# Date 2008-01-16 Time 02:40:55 PST -0800 (1200480055.76 s)
#phil __OFF__

Command line arguments: "../931.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29476
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 931

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.3993, 87.2539, 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: 3.37, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 2.02
Completeness in resolution range: 0.985412
Completeness with d_max=infinity: 0.982249

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1439
                             d_min =   2.0200

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 2.02
Completeness in resolution range: 0.985412
Completeness with d_max=infinity: 0.982249

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1443 -  4.3214 [2087/2110]  1878   209  10.0%
  bin  2:  4.3214 -  3.4433 [2015/2035]  1813   202  10.0%
  bin  3:  3.4433 -  3.0119 [1978/1997]  1781   197  10.0%
  bin  4:  3.0119 -  2.7383 [1933/1963]  1740   193  10.0%
  bin  5:  2.7383 -  2.5430 [1963/1982]  1766   197  10.0%
  bin  6:  2.5430 -  2.3937 [1940/1965]  1747   193   9.9%
  bin  7:  2.3937 -  2.2742 [1926/1954]  1733   193  10.0%
  bin  8:  2.2742 -  2.1755 [1926/1962]  1734   192  10.0%
  bin  9:  2.1755 -  2.0920 [1921/1963]  1728   193  10.0%
  bin 10:  2.0920 -  2.0200 [1900/1948]  1710   190  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_931/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 10
        2.42 -     3.04: 2155
        3.04 -     3.66: 4598
        3.66 -     4.28: 8864
        4.28 -     4.90: 12238
  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 "  1.824 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.273 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27860 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_931/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_931/model_refine_001.geo

CPU time processing inputs: 9.66


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.3993 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4523   r_free= 0.4360   ksol= 0.00   Bsol= 0.00   scale= 0.801    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.248690                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.8194 0.99   1363  152 0.3709 0.3425      6.5478      6.4431|
|  2:  4.8194 -  3.8460 0.99   1299  144 0.3502 0.3770      6.6924      6.7932|
|  3:  3.8460 -  3.3659 0.99   1272  141 0.3996 0.3817      6.6255      6.5996|
|  4:  3.3659 -  3.0609 0.99   1277  142 0.4370 0.3810      6.5054      6.3974|
|  5:  3.0609 -  2.8431 0.99   1255  140 0.4695 0.4510      6.3427      6.3394|
|  6:  2.8431 -  2.6764 0.99   1266  140 0.4780 0.4969      6.2708      6.2261|
|  7:  2.6764 -  2.5430 0.99   1246  139 0.4934 0.4649      6.2225      6.1576|
|  8:  2.5430 -  2.4328 0.98   1249  138 0.4924 0.4454      6.1799      6.1465|
|  9:  2.4328 -  2.3395 0.98   1233  137 0.5023 0.5058       6.108      6.1313|
| 10:  2.3395 -  2.2590 1.00   1237  138 0.5122 0.5088      6.1191      6.1247|
| 11:  2.2590 -  2.1886 0.97   1250  139 0.4993 0.4740      6.0277      6.0588|
| 12:  2.1886 -  2.1262 0.97   1224  136 0.5168 0.4751      6.0016      6.0089|
| 13:  2.1262 -  2.0704 0.99   1229  136 0.5086 0.5104      5.9012      5.8737|
| 14:  2.0704 -  2.0200 0.97   1230  137 0.5270 0.4858      5.8593      5.7683|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.8194  1363   152  0.74  30.69   0.80     0.76      57393.12|
|  2:  4.8194 -  3.8460  1299   144  0.76  30.11   0.89     0.79      81437.23|
|  3:  3.8460 -  3.3659  1272   141  0.69  36.49   0.85     0.76      85709.00|
|  4:  3.3659 -  3.0609  1277   142  0.62  42.48   0.82     0.67      76377.03|
|  5:  3.0609 -  2.8431  1255   140  0.54  49.13   0.75     0.60      64824.33|
|  6:  2.8431 -  2.6764  1266   140  0.50  51.83   0.74     0.56      59805.11|
|  7:  2.6764 -  2.5430  1246   139  0.48  53.96   0.73     0.52      55267.53|
|  8:  2.5430 -  2.4328  1249   138  0.46  55.38   0.77     0.52      51599.66|
|  9:  2.4328 -  2.3395  1233   137  0.46  55.59   0.71     0.51      46537.24|
| 10:  2.3395 -  2.2590  1237   138  0.46  55.32   0.73     0.51      42950.69|
| 11:  2.2590 -  2.1886  1250   139  0.43  57.41   0.76     0.50      40222.50|
| 12:  2.1886 -  2.1262  1224   136  0.41  59.27   0.77     0.49      38521.90|
| 13:  2.1262 -  2.0704  1229   136  0.42  58.89   0.73     0.48      33397.17|
| 14:  2.0704 -  2.0200  1230   137  0.45  55.96   0.71     0.48      25597.20|
|alpha:            min =        0.48 max =            0.79 mean =         0.58|
|beta:             min =    25597.20 max =        85709.00 mean =     54533.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.98 mean =        49.22|
|phase err.(test): min =        0.00 max =           89.99 mean =        49.23|
|-----------------------------------------------------------------------------|

