peak=   -3.155 closest distance to " NH2BARG A 275 " =    1.758
peak=   -3.153 closest distance to " CD  ARG A 195 " =    5.193
peak=   -3.153 closest distance to " CD1 TRP A 274 " =    1.014
peak=   -3.149 closest distance to " NH2 ARG A  66 " =    1.967
peak=   -3.141 closest distance to " CD2 PHE A  61 " =    2.398
peak=   -3.139 closest distance to " CD1 TYR A 247 " =    2.634
peak=   -3.138 closest distance to " N   ALA A 248 " =    1.618
peak=   -3.137 closest distance to " O   VAL A 125 " =    2.355
peak=   -3.137 closest distance to " O   HOH Z 396 " =    1.739
peak=   -3.135 closest distance to " NH2 ARG A  79 " =    1.586
peak=   -3.133 closest distance to " CD1 TYR A 247 " =    2.393
peak=   -3.126 closest distance to " CG2 VAL A 112 " =    2.517
peak=   -3.117 closest distance to " O   HOH Z 149 " =    2.232
peak=   -3.116 closest distance to " O   HOH Z 175 " =    4.278
peak=   -3.114 closest distance to " CG1 VAL A 296 " =    1.298
peak=   -3.113 closest distance to " C   PHE A  59 " =    1.327
peak=   -3.110 closest distance to " O   HOH Z  51 " =    1.375
peak=   -3.106 closest distance to " O   THR A  18 " =    1.566
peak=   -3.096 closest distance to " CB  VAL A 296 " =    1.225
peak=   -3.092 closest distance to " O   HOH Z 389 " =    4.625
peak=   -3.087 closest distance to " O   HOH Z 298 " =    2.792
peak=   -3.076 closest distance to " O   HOH Z 313 " =    1.675
peak=   -3.076 closest distance to " O   HOH Z   6 " =    1.813
peak=   -3.065 closest distance to " O   HOH Z 139 " =    3.039
peak=   -3.063 closest distance to " N   ALA A 248 " =    1.893
peak=   -3.063 closest distance to " O   HOH Z 184 " =    1.663
peak=   -3.029 closest distance to " O   HOH Z 313 " =    1.104

================= 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    :  0.4149 0.4014   6.201321e+00   6.175959e+00
   1_bss:  0.4069 0.3908   6.197284e+00   6.162222e+00
   1_xyz:  0.2942 0.3210   5.953047e+00   6.015185e+00
   1_adp:  0.2220 0.2565   5.703987e+00   5.836273e+00
   1_occ:  0.2215 0.2564   5.702440e+00   5.837527e+00
   2_bss:  0.2163 0.2500   5.699951e+00   5.831354e+00
   2_xyz:  0.1518 0.1916   5.388560e+00   5.578419e+00
   2_adp:  0.1395 0.1794   5.314756e+00   5.514056e+00
   2_occ:  0.1395 0.1795   5.314763e+00   5.514444e+00
   3_bss:  0.1391 0.1789   5.315362e+00   5.515509e+00
   3_xyz:  0.1200 0.1615   5.191753e+00   5.419894e+00
   3_adp:  0.1155 0.1600   5.169771e+00   5.411208e+00
   3_occ:  0.1155 0.1600   5.169648e+00   5.411085e+00
   4_bss:  0.1154 0.1600   5.169298e+00   5.410849e+00
   4_xyz:  0.1130 0.1596   5.159086e+00   5.406035e+00
   4_adp:  0.1149 0.1568   5.157647e+00   5.389713e+00
   4_occ:  0.1148 0.1568   5.157541e+00   5.389708e+00
   5_bss:  0.1151 0.1567   5.158793e+00   5.388554e+00
   5_xyz:  0.1126 0.1555   5.143398e+00   5.381270e+00
   5_adp:  0.1113 0.1563   5.142584e+00   5.387572e+00
   5_occ:  0.1113 0.1563   5.142391e+00   5.387387e+00
   5_bss:  0.1113 0.1563   5.142351e+00   5.387365e+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:  0.342  20.001   8.180   8.079   8.009   0.000   0.000   0.000
