# Date 2008-01-16 Time 03:14:55 PST -0800 (1200482095.29 s)
#phil __OFF__

Command line arguments: "../1161.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29949
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1161

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 47.1647, 86.822, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2319 2.01038
Completeness in resolution range: 0.971869
Completeness with d_max=infinity: 0.968889

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2319
                             d_min =   2.0104

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2319 2.01038
Completeness in resolution range: 0.971869
Completeness with d_max=infinity: 0.968889

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2323 -  4.3018 [2110/2135]  1900   210  10.0%
  bin  2:  4.3018 -  3.4272 [2038/2058]  1833   205  10.1%
  bin  3:  3.4272 -  2.9978 [2006/2025]  1803   203  10.1%
  bin  4:  2.9978 -  2.7254 [1987/2017]  1795   192   9.7%
  bin  5:  2.7254 -  2.5310 [1983/2002]  1787   196   9.9%
  bin  6:  2.5310 -  2.3824 [1965/1990]  1764   201  10.2%
  bin  7:  2.3824 -  2.2634 [1947/1975]  1747   200  10.3%
  bin  8:  2.2634 -  2.1652 [1959/1995]  1765   194   9.9%
  bin  9:  2.1652 -  2.0821 [1950/1992]  1761   189   9.7%
  bin 10:  2.0821 -  2.0104 [1644/1967]  1475   169  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1161/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:
        1.66 -     2.31: 4
        2.31 -     2.96: 1643
        2.96 -     3.61: 4450
        3.61 -     4.25: 9071
        4.25 -     4.90: 12723
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.663 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.242 3.040 -x+1/2,-y+1,z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27886 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_1161/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1161/model_refine_001.geo

CPU time processing inputs: 9.12


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 47.16465 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4474   r_free= 0.4334   ksol= 0.00   Bsol= 0.00   scale= 0.803    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.248055                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.7980 0.99   1380  154 0.3719 0.3430      6.5519      6.4387|
|  2:  4.7980 -  3.8282 0.99   1324  145 0.3467 0.3703      6.6993      6.7409|
|  3:  3.8282 -  3.3502 0.99   1287  143 0.3911 0.3658      6.5967      6.6073|
|  4:  3.3502 -  3.0465 0.99   1284  147 0.4277 0.3754      6.4873      6.3939|
|  5:  3.0465 -  2.8297 0.99   1292  140 0.4680 0.4639      6.3394      6.3822|
|  6:  2.8297 -  2.6638 0.99   1274  141 0.4683 0.4920      6.2575      6.1994|
|  7:  2.6638 -  2.5310 0.99   1277  136 0.5033 0.4832      6.2232      6.2332|
|  8:  2.5310 -  2.4213 0.98   1254  148 0.5048 0.4570      6.1708      6.1323|
|  9:  2.4213 -  2.3284 0.98   1255  137 0.4842 0.5129      6.1002      6.1426|
| 10:  2.3284 -  2.2483 1.00   1268  141 0.4987 0.4647      6.1006      6.0936|
| 11:  2.2483 -  2.1782 0.97   1250  137 0.4957 0.4696      6.0375      6.0316|
| 12:  2.1782 -  2.1161 0.98   1240  142 0.5079 0.5234      5.9823      6.0288|
| 13:  2.1161 -  2.0605 1.00   1258  136 0.5160 0.4980      5.9039      5.8598|
| 14:  2.0605 -  2.0104 0.77    987  112 0.5104 0.4330       5.867      5.6731|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2323 -  4.7980  1380   154  0.74  30.72   0.80     0.77      57990.04|
|  2:  4.7980 -  3.8282  1324   145  0.77  29.31   0.90     0.80      78762.79|
|  3:  3.8282 -  3.3502  1287   143  0.69  36.35   0.85     0.76      84547.24|
|  4:  3.3502 -  3.0465  1284   147  0.61  42.88   0.82     0.68      78328.58|
|  5:  3.0465 -  2.8297  1292   140  0.51  50.93   0.75     0.59      68650.55|
|  6:  2.8297 -  2.6638  1274   141  0.48  53.54   0.76     0.54      62171.94|
|  7:  2.6638 -  2.5310  1277   136  0.44  56.58   0.72     0.49      58346.46|
|  8:  2.5310 -  2.4213  1254   148  0.42  58.76   0.74     0.48      54348.21|
|  9:  2.4213 -  2.3284  1255   137  0.43  57.42   0.73     0.48      48650.53|
| 10:  2.3284 -  2.2483  1268   141  0.44  56.56   0.75     0.50      43562.98|
| 11:  2.2483 -  2.1782  1250   137  0.43  57.30   0.76     0.49      39732.77|
| 12:  2.1782 -  2.1161  1240   142  0.43  57.83   0.76     0.51      37701.47|
| 13:  2.1161 -  2.0605  1258   136  0.45  55.99   0.72     0.53      30865.68|
| 14:  2.0605 -  2.0104   987   112  0.55  48.20   0.71     0.59      21189.21|
|alpha:            min =        0.48 max =            0.80 mean =         0.59|
|beta:             min =    21189.21 max =        84547.24 mean =     55400.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           90.00 mean =        49.24|
|phase err.(test): min =        0.00 max =           89.97 mean =        49.05|
|-----------------------------------------------------------------------------|