============================== 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 = 9.202695              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.374   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.843546              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.264   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      674 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1486 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2567 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3859 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4976 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6513 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7636 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.361 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.630 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.265)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.265)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4581   r_free= 0.4382   ksol= 0.00   Bsol= 0.00   scale= 0.773    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.252700                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4445   r_free= 0.4237   ksol= 0.30   Bsol= 20.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,9.03,9.17,0.00,0.00,0.00); trace/3= 8.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.243739                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.516248              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.737   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.759482              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.049   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4445      final r-factor (work) = 0.3370          |
| start r-factor (free) = 0.4237      final r-factor (free) = 0.3602          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 81.0104 = 8.52 * 0.50 * 6.2585 + 1.00 * 54.3609                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.1122 = 8.52 * 0.50 * 6.1015 + 1.00 * 0.1313                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3370      final r-factor (work) = 0.2835          |
| start r-factor (free) = 0.3602      final r-factor (free) = 0.3233          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6484 = 0.76 * 1.00 * 6.1015 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5400 = 0.76 * 1.00 * 5.9605 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.265)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.10   10.96    None  None   None       |
|    all(noH): 2823   0      0.00    95.10   10.96    None  None   None       |
|    Sol.    : 438    0      0.00    95.10   27.21    None  None   None       |
|    Mac.    : 2385   0      0.00    65.74   7.98     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.510: 1740   |   5:    47.548 -  57.058:   31        |
|      1:     9.510 -  19.019:  607   |   6:    57.058 -  66.568:   13        |
|      2:    19.019 -  28.529:  220   |   7:    66.568 -  76.078:    1        |
|      3:    28.529 -  38.039:  121   |   8:    76.078 -  85.587:    0        |
|      4:    38.039 -  47.548:   89   |   9:    85.587 -  95.097:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2835 r_free = 0.3233             target_work(ml) = 5.916         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2828 r_free = 0.3239             target_work(ml) = 5.915         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2828   r_free= 0.3239   ksol= 0.30   Bsol= 20.00   scale= 1.072   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,9.03,9.17,0.00,0.00,0.00); trace/3= 8.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.915187                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2789   r_free= 0.3176   ksol= 0.33   Bsol= 55.69   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.24,5.71,5.77,0.00,0.00,0.00); trace/3= 5.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.915303                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.100942              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.344   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.436300              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.820  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2789      final r-factor (work) = 0.1923          |
| start r-factor (free) = 0.3176      final r-factor (free) = 0.2316          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3524 = 4.10 * 0.50 * 5.9601 + 1.00 * 0.1313                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8637 = 4.10 * 0.50 * 5.7510 + 1.00 * 0.0714                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1923      final r-factor (work) = 0.1733          |
| start r-factor (free) = 0.2316      final r-factor (free) = 0.2150          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5675 = 0.44 * 1.00 * 5.7510 + 1.00 * 0.0583                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6466 = 0.44 * 1.00 * 5.5320 + 1.00 * 0.2330                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.265)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.94   11.47    None  None   None       |
|    all(noH): 2823   0      0.00    91.94   11.47    None  None   None       |
|    Sol.    : 438    0      0.00    91.94   32.99    None  None   None       |
|    Mac.    : 2385   0      0.00    68.35   7.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.194: 1810   |   5:    45.970 -  55.164:   81        |
|      1:     9.194 -  18.388:  485   |   6:    55.164 -  64.358:   23        |
|      2:    18.388 -  27.582:  162   |   7:    64.358 -  73.552:    5        |
|      3:    27.582 -  36.776:  138   |   8:    73.552 -  82.746:    0        |
|      4:    36.776 -  45.970:  118   |   9:    82.746 -  91.940:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1733 r_free = 0.2150             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1731 r_free = 0.2154             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1731   r_free= 0.2154   ksol= 0.33   Bsol= 55.69   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.24,5.71,5.77,0.00,0.00,0.00); trace/3= 5.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.501119                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1723   r_free= 0.2150   ksol= 0.32   Bsol= 55.69   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.25,4.07,4.70,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.501877                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.290547              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.678  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.952256              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.526   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1723      final r-factor (work) = 0.1298          |
| start r-factor (free) = 0.2150      final r-factor (free) = 0.1711          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9490 = 4.29 * 0.50 * 5.5365 + 1.00 * 0.0716                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6246 = 4.29 * 0.50 * 5.3812 + 1.00 * 0.0805                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1298      final r-factor (work) = 0.1219          |
| start r-factor (free) = 0.1711      final r-factor (free) = 0.1679          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 37.4261 = 6.95 * 1.00 * 5.3812 + 1.00 * 0.0146                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 36.3192 = 6.95 * 1.00 * 5.2214 + 1.00 * 0.0189                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.265)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.03   12.39    None  None   None       |
|    all(noH): 2823   0      0.00    87.03   12.39    None  None   None       |
|    Sol.    : 438    0      0.00    83.41   37.87    None  None   None       |
|    Mac.    : 2385   0      0.00    87.03   7.71     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.703: 1765   |   5:    43.514 -  52.217:   90        |
|      1:     8.703 -  17.406:  501   |   6:    52.217 -  60.920:   74        |
|      2:    17.406 -  26.109:  139   |   7:    60.920 -  69.623:   33        |
|      3:    26.109 -  34.811:  117   |   8:    69.623 -  78.326:   19        |
|      4:    34.811 -  43.514:   77   |   9:    78.326 -  87.029:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1219 r_free = 0.1679             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1219 r_free = 0.1678             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1678   ksol= 0.32   Bsol= 55.69   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.25,4.07,4.70,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.211116                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1685   ksol= 0.33   Bsol= 61.89   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.62,4.50,0.00,0.00,0.00); trace/3= 3.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.212708                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.241884              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.214  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.325341              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.375   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1221      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1685      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9336 = 2.24 * 0.50 * 5.2216 + 1.00 * 0.0805                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8979 = 2.24 * 0.50 * 5.2010 + 1.00 * 0.0679                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1183      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7122 = 0.33 * 1.00 * 5.2010 + 1.00 * 0.0201                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7320 = 0.33 * 1.00 * 5.1965 + 1.00 * 0.0414                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.265)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.53   11.63    None  None   None       |