   1_xyz:  0.342  20.001   8.180   8.079   8.009   0.000   0.000   0.000
   1_adp:  0.342  20.001   8.180   8.079   8.009   0.000   0.000   0.000
   1_occ:  0.342  20.001   8.180   8.079   8.009   0.000   0.000   0.000
   2_bss:  0.347  50.001   4.743   4.397   5.218   0.000   0.000   0.000
   2_xyz:  0.347  50.001   4.743   4.397   5.218   0.000   0.000   0.000
   2_adp:  0.347  50.001   4.743   4.397   5.218   0.000   0.000   0.000
   2_occ:  0.347  50.001   4.743   4.397   5.218   0.000   0.000   0.000
   3_bss:  0.334  47.946   3.571   3.549   4.459   0.000   0.000   0.000
   3_xyz:  0.334  47.946   3.571   3.549   4.459   0.000   0.000   0.000
   3_adp:  0.334  47.946   3.571   3.549   4.459   0.000   0.000   0.000
   3_occ:  0.334  47.946   3.571   3.549   4.459   0.000   0.000   0.000
   4_bss:  0.326  47.946   3.468   3.518   4.394   0.000   0.000   0.000
   4_xyz:  0.326  47.946   3.468   3.518   4.394   0.000   0.000   0.000
   4_adp:  0.326  47.946   3.468   3.518   4.394   0.000   0.000   0.000
   4_occ:  0.326  47.946   3.468   3.518   4.394   0.000   0.000   0.000
   5_bss:  0.326  47.946   3.468   3.518   4.394   0.000   0.000   0.000
   5_xyz:  0.326  47.946   3.468   3.518   4.394   0.000   0.000   0.000
   5_adp:  0.326  47.946   3.468   3.518   4.394   0.000   0.000   0.000
   5_occ:  0.326  47.946   3.468   3.518   4.394   0.000   0.000   0.000
   5_bss:  0.326  51.625  -0.343  -0.266   0.610   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.020 0.5963  0.6597    46339.775
   1_bss:  44.001 0.5942  0.8383    44034.786
   1_xyz:  34.000 0.7120  0.9748    27719.336
   1_adp:  25.187 0.8105  1.0636    16797.455
   1_occ:  25.200 0.8103  1.0629    16803.892
   2_bss:  24.932 0.8130  0.9460    16512.651
   2_xyz:  18.063 0.8799  0.9942     9257.395
   2_adp:  16.438 0.8950  1.0062     8144.991
   2_occ:  16.448 0.8950  1.0060     8150.278
   3_bss:  16.471 0.8948  0.9721     8189.218
   3_xyz:  14.537 0.9107  0.9796     6757.977
   3_adp:  14.371 0.9122  0.9796     6628.238
   3_occ:  14.367 0.9122  0.9796     6625.940
   4_bss:  14.362 0.9123  0.9771     6618.050
   4_xyz:  14.213 0.9136  0.9766     6536.044
   4_adp:  13.814 0.9169  0.9793     6343.537
   4_occ:  13.812 0.9170  0.9792     6337.979
   5_bss:  13.807 0.9170  0.9782     6319.248
   5_xyz:  13.677 0.9180  0.9784     6225.911
   5_adp:  13.843 0.9166  0.9761     6311.797
   5_occ:  13.840 0.9167  0.9761     6310.054
   5_bss:  13.839 0.9167  0.9721     6309.026
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3896e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3896e+01
   1_xyz:   1.444  0.011  0.098 17.881  0.006  4.123   1.0959e-01
   1_adp:   1.444  0.011  0.098 17.881  0.006  4.123   1.0959e-01
   1_occ:   1.444  0.011  0.098 17.881  0.006  4.123   1.0959e-01
   2_bss:   1.444  0.011  0.098 17.881  0.006  4.123   1.0959e-01
   2_xyz:   0.962  0.006  0.072 16.273  0.004  4.124   6.0228e-02
   2_adp:   0.962  0.006  0.072 16.273  0.004  4.124   6.0228e-02
   2_occ:   0.962  0.006  0.072 16.273  0.004  4.124   6.0228e-02