============================== 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 = 9.671556              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.661   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.738507              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.122   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      675 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1483 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2587 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3866 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4969 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6521 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7604 |
|-----------------------------------------------------------------------------|
|-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 |       54.375 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.608 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    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 = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4543   r_free= 0.4381   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.250341                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4406   r_free= 0.4212   ksol= 0.30   Bsol= 20.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.43,7.84,8.12,0.00,0.00,0.00); trace/3= 8.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.242774                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.900853              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.080   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.725820              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.281   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4406      final r-factor (work) = 0.3334          |
| start r-factor (free) = 0.4212      final r-factor (free) = 0.3610          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.2139 = 8.90 * 0.50 * 6.2554 + 1.00 * 54.3748                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2806 = 8.90 * 0.50 * 6.1006 + 1.00 * 0.1303                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3334      final r-factor (work) = 0.2801          |
| start r-factor (free) = 0.3610      final r-factor (free) = 0.3199          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4424 = 0.73 * 1.00 * 6.1006 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3434 = 0.73 * 1.00 * 5.9671 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.35   10.57    None  None   None       |
|    all(noH): 2823   0      0.00    73.35   10.57    None  None   None       |
|    Sol.    : 438    0      0.00    73.35   26.20    None  None   None       |
|    Mac.    : 2385   0      0.00    59.96   7.70     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.335: 1459   |   5:    36.677 -  44.012:   69        |
|      1:     7.335 -  14.671:  735   |   6:    44.012 -  51.348:   34        |
|      2:    14.671 -  22.006:  256   |   7:    51.348 -  58.683:   15        |
|      3:    22.006 -  29.342:  153   |   8:    58.683 -  66.019:    4        |
|      4:    29.342 -  36.677:   97   |   9:    66.019 -  73.354:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2801 r_free = 0.3199             target_work(ml) = 5.920         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2794 r_free = 0.3204             target_work(ml) = 5.919         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2794   r_free= 0.3204   ksol= 0.30   Bsol= 20.00   scale= 1.068   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.43,7.84,8.12,0.00,0.00,0.00); trace/3= 8.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.918740                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2765   r_free= 0.3163   ksol= 0.33   Bsol= 50.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.18,4.84,5.40,0.00,0.00,0.00); trace/3= 5.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.918249                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.508260              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.062   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.451301              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.410  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2765      final r-factor (work) = 0.1996          |
| start r-factor (free) = 0.3163      final r-factor (free) = 0.2466          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5946 = 3.51 * 0.50 * 5.9655 + 1.00 * 0.1303                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1999 = 3.51 * 0.50 * 5.7770 + 1.00 * 0.0663                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1996      final r-factor (work) = 0.1837          |
| start r-factor (free) = 0.2466      final r-factor (free) = 0.2309          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6468 = 0.45 * 1.00 * 5.7770 + 1.00 * 0.0396                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7343 = 0.45 * 1.00 * 5.5922 + 1.00 * 0.2105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.66   11.16    None  None   None       |