|    all(noH): 2823   0      0.00    85.53   11.63    None  None   None       |
|    Sol.    : 438    0      0.77    83.56   34.68    None  None   None       |
|    Mac.    : 2385   0      0.00    85.53   7.40     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.553: 1767   |   5:    42.763 -  51.316:   88        |
|      1:     8.553 -  17.105:  507   |   6:    51.316 -  59.869:   48        |
|      2:    17.105 -  25.658:  159   |   7:    59.869 -  68.421:   20        |
|      3:    25.658 -  34.211:  115   |   8:    68.421 -  76.974:   14        |
|      4:    34.211 -  42.763:  101   |   9:    76.974 -  85.527:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1187 r_free = 0.1628             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1185 r_free = 0.1628             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1628   ksol= 0.33   Bsol= 61.89   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.62,4.50,0.00,0.00,0.00); trace/3= 3.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.188409                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1628   ksol= 0.33   Bsol= 61.89   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.62,4.50,0.00,0.00,0.00); trace/3= 3.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.188433                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.490768              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.650  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.364988              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.874   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1185      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1367 = 3.49 * 0.50 * 5.1959 + 1.00 * 0.0679                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1030 = 3.49 * 0.50 * 5.1647 + 1.00 * 0.0887                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8988 = 0.36 * 1.00 * 5.1647 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8930 = 0.36 * 1.00 * 5.1535 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.265)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.73   11.45    None  None   None       |
|    all(noH): 2823   0      0.00    84.73   11.45    None  None   None       |
|    Sol.    : 438    0      1.05    82.92   34.21    None  None   None       |
|    Mac.    : 2385   0      0.00    84.73   7.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.473: 1777   |   5:    42.363 -  50.835:   94        |
|      1:     8.473 -  16.945:  502   |   6:    50.835 -  59.308:   45        |
|      2:    16.945 -  25.418:  155   |   7:    59.308 -  67.780:   20        |
|      3:    25.418 -  33.890:  116   |   8:    67.780 -  76.253:   12        |
|      4:    33.890 -  42.363:   98   |   9:    76.253 -  84.725:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1601             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1122 r_free = 0.1602             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1602   ksol= 0.33   Bsol= 61.89   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.62,4.50,0.00,0.00,0.00); trace/3= 3.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153091                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.8194 0.99   1363  152 0.1019 0.1369      5.4151      5.5479|
|  2:  4.8194 -  3.8460 0.99   1299  144 0.0847 0.1131      5.4413      5.6519|
|  3:  3.8460 -  3.3659 0.99   1272  141 0.1040 0.1449      5.4771      5.8298|
|  4:  3.3659 -  3.0609 0.99   1277  142 0.1181 0.1546      5.4456       5.616|
|  5:  3.0609 -  2.8431 0.99   1255  140 0.1322 0.1767      5.3444      5.5466|
|  6:  2.8431 -  2.6764 0.99   1266  140 0.1227 0.1849      5.2421      5.4979|
|  7:  2.6764 -  2.5430 0.99   1246  139 0.1295 0.1796      5.1974       5.415|
|  8:  2.5430 -  2.4328 0.98   1249  138 0.1193 0.1728       5.113      5.3841|
|  9:  2.4328 -  2.3395 0.98   1233  137 0.1183 0.1728      5.0612      5.2873|
| 10:  2.3395 -  2.2590 1.00   1237  138 0.1169 0.1941      5.0145      5.3411|
| 11:  2.2590 -  2.1886 0.97   1250  139 0.1156 0.1638      4.9636      5.2129|
| 12:  2.1886 -  2.1262 0.97   1224  136 0.1141 0.1851      4.9041      5.2841|
| 13:  2.1262 -  2.0704 0.99   1229  136 0.1130 0.1749      4.8068      5.0646|
| 14:  2.0704 -  2.0200 0.97   1230  137 0.1038 0.1669      4.6465      4.9355|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.8194  1363   152  0.94   9.60   0.97     0.94       7936.54|
|  2:  4.8194 -  3.8460  1299   144  0.95   8.27   1.00     0.98       9408.18|
|  3:  3.8460 -  3.3659  1272   141  0.94  11.05   1.01     1.01      10434.42|
|  4:  3.3659 -  3.0609  1277   142  0.92  13.11   1.00     0.98      10036.58|
|  5:  3.0609 -  2.8431  1255   140  0.90  15.87   0.99     0.96       8601.85|
|  6:  2.8431 -  2.6764  1266   140  0.90  16.13   0.98     0.95       7485.77|
|  7:  2.6764 -  2.5430  1246   139  0.90  16.16   0.98     0.95       6576.30|
|  8:  2.5430 -  2.4328  1249   138  0.91  15.40   0.98     0.96       5800.90|
|  9:  2.4328 -  2.3395  1233   137  0.90  16.12   1.00     0.96       5429.60|
| 10:  2.3395 -  2.2590  1237   138  0.90  16.02   0.99     0.95       4773.96|
| 11:  2.2590 -  2.1886  1250   139  0.90  16.35   0.99     0.95       4589.47|
| 12:  2.1886 -  2.1262  1224   136  0.91  15.57   1.00     0.98       4112.44|
| 13:  2.1262 -  2.0704  1229   136  0.91  15.49   0.99     0.98       3399.66|
| 14:  2.0704 -  2.0200  1230   137  0.92  14.15   0.96     0.93       2395.16|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2395.16 max =        10434.42 mean =      6541.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.18|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.67|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1601   ksol= 0.32   Bsol= 58.31   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.21,0.81,-0.00,0.00,0.00); trace/3= -0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.152951                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1601   ksol= 0.32   Bsol= 58.31   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.21,0.81,-0.00,0.00,0.00); trace/3= -0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.152951                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.8194 0.99   1363  152 0.1014 0.1365      5.4108      5.5443|
|  2:  4.8194 -  3.8460 0.99   1299  144 0.0843 0.1124      5.4367      5.6453|
|  3:  3.8460 -  3.3659 0.99   1272  141 0.1038 0.1450      5.4751      5.8297|
|  4:  3.3659 -  3.0609 0.99   1277  142 0.1183 0.1549       5.447      5.6177|
|  5:  3.0609 -  2.8431 0.99   1255  140 0.1326 0.1772      5.3469      5.5487|
|  6:  2.8431 -  2.6764 0.99   1266  140 0.1230 0.1851       5.244      5.4996|
|  7:  2.6764 -  2.5430 0.99   1246  139 0.1297 0.1801      5.1989       5.417|
|  8:  2.5430 -  2.4328 0.98   1249  138 0.1196 0.1729      5.1139      5.3845|
|  9:  2.4328 -  2.3395 0.98   1233  137 0.1183 0.1725      5.0615      5.2869|
| 10:  2.3395 -  2.2590 1.00   1237  138 0.1169 0.1943       5.015      5.3426|
| 11:  2.2590 -  2.1886 0.97   1250  139 0.1158 0.1639      4.9642      5.2138|
| 12:  2.1886 -  2.1262 0.97   1224  136 0.1140 0.1852      4.9044      5.2843|
| 13:  2.1262 -  2.0704 0.99   1229  136 0.1131 0.1751      4.8067      5.0651|
| 14:  2.0704 -  2.0200 0.97   1230  137 0.1039 0.1667      4.6462      4.9345|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.8194  1363   152  0.94   9.56   0.97     0.94       7865.99|
|  2:  4.8194 -  3.8460  1299   144  0.95   8.20   1.00     0.99       9327.75|
|  3:  3.8460 -  3.3659  1272   141  0.94  11.02   1.02     1.01      10381.61|
|  4:  3.3659 -  3.0609  1277   142  0.92  13.13   1.00     0.98      10063.67|
|  5:  3.0609 -  2.8431  1255   140  0.90  15.90   0.99     0.96       8640.40|
|  6:  2.8431 -  2.6764  1266   140  0.90  16.17   0.98     0.95       7518.05|
|  7:  2.6764 -  2.5430  1246   139  0.90  16.18   0.98     0.96       6596.57|
|  8:  2.5430 -  2.4328  1249   138  0.91  15.41   0.98     0.96       5807.66|
|  9:  2.4328 -  2.3395  1233   137  0.90  16.14   1.00     0.96       5434.52|
| 10:  2.3395 -  2.2590  1237   138  0.90  16.03   0.99     0.95       4777.11|
| 11:  2.2590 -  2.1886  1250   139  0.90  16.36   0.99     0.95       4597.28|
| 12:  2.1886 -  2.1262  1224   136  0.91  15.58   1.00     0.98       4118.00|
| 13:  2.1262 -  2.0704  1229   136  0.91  15.49   0.99     0.98       3399.93|
| 14:  2.0704 -  2.0200  1230   137  0.92  14.13   0.97     0.93       2390.97|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2390.97 max =        10381.61 mean =      6536.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.18|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.67|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.265)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.79    88.51   15.24    None  None   None       |
|    all(noH): 2823   0      3.79    88.51   15.24    None  None   None       |
|    Sol.    : 438    0      4.83    86.70   38.00    None  None   None       |
|    Mac.    : 2385   0      3.79    88.51   11.06    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:     3.786 -  12.259: 1777   |   5:    46.149 -  54.621:   94        |
|      1:    12.259 -  20.731:  502   |   6:    54.621 -  63.094:   45        |
|      2:    20.731 -  29.204:  155   |   7:    63.094 -  71.566:   20        |
|      3:    29.204 -  37.676:  116   |   8:    71.566 -  80.039:   12        |
|      4:    37.676 -  46.149:   98   |   9:    80.039 -  88.511:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.261 - 5.959
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 317
   mapped sites are within: 0.703 - 5.959