   3_bss:   0.962  0.006  0.072 16.273  0.004  4.124   6.0228e-02
   3_xyz:   1.033  0.008  0.084 16.081  0.004  4.133   6.6355e-02
   3_adp:   1.033  0.008  0.084 16.081  0.004  4.133   6.6355e-02
   3_occ:   1.033  0.008  0.084 16.081  0.004  4.133   6.6355e-02
   4_bss:   1.033  0.008  0.084 16.081  0.004  4.133   6.6355e-02
   4_xyz:   0.971  0.007  0.079 15.791  0.003  4.120   5.9825e-02
   4_adp:   0.971  0.007  0.079 15.791  0.003  4.120   5.9825e-02
   4_occ:   0.971  0.007  0.079 15.791  0.003  4.120   5.9825e-02
   5_bss:   0.971  0.007  0.079 15.791  0.003  4.120   5.9825e-02
   5_xyz:   1.013  0.008  0.083 15.749  0.004  4.121   6.3744e-02
   5_adp:   1.013  0.008  0.083 15.749  0.004  4.121   6.3744e-02
   5_occ:   1.013  0.008  0.083 15.749  0.004  4.121   6.3744e-02
   5_bss:   1.013  0.008  0.083 15.749  0.004  4.121   6.3744e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9886e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9886e+00
   1_xyz:  11.851  0.128  0.391 88.529  0.039  2.263   8.1585e-02
   1_adp:  11.851  0.128  0.391 88.529  0.039  2.263   8.1585e-02
   1_occ:  11.851  0.128  0.391 88.529  0.039  2.263   8.1585e-02
   2_bss:  11.851  0.128  0.391 88.529  0.039  2.263   8.1585e-02
   2_xyz:   6.741  0.061  0.336 81.782  0.036  2.368   4.3889e-02
   2_adp:   6.741  0.061  0.336 81.782  0.036  2.368   4.3889e-02
   2_occ:   6.741  0.061  0.336 81.782  0.036  2.368   4.3889e-02
   3_bss:   6.741  0.061  0.336 81.782  0.036  2.368   4.3889e-02
   3_xyz:   7.216  0.054  0.557 83.803  0.039  2.327   6.7804e-02
   3_adp:   7.216  0.054  0.557 83.803  0.039  2.327   6.7804e-02
   3_occ:   7.216  0.054  0.557 83.803  0.039  2.327   6.7804e-02
   4_bss:   7.216  0.054  0.557 83.803  0.039  2.327   6.7804e-02
   4_xyz:   7.510  0.038  0.518 83.250  0.037  2.351   3.7290e-02
   4_adp:   7.510  0.038  0.518 83.250  0.037  2.351   3.7290e-02
   4_occ:   7.510  0.038  0.518 83.250  0.037  2.351   3.7290e-02
   5_bss:   7.510  0.038  0.518 83.250  0.037  2.351   3.7290e-02
   5_xyz:   7.233  0.044  0.554 83.771  0.039  2.319   4.1190e-02
   5_adp:   7.233  0.044  0.554 83.771  0.039  2.319   4.1190e-02
   5_occ:   7.233  0.044  0.554 83.771  0.039  2.319   4.1190e-02
   5_bss:   7.233  0.044  0.554 83.771  0.039  2.319   4.1190e-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:  55.07   0.00   9.99  55.00   0.00   6.85  55.07   0.00  27.07
   1_occ:  55.07   0.00   9.99  55.00   0.00   6.85  55.07   0.00  27.07
   2_bss:  55.07   0.00   9.99  55.00   0.00   6.85  55.07   0.00  27.07
   2_xyz:  55.07   0.00   9.99  55.00   0.00   6.85  55.07   0.00  27.07
   2_adp:  57.89   0.00  10.63  56.84   0.00   6.92  57.89   0.63  30.84
   2_occ:  57.89   0.00  10.63  56.84   0.00   6.92  57.89   0.63  30.84
   3_bss:  57.89   0.00  10.63  56.84   0.00   6.92  57.89   0.63  30.84
   3_xyz:  57.89   0.00  10.63  56.84   0.00   6.92  57.89   0.63  30.84
   3_adp:  76.24   0.00  11.54  76.24   0.00   7.26  76.24   0.36  34.80
   3_occ:  76.24   0.00  11.54  76.24   0.00   7.26  76.24   0.36  34.80
   4_bss:  76.24   0.00  11.54  76.24   0.00   7.26  76.24   0.36  34.80