|    all(noH): 2823   0      0.00    74.66   11.16    None  None   None       |
|    Sol.    : 438    0      0.00    73.54   30.92    None  None   None       |
|    Mac.    : 2385   0      0.00    74.66   7.53     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.466: 1563   |   5:    37.332 -  44.798:   90        |
|      1:     7.466 -  14.933:  622   |   6:    44.798 -  52.264:   52        |
|      2:    14.933 -  22.399:  211   |   7:    52.264 -  59.731:   21        |
|      3:    22.399 -  29.865:  118   |   8:    59.731 -  67.197:    6        |
|      4:    29.865 -  37.332:  138   |   9:    67.197 -  74.663:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1837 r_free = 0.2309             target_work(ml) = 5.563         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1834 r_free = 0.2310             target_work(ml) = 5.563         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1834   r_free= 0.2310   ksol= 0.33   Bsol= 50.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.18,4.84,5.40,0.00,0.00,0.00); trace/3= 5.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.563073                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1824   r_free= 0.2294   ksol= 0.32   Bsol= 50.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.07,3.60,4.46,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.563387                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.034184              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.845  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.108564              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.056   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1824      final r-factor (work) = 0.1403          |
| start r-factor (free) = 0.2294      final r-factor (free) = 0.1857          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5580 = 3.03 * 0.50 * 5.5973 + 1.00 * 0.0663                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3396 = 3.03 * 0.50 * 5.4492 + 1.00 * 0.0727                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1403      final r-factor (work) = 0.1293          |
| start r-factor (free) = 0.1857      final r-factor (free) = 0.1776          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.8552 = 5.11 * 1.00 * 5.4492 + 1.00 * 0.0177                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.0538 = 5.11 * 1.00 * 5.2925 + 1.00 * 0.0169                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.54   12.44    None  None   None       |
|    all(noH): 2823   0      0.00    89.54   12.44    None  None   None       |
|    Sol.    : 438    0      0.00    89.54   37.74    None  None   None       |
|    Mac.    : 2385   0      0.00    85.28   7.79     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 -   8.954: 1766   |   5:    44.770 -  53.725:   79        |
|      1:     8.954 -  17.908:  505   |   6:    53.725 -  62.679:   69        |
|      2:    17.908 -  26.862:  152   |   7:    62.679 -  71.633:   37        |
|      3:    26.862 -  35.816:  105   |   8:    71.633 -  80.587:   10        |
|      4:    35.816 -  44.770:   95   |   9:    80.587 -  89.541:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1293 r_free = 0.1776             target_work(ml) = 5.272         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1293 r_free = 0.1776             target_work(ml) = 5.272         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1293   r_free= 0.1776   ksol= 0.32   Bsol= 50.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.07,3.60,4.46,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.271783                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1298   r_free= 0.1773   ksol= 0.32   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,3.28,4.26,0.00,0.00,0.00); trace/3= 3.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.272147                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.701812              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.704  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.537092              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.223  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1298      final r-factor (work) = 0.1249          |
| start r-factor (free) = 0.1773      final r-factor (free) = 0.1740          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5770 = 1.70 * 0.50 * 5.2935 + 1.00 * 0.0727                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5334 = 1.70 * 0.50 * 5.2568 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1249      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1740      final r-factor (free) = 0.1714          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8404 = 0.54 * 1.00 * 5.2568 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8412 = 0.54 * 1.00 * 5.2433 + 1.00 * 0.0251                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.68   12.13    None  None   None       |
|    all(noH): 2823   0      0.00    88.68   12.13    None  None   None       |
|    Sol.    : 438    0      0.54    88.68   36.34    None  None   None       |