peak=    9.563 closest distance to " CG2 VAL A 230 " =    1.304
peak=    6.104 closest distance to " NH2 ARG A  56 " =    2.287
peak=    6.033 closest distance to " CG  LEU A   5 " =    1.216
peak=    5.777 closest distance to " CG  LEU A 228 " =    1.194
peak=    5.588 closest distance to " CB  VAL A 296 " =    1.174
peak=    5.374 closest distance to " CB  VAL A 230 " =    1.218
peak=    5.329 closest distance to " CB  GLN A 223 " =    1.463
peak=    5.061 closest distance to " CG  PRO A  54 " =    1.281
peak=    5.012 closest distance to " CB  GLN A 183 " =    1.260
peak=    4.843 closest distance to " CD2 LEU A   5 " =    1.166
peak=    4.813 closest distance to " CB  SER A  63 " =    1.268
peak=    4.737 closest distance to " O   HOH Z 232 " =    2.335
peak=    4.674 closest distance to " NE2 GLN A  11 " =    1.133
peak=    4.616 closest distance to " CG2 VAL A 296 " =    0.992
peak=    4.504 closest distance to " CB  PRO A  54 " =    0.898
peak=    4.447 closest distance to " CB  ARG A 190 " =    1.587
peak=    4.443 closest distance to " C   PRO A 198 " =    1.518
peak=    4.428 closest distance to " O   HOH Z 369 " =    2.105
peak=    4.413 closest distance to " O   HOH Z 265 " =    2.201
peak=    4.324 closest distance to " CZ  PHE A 218 " =    1.124
peak=    4.275 closest distance to " CB  GLU A 152 " =    1.165
peak=    4.254 closest distance to " O   HOH Z 126 " =    1.909
peak=    4.243 closest distance to " O   HOH Z 303 " =    2.149
peak=    4.202 closest distance to " O   SER A  87 " =    2.260
peak=    4.197 closest distance to " CB  ARG A 275 " =    0.891
peak=    4.175 closest distance to " O   HOH Z 423 " =    1.827
peak=    4.172 closest distance to " O   HOH Z 234 " =    3.729
peak=    4.147 closest distance to " CB  ARG A  79 " =    1.509
peak=    4.144 closest distance to " O   HOH Z 368 " =    2.323
peak=    4.139 closest distance to " CB  ASP A 140 " =    0.967
peak=    4.128 closest distance to " O   HOH Z 427 " =    3.052
peak=    4.121 closest distance to " CB  ASN A 148 " =    1.425
peak=    4.120 closest distance to " CB  GLU A 277 " =    3.680
peak=    4.101 closest distance to " CA  ALA A  51 " =    0.982
peak=    4.077 closest distance to " O   HOH Z 272 " =    1.927
peak=    4.061 closest distance to " CG  PRO A 213 " =    1.178
peak=    4.049 closest distance to " O   HOH Z 298 " =    1.905
peak=    4.048 closest distance to " CA  TYR A  30 " =    0.955
peak=    4.047 closest distance to " CB  TRP A 266 " =    0.975
peak=    4.044 closest distance to " ND2 ASN A 187 " =    1.553
peak=    4.026 closest distance to " O   HOH Z 236 " =    1.947
peak=    4.015 closest distance to " O   HOH Z  63 " =    1.926
peak=    4.007 closest distance to " CG  PRO A 243 " =    1.136
peak=    4.001 closest distance to " OD1 ASN A  69 " =    2.603
peak=    3.993 closest distance to " O   HOH Z 280 " =    2.938
peak=    3.989 closest distance to " OG BSER A 164 " =    2.208
peak=    3.972 closest distance to " O   HOH Z  44 " =    2.108
peak=    3.972 closest distance to " O   HOH Z  61 " =    1.596
peak=    3.961 closest distance to " O   HOH Z 403 " =    1.639
peak=    3.961 closest distance to " O   HOH Z 411 " =    3.780
peak=    3.955 closest distance to " O   HOH Z 422 " =    2.732
peak=    3.954 closest distance to " ND2 ASN A 249 " =    1.964
peak=    3.945 closest distance to " O   HOH Z 126 " =    1.617
peak=    3.935 closest distance to " CB  GLU A 128 " =    1.048
peak=    3.916 closest distance to " CB  VAL A 265 " =    1.332
peak=    3.908 closest distance to " O   HOH Z 142 " =    1.576
peak=    3.907 closest distance to " NH1AARG A 145 " =    1.216
peak=    3.904 closest distance to " O   HOH Z 158 " =    3.220
peak=    3.903 closest distance to " CG1 VAL A 296 " =    1.134
peak=    3.898 closest distance to " O   HOH Z 214 " =    2.272
peak=    3.888 closest distance to " CB  VAL A 202 " =    1.537
peak=    3.884 closest distance to " O   HOH Z  78 " =    1.613
peak=    3.863 closest distance to " CD  LYS A 166 " =    1.277
peak=    3.860 closest distance to " OG  SER A  97 " =    2.936
peak=    3.847 closest distance to " O   HOH Z 203 " =    1.800
peak=    3.830 closest distance to " O   HOH Z 248 " =    1.641
peak=    3.826 closest distance to " O   HOH Z 316 " =    3.117
peak=    3.824 closest distance to " CG  MET A 185 " =    1.196
peak=    3.814 closest distance to " O   HOH Z 261 " =    1.924
peak=    3.808 closest distance to " O   HOH Z 346 " =    1.543
peak=    3.803 closest distance to " O   HOH Z 402 " =    1.513
peak=    3.799 closest distance to " O   HOH Z 425 " =    1.379
peak=    3.791 closest distance to " O   HOH Z  48 " =    1.699
peak=    3.787 closest distance to " CB  GLU A  46 " =    0.961
peak=    3.782 closest distance to " O   HOH Z  40 " =    1.774
peak=    3.777 closest distance to " CB  LEU A 143 " =    1.205
peak=    3.777 closest distance to " CA  PRO A  54 " =    1.360
peak=    3.773 closest distance to " CB  ASN A 142 " =    1.043
peak=    3.766 closest distance to " CG  PRO A 198 " =    1.325
peak=    3.756 closest distance to " CB  ALA A   9 " =    1.637
peak=    3.738 closest distance to " O   HOH Z  80 " =    1.716
peak=    3.738 closest distance to " CG1 ILE A  49 " =    1.550
peak=    3.734 closest distance to " CG2 THR A 221 " =    1.098
peak=    3.733 closest distance to " O   HOH Z  15 " =    2.085
peak=    3.732 closest distance to " O   HOH Z 227 " =    1.799
peak=    3.728 closest distance to " O   HOH Z  43 " =    2.000
peak=    3.721 closest distance to " CB  ASN A  39 " =    0.837
peak=    3.719 closest distance to " CD1 LEU A   5 " =    1.326
peak=    3.716 closest distance to " O   HOH Z 193 " =    2.119
peak=    3.709 closest distance to " O   MET A 105 " =    1.877
peak=    3.693 closest distance to " O   HOH Z 285 " =    2.701
peak=    3.686 closest distance to " CG1 VAL A 153 " =    1.002
peak=    3.684 closest distance to " O   HOH Z  97 " =    2.004
peak=    3.684 closest distance to " O   HOH Z 197 " =    2.782
peak=    3.677 closest distance to " CB  ASN A 187 " =    1.131
peak=    3.677 closest distance to " NH2 ARG A 156 " =    1.152
peak=    3.676 closest distance to " N   ASN A  39 " =    1.241
peak=    3.659 closest distance to " O   HOH Z 313 " =    1.761
peak=    3.648 closest distance to " CD ALYS A 290 " =    1.083
peak=    3.641 closest distance to " O   HOH Z  19 " =    2.072
peak=    3.638 closest distance to " CD1 LEU A 300 " =    1.183
peak=    3.637 closest distance to " CD  ARG A 159 " =    0.766
peak=    3.632 closest distance to " O  BHOH Z 338 " =    2.412
peak=    3.629 closest distance to " CA  THR A 264 " =    0.759
peak=    3.624 closest distance to " O   HOH Z 371 " =    3.024
peak=    3.615 closest distance to " NE2 GLN A  77 " =    3.366
peak=    3.614 closest distance to " O   HOH Z 147 " =    1.812
peak=    3.612 closest distance to " CD2 LEU A 228 " =    1.092
peak=    3.603 closest distance to " CB  THR A  31 " =    1.595
peak=    3.598 closest distance to " O   HOH Z 193 " =    1.881
peak=    3.596 closest distance to " CD  ARG A  66 " =    2.613
peak=    3.595 closest distance to " CA  ARG A 195 " =    1.209
peak=    3.594 closest distance to " O   HOH Z 406 " =    1.529
peak=    3.592 closest distance to " CD2 TRP A 179 " =    1.345
peak=    3.591 closest distance to " CG1BVAL A  72 " =    1.829
peak=    3.573 closest distance to " O   HOH Z 180 " =    2.124
peak=    3.563 closest distance to " CA  ALA A 158 " =    1.197
peak=    3.559 closest distance to " NZ  LYS A  48 " =    1.352
peak=    3.556 closest distance to " CA  ASP A 162 " =    1.022
peak=    3.555 closest distance to " CB  ALA A 100 " =    1.245
peak=    3.552 closest distance to " CA  ALA A 295 " =    1.052
peak=    3.550 closest distance to " N   VAL A 126 " =    1.407
peak=    3.547 closest distance to " O   HOH Z  21 " =    1.722
peak=    3.546 closest distance to " CE1 TYR A 186 " =    1.263
peak=    3.537 closest distance to " O   ALA A 158 " =    1.355
peak=    3.536 closest distance to " O   HOH Z 172 " =    3.879
peak=    3.536 closest distance to " O   HOH Z 213 " =    1.748
peak=    3.525 closest distance to " CB  TRP A 179 " =    1.447
peak=    3.524 closest distance to " O   HOH Z 126 " =    1.772
peak=    3.523 closest distance to " CB  SER A   3 " =    1.282
peak=    3.522 closest distance to " O   HOH Z 171 " =    3.896
peak=    3.521 closest distance to " CA  THR A 221 " =    0.888
peak=    3.519 closest distance to " O   HOH Z 133 " =    2.322
peak=    3.519 closest distance to " CB  ALA A 248 " =    1.110
peak=    3.518 closest distance to " O   HOH Z 108 " =    2.699
peak=    3.518 closest distance to " CB  ALA A 104 " =    0.731
peak=    3.517 closest distance to " CG1 ILE A  33 " =    1.254
peak=    3.509 closest distance to " O   HOH Z 299 " =    4.314
peak=    3.506 closest distance to " OG  SER A  22 " =    2.810
peak=    3.501 closest distance to " CA  ILE A 106 " =    0.743
peak=    3.499 closest distance to " CB  TRP A 150 " =    1.394
peak=    3.494 closest distance to " CA  SER A  87 " =    1.038
peak=    3.491 closest distance to " CB  GLN A  88 " =    1.214
peak=    3.486 closest distance to " CD  ARG A 269 " =    0.871
peak=    3.485 closest distance to " O   HOH Z 102 " =    1.339
peak=    3.484 closest distance to " O   HOH Z 193 " =    1.714
peak=    3.484 closest distance to " CA  ALA A 291 " =    0.890
peak=    3.479 closest distance to " O   HOH Z 112 " =    1.678
peak=    3.479 closest distance to " CB BVAL A  41 " =    1.106
peak=    3.478 closest distance to " CA  LYS A 117 " =    1.256
peak=    3.477 closest distance to " O   ASP A 124 " =    1.200
peak=    3.461 closest distance to " CA  TYR A 116 " =    1.440
peak=    3.459 closest distance to " O   HOH Z  68 " =    2.135
peak=    3.455 closest distance to " C   TYR A 214 " =    1.562