   4_xyz:  76.24   0.00  11.54  76.24   0.00   7.26  76.24   0.36  34.80
   4_adp:  75.65   0.00  11.20  75.65   0.00   7.15  71.92   0.90  33.23
   4_occ:  75.65   0.00  11.20  75.65   0.00   7.15  71.92   0.90  33.23
   5_bss:  75.65   0.00  11.20  75.65   0.00   7.15  71.92   0.90  33.23
   5_xyz:  75.65   0.00  11.20  75.65   0.00   7.15  71.92   0.90  33.23
   5_adp:  75.98   0.00  11.19  75.98   0.00   7.14  71.48   1.05  33.28
   5_occ:  75.98   0.00  11.19  75.98   0.00   7.14  71.48   1.05  33.28
   5_bss:  79.66   3.68  14.87  79.66   3.68  10.82  75.16   4.73  36.96
------------------------------------------------------------------------
 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:    1.152    0.011    0.398
   1_adp:    1.152    0.011    0.398
   1_occ:    1.152    0.011    0.398
   2_bss:    1.152    0.011    0.398
   2_xyz:    1.398    0.023    0.473
   2_adp:    1.398    0.023    0.473
   2_occ:    1.398    0.023    0.473
   3_bss:    1.398    0.023    0.473
   3_xyz:    1.381    0.026    0.504
   3_adp:    1.381    0.026    0.504
   3_occ:    1.381    0.026    0.504
   4_bss:    1.381    0.026    0.504
   4_xyz:    1.511    0.038    0.512
   4_adp:    1.511    0.038    0.512
   4_occ:    1.511    0.038    0.512
   5_bss:    1.511    0.038    0.512
   5_xyz:    1.567    0.046    0.522
   5_adp:    1.567    0.046    0.522
   5_occ:    1.567    0.046    0.522
   5_bss:    1.567    0.046    0.522
------------------------------------------------------------------------

CPU time actual refinement: 334.17


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_906/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_906/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_906/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_906/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_906/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.01 
  Macro-tasks:
    bulk solvent and scale       = 40.38  
    individual site refinement   = 140.42 
    weights calculation          = 32.59  
    collect and process          = 6.88   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 220.40 
  Micro-tasks:
    mask                            = 1.73   
    f_calc                          = 101.54 
    alpha_beta                      = 8.33   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 114.40 
    fmodel                         = 7.56   
    r_factors                      = 0.32   
    phase_errors                   = 11.15  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 246.45 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.613 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    669 calls, 101.12 s
gradients_fft:          615 calls,  99.99 s

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

# Date 2008-01-16 Time 02:43:20 PST -0800 (1200480200.07 s)
Start R-work = 0.4149, R-free = 0.4014 (no bulk solvent and anisotropic scale)
Final R-work = 0.1282, R-free = 0.1720 (no bulk solvent and anisotropic scale)

Start R-work = 0.4069, R-free = 0.3908
Final R-work = 0.1113, R-free = 0.1563