peak=    3.442 closest distance to " O   HOH Z 128 " =    2.158
peak=    3.442 closest distance to " CB  ALA A 291 " =    1.356
peak=    3.435 closest distance to " CB  THR A  82 " =    1.410
peak=    3.434 closest distance to " O   HOH Z 359 " =    1.470
peak=    3.432 closest distance to " O   HOH Z  97 " =    2.452
peak=    3.432 closest distance to " O   LYS A 290 " =    2.442
peak=    3.424 closest distance to " CG  LEU A 167 " =    1.198
peak=    3.424 closest distance to " CB  LEU A 228 " =    1.200
peak=    3.423 closest distance to " CA  ASP A 191 " =    0.823
peak=    3.421 closest distance to " CA  ALA A  21 " =    1.145
peak=    3.416 closest distance to " O   HOH Z 273 " =    2.827
peak=    3.409 closest distance to " CB  LEU A  83 " =    0.728
peak=    3.408 closest distance to " O   HOH Z 251 " =    1.447
peak=    3.408 closest distance to " O   HOH Z 163 " =    1.636
peak=    3.403 closest distance to " CB  ILE A 120 " =    1.310
peak=    3.402 closest distance to " O   HOH Z 245 " =    1.394
peak=    3.401 closest distance to " CB  THR A  52 " =    1.103
peak=    3.400 closest distance to " O   HOH Z  88 " =    3.273
peak=    3.400 closest distance to " O   HOH Z 437 " =    1.725
peak=    3.398 closest distance to " N   SER A 135 " =    1.492
peak=    3.397 closest distance to " CB  SER A 212 " =    1.216
peak=    3.396 closest distance to " CB  ARG A  79 " =    0.926
peak=    3.396 closest distance to " O   HOH Z 383 " =    2.052
peak=    3.396 closest distance to " CZ  PHE A 192 " =    0.972
peak=    3.396 closest distance to " CB  MET A  40 " =    0.778
peak=    3.388 closest distance to " CB  THR A 157 " =    1.143
peak=    3.385 closest distance to " O   HOH Z 128 " =    2.367
peak=    3.385 closest distance to " CG  GLN A  58 " =    2.955
peak=    3.384 closest distance to " NH2 ARG A  79 " =    1.269
peak=    3.378 closest distance to " O   HOH Z 199 " =    1.654
peak=    3.373 closest distance to " CG  MET A 185 " =    1.014
peak=    3.371 closest distance to " O   HOH Z  59 " =    2.391
peak=    3.371 closest distance to " CE  LYS A  76 " =    0.865
peak=    3.369 closest distance to " O   HOH Z 327 " =    1.816
peak=    3.368 closest distance to " O   HOH Z 134 " =    1.390
peak=    3.368 closest distance to " CA  MET A  40 " =    1.191
peak=    3.363 closest distance to " ND1 HIS A  81 " =    1.677
peak=    3.358 closest distance to " CA  VAL A 125 " =    1.263
peak=    3.355 closest distance to " N   ASP A 162 " =    1.307
peak=    3.352 closest distance to " CB  ARG A 139 " =    0.956
peak=    3.346 closest distance to " CB  SER A  26 " =    1.776
peak=    3.344 closest distance to " CG BARG A 275 " =    1.357
peak=    3.340 closest distance to " CA  LEU A 282 " =    1.032
peak=    3.338 closest distance to " CB  GLN A 103 " =    0.998
peak=    3.331 closest distance to " O   THR A  31 " =    1.604
peak=    3.327 closest distance to " O   HOH Z 132 " =    2.719
peak=    3.327 closest distance to " CB  GLN A 205 " =    1.092
peak=    3.324 closest distance to " CB  GLN A 278 " =    0.855
peak=    3.322 closest distance to " NE  ARG A  79 " =    1.211
peak=    3.320 closest distance to " O   HOH Z 133 " =    1.631
peak=    3.319 closest distance to " CB  HIS A 108 " =    0.761
peak=    3.318 closest distance to " O   HOH Z  10 " =    1.771
peak=    3.315 closest distance to " O   HOH Z 238 " =    2.325
peak=    3.314 closest distance to " O   HOH Z 141 " =    1.646
peak=    3.312 closest distance to " CA  LYS A 181 " =    1.080
peak=    3.307 closest distance to " NZ  LYS A 117 " =    3.297
peak=    3.305 closest distance to " O   TRP A 274 " =    1.881
peak=    3.301 closest distance to " O   GLN A 278 " =    1.538
peak=    3.300 closest distance to " CA  MET A 105 " =    0.961
peak=    3.294 closest distance to " O   HOH Z 148 " =    3.192
peak=    3.293 closest distance to " O   HOH Z 145 " =    2.074
peak=    3.291 closest distance to " O   HOH Z 368 " =    3.581
peak=    3.289 closest distance to " O   HOH Z 146 " =    2.297
peak=    3.285 closest distance to " CA  ARG A  36 " =    1.112
peak=    3.282 closest distance to " O   HOH Z 130 " =    2.264
peak=    3.281 closest distance to " CG2 VAL A 257 " =    0.787
peak=    3.275 closest distance to " O   ALA A 165 " =    1.434
peak=    3.272 closest distance to " O   HOH Z 417 " =    3.268
peak=    3.270 closest distance to " CB  ASN A 110 " =    1.179
peak=    3.270 closest distance to " O   HOH Z 250 " =    1.368
peak=    3.269 closest distance to " O   HOH Z 305 " =    3.663
peak=    3.268 closest distance to " O   HOH Z 187 " =    2.335
peak=    3.265 closest distance to " OD1 ASN A 217 " =    1.612
peak=    3.263 closest distance to " CA  ALA A 154 " =    0.964
peak=    3.261 closest distance to " CB  ALA A  34 " =    0.783
peak=    3.261 closest distance to " O   GLU A   2 " =    1.675
peak=    3.258 closest distance to " CB  ALA A   1 " =    4.845
peak=    3.247 closest distance to " N   PHE A 130 " =    1.234
peak=    3.244 closest distance to " O   HOH Z 291 " =    1.590
peak=    3.244 closest distance to " O   HOH Z 325 " =    2.288
peak=    3.243 closest distance to " O   HOH Z 403 " =    1.432
peak=    3.243 closest distance to " CE2 TYR A  30 " =    0.831
peak=    3.242 closest distance to " O   HOH Z 295 " =    1.530
peak=    3.239 closest distance to " O   HOH Z 313 " =    1.635
peak=    3.239 closest distance to " CG  GLN A  88 " =    1.072
peak=    3.237 closest distance to " O   HOH Z 353 " =    2.678
peak=    3.234 closest distance to " CZ3 TRP A 274 " =    4.561
peak=    3.231 closest distance to " O   PRO A  90 " =    1.307
peak=    3.219 closest distance to " CB  GLN A  89 " =    1.130
peak=    3.216 closest distance to " CG  PHE A 204 " =    0.920
peak=    3.213 closest distance to " O   HOH Z 247 " =    1.378
peak=    3.213 closest distance to " CG1 ILE A 151 " =    1.120
peak=    3.213 closest distance to " CA  ASN A 215 " =    1.202
peak=    3.212 closest distance to " O   HOH Z  49 " =    3.418
peak=    3.212 closest distance to " O   HOH Z 420 " =    5.959
peak=    3.206 closest distance to " O   HOH Z 365 " =    2.920
peak=    3.203 closest distance to " O   HOH Z  85 " =    2.236
peak=    3.197 closest distance to " O   HOH Z 435 " =    1.965
peak=    3.195 closest distance to " OG  SER A 245 " =    1.618
peak=    3.189 closest distance to " O   HOH Z 258 " =    2.123
peak=    3.187 closest distance to " CD  LYS A 119 " =    1.943
peak=    3.186 closest distance to " CB  PRO A  90 " =    1.287
peak=    3.185 closest distance to " CA  GLY A 211 " =    1.324
peak=    3.184 closest distance to " O   HOH Z 384 " =    3.149
peak=    3.184 closest distance to " CZ3 TRP A  85 " =    1.058
peak=    3.183 closest distance to " O   HOH Z 171 " =    2.445
peak=    3.181 closest distance to " O   HOH Z 344 " =    2.997
peak=    3.181 closest distance to " CG2 ILE A  20 " =    1.425
peak=    3.176 closest distance to " O   HOH Z 420 " =    2.020
peak=    3.176 closest distance to " CA  ALA A 233 " =    1.529
peak=    3.170 closest distance to " O   HOH Z 263 " =    1.638
peak=    3.166 closest distance to " CB  ASN A 224 " =    0.999
peak=    3.165 closest distance to " CB  LYS A 117 " =    1.200
peak=    3.164 closest distance to " CG2 ILE A 234 " =    0.854
peak=    3.163 closest distance to " O   ASN A 284 " =    1.827
peak=    3.162 closest distance to " CZ  PHE A  38 " =    1.150
peak=    3.162 closest distance to " O   HOH Z 188 " =    1.947
peak=    3.161 closest distance to " CB  ASN A 285 " =    0.914
peak=    3.157 closest distance to " O   HOH Z 256 " =    2.334
peak=    3.155 closest distance to " CB  LEU A 261 " =    0.811
peak=    3.154 closest distance to " CB  PRO A 243 " =    1.580
peak=    3.153 closest distance to " CG BARG A 102 " =    1.782
peak=    3.153 closest distance to " O   HOH Z 116 " =    1.823
peak=    3.147 closest distance to " CB  PHE A 204 " =    0.904
peak=    3.142 closest distance to " CD1 ILE A  33 " =    1.690
peak=    3.141 closest distance to " O   HOH Z 294 " =    1.560
peak=    3.139 closest distance to " NZ  LYS A  76 " =    1.560
peak=    3.134 closest distance to " O   HOH Z  46 " =    1.532
peak=    3.128 closest distance to " O   ILE A  20 " =    2.249
peak=    3.127 closest distance to " N   CYS A 260 " =    0.703
peak=    3.127 closest distance to " CZ3 TRP A  92 " =    1.397
peak=    3.122 closest distance to " CB  TYR A 116 " =    0.898
peak=    3.122 closest distance to " CB  PHE A 204 " =    0.900
peak=    3.120 closest distance to " CA  VAL A  41 " =    0.841
peak=    3.118 closest distance to " O   HOH Z 261 " =    1.604
peak=    3.117 closest distance to " CG2 VAL A 197 " =    1.018
peak=    3.116 closest distance to " O   HOH Z 329 " =    4.073
peak=    3.114 closest distance to " CB  VAL A 268 " =    0.848
peak=    3.113 closest distance to " O   HOH Z 201 " =    3.079
peak=    3.108 closest distance to " CA  ASN A 217 " =    1.261
peak=    3.107 closest distance to " O   HOH Z 293 " =    1.747
peak=    3.104 closest distance to " CB  ASN A 215 " =    1.174
peak=    3.103 closest distance to " O   HOH Z 421 " =    3.119
peak=    3.089 closest distance to " CB  VAL A 257 " =    0.731
peak=    3.084 closest distance to " CB  ALA A 114 " =    1.281
peak=    3.084 closest distance to " CB  LEU A  96 " =    1.315
peak=    3.076 closest distance to " CB  ARG A 138 " =    1.015
peak=    3.073 closest distance to " O   HOH Z 184 " =    1.434
peak=    3.060 closest distance to " OE2 GLU A   2 " =    1.872
peak=    3.060 closest distance to " CD1 ILE A 106 " =    1.039
peak=    3.045 closest distance to " CD  ARG A  79 " =    1.943
peak=    3.029 closest distance to " O   HOH Z 358 " =    3.725
peak=    3.024 closest distance to " O   HOH Z 430 " =    4.002

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 222         
Filter by distance & map next to the model:
   mapped sites are within: 0.780 - 5.283
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 221 from: 222
   mapped sites are within: 0.780 - 5.283

peak=   -5.567 closest distance to " CG2 VAL A 230 " =    0.864
peak=   -4.587 closest distance to " CD  ARG A 156 " =    2.063
peak=   -4.421 closest distance to " CD  GLN A  58 " =    1.022
peak=   -4.345 closest distance to " CB  PRO A 243 " =    2.644
peak=   -4.292 closest distance to " O   HOH Z 266 " =    5.283
peak=   -4.261 closest distance to " CD  ARG A  14 " =    3.264
peak=   -4.220 closest distance to " O   HOH Z 196 " =    2.247
peak=   -4.077 closest distance to " CG2BVAL A  41 " =    2.626
peak=   -4.075 closest distance to " CG1 VAL A 250 " =    2.804
peak=   -4.072 closest distance to " OG  SER A  97 " =    2.336
peak=   -4.033 closest distance to " CE2 TYR A  30 " =    2.742
peak=   -4.015 closest distance to " O   ILE A 109 " =    2.634
peak=   -3.962 closest distance to " OE1 GLN A 223 " =    2.121
peak=   -3.957 closest distance to " O   VAL A  67 " =    2.793
peak=   -3.944 closest distance to " CZ3 TRP A 179 " =    1.181
peak=   -3.934 closest distance to " CA  ASP A 298 " =    1.070
peak=   -3.899 closest distance to " O   HOH Z  37 " =    1.926
peak=   -3.872 closest distance to " O   HOH Z 290 " =    1.251
peak=   -3.862 closest distance to " C   HIS A 108 " =    1.165
peak=   -3.848 closest distance to " O   HOH Z  73 " =    2.257
peak=   -3.841 closest distance to " CG1 VAL A 112 " =    2.602
peak=   -3.840 closest distance to " NH2AARG A 275 " =    5.218
peak=   -3.835 closest distance to " CA  GLY A 241 " =    3.120
peak=   -3.834 closest distance to " O   HOH Z  52 " =    1.637
peak=   -3.800 closest distance to " OG BSER A 134 " =    1.272
peak=   -3.787 closest distance to " CG  ARG A 269 " =    2.453
peak=   -3.772 closest distance to " O   HOH Z 231 " =    2.175
peak=   -3.765 closest distance to " OXT GLY A 302 " =    2.956
peak=   -3.762 closest distance to " O   HOH Z 394 " =    1.564
peak=   -3.759 closest distance to " O   HOH Z 351 " =    1.587
peak=   -3.756 closest distance to " CZ2 TRP A  92 " =    2.854
peak=   -3.743 closest distance to " NE2 GLN A 194 " =    1.905
peak=   -3.742 closest distance to " CB  PHE A 192 " =    1.929
peak=   -3.737 closest distance to " C   ALA A 158 " =    1.352
peak=   -3.731 closest distance to " N   ALA A  43 " =    2.649
peak=   -3.722 closest distance to " O   HOH Z 185 " =    2.414
peak=   -3.718 closest distance to " O   HOH Z 166 " =    1.884
peak=   -3.717 closest distance to " CD1 PHE A  59 " =    2.008
peak=   -3.711 closest distance to " CG1 VAL A 296 " =    1.306
peak=   -3.700 closest distance to " O   HOH Z 211 " =    1.540
peak=   -3.688 closest distance to " O   HOH Z  10 " =    1.521
peak=   -3.680 closest distance to " O   HOH Z 114 " =    3.120
peak=   -3.671 closest distance to " CD1 LEU A 101 " =    2.450
peak=   -3.647 closest distance to " O   SER A 271 " =    2.167
peak=   -3.641 closest distance to " N   ALA A 226 " =    2.128
peak=   -3.621 closest distance to " CG  ASP A 231 " =    0.780
peak=   -3.617 closest distance to " CB  ALA A 248 " =    2.352
peak=   -3.612 closest distance to " OD1 ASN A 148 " =    1.497
peak=   -3.607 closest distance to " NE2 GLN A 103 " =    1.744
peak=   -3.603 closest distance to " CD2 PHE A  61 " =    2.511
peak=   -3.595 closest distance to " CD2 LEU A 300 " =    2.793
peak=   -3.595 closest distance to " O   PRO A 163 " =    2.160
peak=   -3.593 closest distance to " CD2 TYR A 293 " =    2.080
peak=   -3.593 closest distance to " CG1 VAL A 112 " =    2.769
peak=   -3.590 closest distance to " O   HOH Z 241 " =    1.154
peak=   -3.588 closest distance to " CE3 TRP A 150 " =    2.293
peak=   -3.566 closest distance to " CE BMET A  47 " =    2.110
peak=   -3.549 closest distance to " O   HOH Z  11 " =    1.927
peak=   -3.540 closest distance to " CB  ALA A 248 " =    2.159
peak=   -3.532 closest distance to " O   HOH Z 222 " =    1.508
peak=   -3.528 closest distance to " C   LEU A 143 " =    1.006
peak=   -3.526 closest distance to " O   HOH Z  44 " =    2.155
peak=   -3.516 closest distance to " CG  TRP A 266 " =    1.852
peak=   -3.510 closest distance to " O   HOH Z 128 " =    2.691
peak=   -3.508 closest distance to " CD2 LEU A 167 " =    1.790
peak=   -3.498 closest distance to " O   HOH Z 407 " =    3.263
peak=   -3.494 closest distance to " ND2 ASN A  45 " =    1.916
peak=   -3.491 closest distance to " CB  VAL A 230 " =    1.013
peak=   -3.481 closest distance to " O   VAL A 189 " =    2.624
peak=   -3.476 closest distance to " O   PRO A 198 " =    1.260
peak=   -3.462 closest distance to " N   ASP A 171 " =    2.328
peak=   -3.459 closest distance to " CB  ALA A  43 " =    2.555
peak=   -3.455 closest distance to " O   HOH Z 136 " =    2.392
peak=   -3.454 closest distance to " O   HOH Z 377 " =    2.119
peak=   -3.450 closest distance to " O   HOH Z 234 " =    4.357
peak=   -3.448 closest distance to " CG  GLU A 277 " =    1.154
peak=   -3.447 closest distance to " O   HOH Z 353 " =    2.140
peak=   -3.446 closest distance to " NE2 GLN A  88 " =    2.094
peak=   -3.445 closest distance to " CB  ALA A 291 " =    2.223
peak=   -3.436 closest distance to " CB  PRO A 163 " =    2.560
peak=   -3.431 closest distance to " O   HOH Z 177 " =    1.756
peak=   -3.426 closest distance to " N   THR A 235 " =    1.309
peak=   -3.421 closest distance to " OG ASER A 134 " =    1.344
peak=   -3.419 closest distance to " O   HOH Z  38 " =    1.555
peak=   -3.419 closest distance to " ND2 ASN A 187 " =    1.654
peak=   -3.413 closest distance to " O   HOH Z 166 " =    1.639
peak=   -3.409 closest distance to " O   HOH Z 292 " =    4.664
peak=   -3.408 closest distance to " O   HOH Z  15 " =    1.519
peak=   -3.402 closest distance to " CD1 ILE A 199 " =    2.590
peak=   -3.399 closest distance to " NH2 ARG A 159 " =    2.435
peak=   -3.398 closest distance to " O   HOH Z 434 " =    1.826
peak=   -3.395 closest distance to " O   HOH Z 435 " =    2.604
peak=   -3.393 closest distance to " CG2 ILE A 263 " =    2.405
peak=   -3.393 closest distance to " O   HOH Z  17 " =    1.413
peak=   -3.393 closest distance to " NE2 GLN A  88 " =    0.995
peak=   -3.385 closest distance to " CZ  TYR A 169 " =    1.762
peak=   -3.384 closest distance to " CA  GLY A 241 " =    2.375
peak=   -3.376 closest distance to " CB  ALA A 291 " =    2.331
peak=   -3.375 closest distance to " NH2 ARG A  79 " =    1.652
peak=   -3.375 closest distance to " CB  ASP A 132 " =    2.332
peak=   -3.372 closest distance to " CG2 VAL A 296 " =    1.238
peak=   -3.372 closest distance to " CD1 LEU A 228 " =    2.337
peak=   -3.369 closest distance to " O   HOH Z 113 " =    2.409
peak=   -3.368 closest distance to " CB  ASP A 171 " =    2.354
peak=   -3.368 closest distance to " CD  PRO A 213 " =    2.205
peak=   -3.364 closest distance to " O   HOH Z 389 " =    1.985
peak=   -3.359 closest distance to " OG BSER A 134 " =    1.892
peak=   -3.358 closest distance to " O   HOH Z 426 " =    1.728
peak=   -3.355 closest distance to " O   HOH Z 252 " =    3.884
peak=   -3.355 closest distance to " CB  ALA A 114 " =    2.532
peak=   -3.354 closest distance to " OG  SER A  87 " =    1.511
peak=   -3.353 closest distance to " O   HOH Z 216 " =    1.582
peak=   -3.352 closest distance to " CD1 ILE A 151 " =    2.397
peak=   -3.347 closest distance to " CG  PRO A 163 " =    2.525
peak=   -3.345 closest distance to " N   SER A   3 " =    2.070
peak=   -3.341 closest distance to " NH2 ARG A  79 " =    2.029
peak=   -3.340 closest distance to " CG1 VAL A 197 " =    2.239
peak=   -3.337 closest distance to " N   THR A  52 " =    1.684
peak=   -3.331 closest distance to " O   HOH Z 377 " =    1.506
peak=   -3.327 closest distance to " ND2 ASN A  69 " =    1.817
peak=   -3.298 closest distance to " C   ASN A 187 " =    1.848
peak=   -3.297 closest distance to " O   HOH Z 102 " =    1.657
peak=   -3.294 closest distance to " O   SER A 276 " =    1.719
peak=   -3.293 closest distance to " O   SER A 210 " =    1.969
peak=   -3.293 closest distance to " N   ALA A 248 " =    2.492
peak=   -3.292 closest distance to " CD  GLN A 223 " =    1.239
peak=   -3.291 closest distance to " O   ARG A  24 " =    2.108
peak=   -3.291 closest distance to " O   GLY A 196 " =    1.179
peak=   -3.287 closest distance to " O   HOH Z 275 " =    1.507
peak=   -3.286 closest distance to " O   HOH Z 313 " =    1.214
peak=   -3.285 closest distance to " CD  ARG A 139 " =    1.690
peak=   -3.284 closest distance to " O   HOH Z  60 " =    1.884
peak=   -3.280 closest distance to " ND2 ASN A  45 " =    1.189
peak=   -3.279 closest distance to " OD1 ASP A 171 " =    1.633
peak=   -3.278 closest distance to " OG  SER A  26 " =    1.301
peak=   -3.274 closest distance to " CG2 VAL A 189 " =    2.081
peak=   -3.273 closest distance to " OG  SER A  62 " =    1.772
peak=   -3.268 closest distance to " CG1 VAL A 112 " =    2.883
peak=   -3.265 closest distance to " O   HOH Z 396 " =    1.969
peak=   -3.259 closest distance to " O   HOH Z  13 " =    1.541
peak=   -3.259 closest distance to " CD  GLN A 223 " =    0.780
peak=   -3.250 closest distance to " CA  GLY A 133 " =    2.302
peak=   -3.250 closest distance to " O   HOH Z 264 " =    1.729
peak=   -3.249 closest distance to " CE3 TRP A  70 " =    1.797
peak=   -3.246 closest distance to " C   MET A 188 " =    1.364
peak=   -3.246 closest distance to " C   ASN A 285 " =    2.421
peak=   -3.245 closest distance to " N   THR A 157 " =    1.563
peak=   -3.243 closest distance to " CD  PRO A 243 " =    2.093
peak=   -3.239 closest distance to " CD1 LEU A   5 " =    2.550
peak=   -3.233 closest distance to " O   HOH Z  19 " =    2.292
peak=   -3.233 closest distance to " O   ILE A 234 " =    1.286
peak=   -3.229 closest distance to " C   SER A 206 " =    1.439
peak=   -3.228 closest distance to " CG  LYS A 166 " =    2.219
peak=   -3.227 closest distance to " O   HOH Z  49 " =    1.314
peak=   -3.227 closest distance to " O   HOH Z 353 " =    2.095
peak=   -3.227 closest distance to " CG  ARG A  66 " =    2.495
peak=   -3.226 closest distance to " CE2 PHE A 218 " =    2.555
peak=   -3.225 closest distance to " CG1 VAL A  67 " =    2.836
peak=   -3.224 closest distance to " C   PHE A  59 " =    1.293
peak=   -3.219 closest distance to " O   HOH Z 133 " =    1.449
peak=   -3.218 closest distance to " CB  ALA A  10 " =    2.315
peak=   -3.214 closest distance to " CG1 VAL A 125 " =    2.019
peak=   -3.213 closest distance to " N   GLN A  58 " =    1.633
peak=   -3.211 closest distance to " CD1 LEU A 101 " =    2.852
peak=   -3.210 closest distance to " CE  MET A 105 " =    2.192
peak=   -3.210 closest distance to " CG  GLU A  53 " =    1.712
peak=   -3.210 closest distance to " ND2 ASN A  60 " =    1.290
peak=   -3.205 closest distance to " O   HOH Z  90 " =    1.639
peak=   -3.205 closest distance to " O   HOH Z 409 " =    4.783
peak=   -3.204 closest distance to " O   HOH Z 236 " =    1.422
peak=   -3.199 closest distance to " O   HOH Z 380 " =    1.436
peak=   -3.199 closest distance to " O   HOH Z   6 " =    1.635
peak=   -3.195 closest distance to " OG  SER A 206 " =    1.722
peak=   -3.195 closest distance to " O   HOH Z 295 " =    1.556
peak=   -3.194 closest distance to " O   HOH Z 139 " =    3.083
peak=   -3.188 closest distance to " CA  GLY A  98 " =    2.036
peak=   -3.185 closest distance to " O   HOH Z 350 " =    2.010
peak=   -3.184 closest distance to " O   HOH Z  43 " =    1.655
peak=   -3.175 closest distance to " N   PHE A  59 " =    2.125
peak=   -3.173 closest distance to " O   HOH Z 262 " =    2.893
peak=   -3.173 closest distance to " OG BSER A 210 " =    1.462
peak=   -3.172 closest distance to " CG2 VAL A 112 " =    2.547
peak=   -3.171 closest distance to " O   HOH Z 174 " =    2.309
peak=   -3.169 closest distance to " O   VAL A 125 " =    2.347
peak=   -3.168 closest distance to " N   SER A 276 " =    1.445
peak=   -3.165 closest distance to " O   HOH Z 311 " =    3.812
peak=   -3.163 closest distance to " OD1 ASN A 173 " =    1.435
peak=   -3.159 closest distance to " O   HOH Z 298 " =    2.784
peak=   -3.158 closest distance to " O   HOH Z 193 " =    1.930
peak=   -3.157 closest distance to " O   HOH Z 176 " =    0.819
peak=   -3.145 closest distance to " OD2 ASP A  50 " =    2.241
peak=   -3.144 closest distance to " O   HOH Z 165 " =    1.822
peak=   -3.143 closest distance to " O   HOH Z 431 " =    1.932
peak=   -3.141 closest distance to " O   GLY A  80 " =    2.620
peak=   -3.136 closest distance to " CG  PHE A 283 " =    2.653
peak=   -3.132 closest distance to " O   HOH Z 111 " =    2.054
peak=   -3.132 closest distance to " NE2 GLN A 278 " =    1.879
peak=   -3.126 closest distance to " ND2 ASN A  60 " =    1.895
peak=   -3.124 closest distance to " CA  SER A  62 " =    2.476
peak=   -3.122 closest distance to " CD  ARG A 195 " =    5.153
peak=   -3.120 closest distance to " CD2 LEU A 237 " =    2.834
peak=   -3.119 closest distance to " CG  ARG A 269 " =    2.063
peak=   -3.114 closest distance to " OE1 GLN A  77 " =    1.842
peak=   -3.112 closest distance to " O   HOH Z 175 " =    4.309
peak=   -3.112 closest distance to " O   PRO A 198 " =    1.346
peak=   -3.103 closest distance to " O   HOH Z 184 " =    1.515
peak=   -3.093 closest distance to " CG  LEU A 228 " =    0.984
peak=   -3.091 closest distance to " OD1 ASN A 187 " =    1.595
peak=   -3.089 closest distance to " OE1 GLN A  88 " =    0.939
peak=   -3.085 closest distance to " OD1 ASN A 249 " =    2.259
peak=   -3.082 closest distance to " C   ASP A 270 " =    1.231
peak=   -3.082 closest distance to " N   ALA A 248 " =    2.056
peak=   -3.080 closest distance to " CE1 HIS A  81 " =    1.395
peak=   -3.077 closest distance to " CD  GLN A  88 " =    0.833
peak=   -3.070 closest distance to " NH2 ARG A  66 " =    1.920
peak=   -3.061 closest distance to " O   LYS A 289 " =    2.948
peak=   -3.059 closest distance to " O   HOH Z  31 " =    1.574
peak=   -3.039 closest distance to " CA  GLY A 241 " =    2.855
peak=   -3.037 closest distance to " O   HOH Z 106 " =    1.830
peak=   -3.033 closest distance to " CB  ASP A 132 " =    2.382
peak=   -3.026 closest distance to " OD1 ASN A 301 " =    2.019

================= 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    :  0.4523 0.4360   6.248690e+00   6.224354e+00
   1_bss:  0.4445 0.4237   6.243739e+00   6.212893e+00
   1_xyz:  0.3370 0.3602   6.057496e+00   6.097328e+00
   1_adp:  0.2835 0.3233   5.916241e+00   6.015094e+00
   1_occ:  0.2828 0.3239   5.915187e+00   6.016244e+00
   2_bss:  0.2789 0.3176   5.915303e+00   6.013099e+00
   2_xyz:  0.1923 0.2316   5.587089e+00   5.744464e+00
   2_adp:  0.1733 0.2150   5.501221e+00   5.677405e+00
   2_occ:  0.1731 0.2154   5.501119e+00   5.678087e+00
   3_bss:  0.1723 0.2150   5.501877e+00   5.678104e+00
   3_xyz:  0.1298 0.1711   5.251149e+00   5.471552e+00
   3_adp:  0.1219 0.1679   5.211421e+00   5.449864e+00
   3_occ:  0.1219 0.1678   5.211116e+00   5.449617e+00
   4_bss:  0.1221 0.1685   5.212708e+00   5.450437e+00
   4_xyz:  0.1183 0.1658   5.193439e+00   5.434935e+00
   4_adp:  0.1187 0.1628   5.188333e+00   5.421681e+00
   4_occ:  0.1185 0.1628   5.188409e+00   5.422266e+00
   5_bss:  0.1185 0.1628   5.188433e+00   5.422267e+00
   5_xyz:  0.1124 0.1606   5.154640e+00   5.406690e+00
   5_adp:  0.1122 0.1601   5.152871e+00   5.404309e+00
   5_occ:  0.1122 0.1602   5.153091e+00   5.404888e+00
   5_bss:  0.1122 0.1601   5.152951e+00   5.404799e+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:  0.300  20.000   7.385   9.028   9.171   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.385   9.028   9.171   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.385   9.028   9.171   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.385   9.028   9.171   0.000   0.000   0.000
   2_bss:  0.330  55.694   4.245   5.706   5.767   0.000   0.000   0.000
   2_xyz:  0.330  55.694   4.245   5.706   5.767   0.000   0.000   0.000
   2_adp:  0.330  55.694   4.245   5.706   5.767   0.000   0.000   0.000
   2_occ:  0.330  55.694   4.245   5.706   5.767   0.000   0.000   0.000
   3_bss:  0.323  55.694   3.252   4.066   4.698   0.000   0.000   0.000
   3_xyz:  0.323  55.694   3.252   4.066   4.698   0.000   0.000   0.000
   3_adp:  0.323  55.694   3.252   4.066   4.698   0.000   0.000   0.000
   3_occ:  0.323  55.694   3.252   4.066   4.698   0.000   0.000   0.000
   4_bss:  0.328  61.892   3.121   3.618   4.501   0.000   0.000   0.000
   4_xyz:  0.328  61.892   3.121   3.618   4.501   0.000   0.000   0.000
   4_adp:  0.328  61.892   3.121   3.618   4.501   0.000   0.000   0.000
   4_occ:  0.328  61.892   3.121   3.618   4.501   0.000   0.000   0.000
   5_bss:  0.329  61.892   3.121   3.618   4.501   0.000   0.000   0.000
   5_xyz:  0.329  61.892   3.121   3.618   4.501   0.000   0.000   0.000
   5_adp:  0.329  61.892   3.121   3.618   4.501   0.000   0.000   0.000
   5_occ:  0.329  61.892   3.121   3.618   4.501   0.000   0.000   0.000
   5_bss:  0.321  58.305  -0.604  -0.208   0.812  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.222 0.5316  0.5850    54532.191
   1_bss:  48.240 0.5429  0.7721    52485.463
   1_xyz:  39.525 0.6475  0.8928    35734.180
   1_adp:  33.352 0.7206  0.9813    27465.417
   1_occ:  33.395 0.7201  0.9806    27552.530
   2_bss:  33.242 0.7218  0.8741    27303.966
   2_xyz:  22.858 0.8332  0.9790    13755.895
   2_adp:  20.684 0.8555  0.9938    11814.989
   2_occ:  20.708 0.8553  0.9934    11836.649
   3_bss:  20.690 0.8556  0.9499    11843.553
   3_xyz:  15.687 0.9007  0.9780     7415.249
   3_adp:  15.193 0.9051  0.9761     7109.771
   3_occ:  15.187 0.9052  0.9761     7107.044
   4_bss:  15.223 0.9049  0.9666     7152.604
   4_xyz:  14.784 0.9091  0.9667     6906.771
   4_adp:  14.461 0.9118  0.9644     6757.659
   4_occ:  14.475 0.9117  0.9641     6765.965
   5_bss:  14.475 0.9117  0.9641     6766.201
   5_xyz:  14.177 0.9139  0.9664     6566.279
   5_adp:  14.118 0.9144  0.9633     6537.053
   5_occ:  14.128 0.9143  0.9631     6541.904
   5_bss:  14.128 0.9144  0.9645     6536.882
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4361e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4361e+01
   1_xyz:   1.628  0.013  0.106 17.849  0.006  4.113   1.3133e-01
   1_adp:   1.628  0.013  0.106 17.849  0.006  4.113   1.3133e-01
   1_occ:   1.628  0.013  0.106 17.849  0.006  4.113   1.3133e-01
   2_bss:   1.628  0.013  0.106 17.849  0.006  4.113   1.3133e-01
   2_xyz:   1.090  0.008  0.074 16.215  0.004  4.133   7.1424e-02
   2_adp:   1.090  0.008  0.074 16.215  0.004  4.133   7.1424e-02
   2_occ:   1.090  0.008  0.074 16.215  0.004  4.133   7.1424e-02
   3_bss:   1.090  0.008  0.074 16.215  0.004  4.133   7.1424e-02
   3_xyz:   1.147  0.010  0.089 15.890  0.004  4.114   8.0476e-02
   3_adp:   1.147  0.010  0.089 15.890  0.004  4.114   8.0476e-02
   3_occ:   1.147  0.010  0.089 15.890  0.004  4.114   8.0476e-02
   4_bss:   1.147  0.010  0.089 15.890  0.004  4.114   8.0476e-02
   4_xyz:   1.046  0.009  0.084 15.504  0.004  4.117   6.7875e-02
   4_adp:   1.046  0.009  0.084 15.504  0.004  4.117   6.7875e-02
   4_occ:   1.046  0.009  0.084 15.504  0.004  4.117   6.7875e-02
   5_bss:   1.046  0.009  0.084 15.504  0.004  4.117   6.7875e-02
   5_xyz:   1.197  0.012  0.097 15.699  0.004  4.121   8.8694e-02
   5_adp:   1.197  0.012  0.097 15.699  0.004  4.121   8.8694e-02
   5_occ:   1.197  0.012  0.097 15.699  0.004  4.121   8.8694e-02
   5_bss:   1.197  0.012  0.097 15.699  0.004  4.121   8.8694e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0487e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0487e+00
   1_xyz:  14.147  0.157  0.450 86.548  0.038  2.309   9.9620e-02
   1_adp:  14.147  0.157  0.450 86.548  0.038  2.309   9.9620e-02
   1_occ:  14.147  0.157  0.450 86.548  0.038  2.309   9.9620e-02
   2_bss:  14.147  0.157  0.450 86.548  0.038  2.309   9.9620e-02
   2_xyz:   6.937  0.093  0.228 86.630  0.038  2.216   6.2027e-02
   2_adp:   6.937  0.093  0.228 86.630  0.038  2.216   6.2027e-02
   2_occ:   6.937  0.093  0.228 86.630  0.038  2.216   6.2027e-02
   3_bss:   6.937  0.093  0.228 86.630  0.038  2.216   6.2027e-02
   3_xyz:   7.451  0.055  0.486 83.879  0.042  2.374   6.4265e-02
   3_adp:   7.451  0.055  0.486 83.879  0.042  2.374   6.4265e-02
   3_occ:   7.451  0.055  0.486 83.879  0.042  2.374   6.4265e-02
   4_bss:   7.451  0.055  0.486 83.879  0.042  2.374   6.4265e-02
   4_xyz:   7.454  0.045  0.449 82.120  0.040  2.384   4.3412e-02
   4_adp:   7.454  0.045  0.449 82.120  0.040  2.384   4.3412e-02
   4_occ:   7.454  0.045  0.449 82.120  0.040  2.384   4.3412e-02
   5_bss:   7.454  0.045  0.449 82.120  0.040  2.384   4.3412e-02
   5_xyz:   7.981  0.058  0.596 82.011  0.042  2.311   6.4391e-02
   5_adp:   7.981  0.058  0.596 82.011  0.042  2.311   6.4391e-02
   5_occ:   7.981  0.058  0.596 82.011  0.042  2.311   6.4391e-02
   5_bss:   7.981  0.058  0.596 82.011  0.042  2.311   6.4391e-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:  95.10   0.00  10.96  65.74   0.00   7.98  95.10   0.00  27.21
   1_occ:  95.10   0.00  10.96  65.74   0.00   7.98  95.10   0.00  27.21
   2_bss:  95.10   0.00  10.96  65.74   0.00   7.98  95.10   0.00  27.21
   2_xyz:  95.10   0.00  10.96  65.74   0.00   7.98  95.10   0.00  27.21
   2_adp:  91.94   0.00  11.47  68.35   0.00   7.51  91.94   0.00  32.99
   2_occ:  91.94   0.00  11.47  68.35   0.00   7.51  91.94   0.00  32.99
   3_bss:  91.94   0.00  11.47  68.35   0.00   7.51  91.94   0.00  32.99
   3_xyz:  91.94   0.00  11.47  68.35   0.00   7.51  91.94   0.00  32.99
   3_adp:  87.03   0.00  12.39  87.03   0.00   7.71  83.41   0.00  37.87
   3_occ:  87.03   0.00  12.39  87.03   0.00   7.71  83.41   0.00  37.87
   4_bss:  87.03   0.00  12.39  87.03   0.00   7.71  83.41   0.00  37.87
   4_xyz:  87.03   0.00  12.39  87.03   0.00   7.71  83.41   0.00  37.87
   4_adp:  85.53   0.00  11.63  85.53   0.00   7.40  83.56   0.77  34.68
   4_occ:  85.53   0.00  11.63  85.53   0.00   7.40  83.56   0.77  34.68
   5_bss:  85.53   0.00  11.63  85.53   0.00   7.40  83.56   0.77  34.68
   5_xyz:  85.53   0.00  11.63  85.53   0.00   7.40  83.56   0.77  34.68
   5_adp:  84.73   0.00  11.45  84.73   0.00   7.27  82.92   1.05  34.21
   5_occ:  84.73   0.00  11.45  84.73   0.00   7.27  82.92   1.05  34.21
   5_bss:  88.51   3.79  15.24  88.51   3.79  11.06  86.70   4.83  38.00
------------------------------------------------------------------------
 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:    1.233    0.024    0.410
   1_adp:    1.233    0.024    0.410
   1_occ:    1.233    0.024    0.410
   2_bss:    1.233    0.024    0.410
   2_xyz:    1.614    0.032    0.541
   2_adp:    1.614    0.032    0.541
   2_occ:    1.614    0.032    0.541
   3_bss:    1.614    0.032    0.541
   3_xyz:    1.497    0.041    0.595
   3_adp:    1.497    0.041    0.595
   3_occ:    1.497    0.041    0.595
   4_bss:    1.497    0.041    0.595
   4_xyz:    1.598    0.025    0.607
   4_adp:    1.598    0.025    0.607
   4_occ:    1.598    0.025    0.607
   5_bss:    1.598    0.025    0.607
   5_xyz:    1.516    0.033    0.621
   5_adp:    1.516    0.033    0.621
   5_occ:    1.516    0.033    0.621
   5_bss:    1.516    0.033    0.621
------------------------------------------------------------------------

CPU time actual refinement: 336.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_931/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_931/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_931/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_931/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_931/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.86 
  Macro-tasks:
    bulk solvent and scale       = 42.16  
    individual site refinement   = 140.32 
    weights calculation          = 32.15  
    collect and process          = 6.61   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 221.37 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 102.37 
    alpha_beta                      = 8.21   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 114.28 
    fmodel                         = 7.45   
    r_factors                      = 0.29   
    phase_errors                   = 10.58  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 246.35 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.665 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    665 calls, 101.98 s
gradients_fft:          609 calls, 100.18 s

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

# Date 2008-01-16 Time 02:46:45 PST -0800 (1200480405.55 s)
Start R-work = 0.4523, R-free = 0.4360 (no bulk solvent and anisotropic scale)
Final R-work = 0.1289, R-free = 0.1750 (no bulk solvent and anisotropic scale)

Start R-work = 0.4445, R-free = 0.4237
Final R-work = 0.1122, R-free = 0.1601