|    Mac.    : 2385   0      0.00    86.68   7.68     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 -   8.868: 1768   |   5:    44.341 -  53.209:   80        |
|      1:     8.868 -  17.736:  509   |   6:    53.209 -  62.077:   63        |
|      2:    17.736 -  26.605:  159   |   7:    62.077 -  70.946:   26        |
|      3:    26.605 -  35.473:  113   |   8:    70.946 -  79.814:   10        |
|      4:    35.473 -  44.341:   89   |   9:    79.814 -  88.682:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1241 r_free = 0.1714             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1239 r_free = 0.1712             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1239   r_free= 0.1712   ksol= 0.32   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,3.28,4.26,0.00,0.00,0.00); trace/3= 3.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.233649                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1239   r_free= 0.1712   ksol= 0.32   Bsol= 58.56   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,3.26,4.26,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.233335                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.462322              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.488  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.323670              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.946   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1239      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1712      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5145 = 2.46 * 0.50 * 5.2423 + 1.00 * 0.0603                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4863 = 2.46 * 0.50 * 5.2074 + 1.00 * 0.0752                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1661      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7033 = 0.32 * 1.00 * 5.2074 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6975 = 0.32 * 1.00 * 5.1925 + 1.00 * 0.0169                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.09   11.56    None  None   None       |
|    all(noH): 2823   0      0.00    85.09   11.56    None  None   None       |
|    Sol.    : 438    0      1.01    85.09   33.92    None  None   None       |
|    Mac.    : 2385   0      0.00    84.55   7.45     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 -   8.509: 1763   |   5:    42.545 -  51.054:   99        |
|      1:     8.509 -  17.018:  511   |   6:    51.054 -  59.563:   42        |
|      2:    17.018 -  25.527:  155   |   7:    59.563 -  68.071:   17        |
|      3:    25.527 -  34.036:  123   |   8:    68.071 -  76.580:    5        |
|      4:    34.036 -  42.545:  101   |   9:    76.580 -  85.089:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1172 r_free = 0.1648             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1172 r_free = 0.1648             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1648   ksol= 0.32   Bsol= 58.56   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,3.26,4.26,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.188035                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.7980 0.99   1380  154 0.1023 0.1359      5.4093      5.5554|
|  2:  4.7980 -  3.8282 0.99   1324  145 0.0885 0.1154      5.4675      5.6713|
|  3:  3.8282 -  3.3502 0.99   1287  143 0.1072 0.1523      5.5028      5.8498|
|  4:  3.3502 -  3.0465 0.99   1284  147 0.1241 0.1616      5.4863      5.6409|
|  5:  3.0465 -  2.8297 0.99   1292  140 0.1419 0.1876      5.3849      5.6185|
|  6:  2.8297 -  2.6638 0.99   1274  141 0.1284 0.1992      5.2739      5.5045|
|  7:  2.6638 -  2.5310 0.99   1277  136 0.1346 0.1728      5.2282      5.4286|
|  8:  2.5310 -  2.4213 0.98   1254  148 0.1255 0.1779      5.1316      5.3853|
|  9:  2.4213 -  2.3284 0.98   1255  137 0.1247 0.1783      5.0953      5.3338|
| 10:  2.3284 -  2.2483 1.00   1268  141 0.1208 0.1864       5.016      5.3017|
| 11:  2.2483 -  2.1782 0.97   1250  137 0.1206 0.1780      4.9983      5.2614|
| 12:  2.1782 -  2.1161 0.98   1240  142 0.1173 0.1867      4.9183      5.2718|
| 13:  2.1161 -  2.0605 1.00   1258  136 0.1224 0.1806      4.8443      5.1265|
| 14:  2.0605 -  2.0104 0.77    987  112 0.1156 0.1750      4.7127      4.9302|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2323 -  4.7980  1380   154  0.94   9.48   0.97     0.95       7724.82|
|  2:  4.7980 -  3.8282  1324   145  0.95   8.33   1.00     0.98       9677.34|
|  3:  3.8282 -  3.3502  1287   143  0.93  11.73   1.01     1.01      11210.26|
|  4:  3.3502 -  3.0465  1284   147  0.92  13.94   1.00     0.98      10911.99|
|  5:  3.0465 -  2.8297  1292   140  0.89  17.07   0.99     0.96       9274.79|
|  6:  2.8297 -  2.6638  1274   141  0.90  16.63   0.98     0.96       8049.27|
|  7:  2.6638 -  2.5310  1277   136  0.90  16.64   0.98     0.95       6975.07|
|  8:  2.5310 -  2.4213  1254   148  0.90  16.24   0.98     0.96       5977.54|
|  9:  2.4213 -  2.3284  1255   137  0.90  16.36   1.00     0.96       5634.73|
| 10:  2.3284 -  2.2483  1268   141  0.90  15.97   0.99     0.95       4709.46|
| 11:  2.2483 -  2.1782  1250   137  0.89  17.36   0.99     0.95       4873.53|
| 12:  2.1782 -  2.1161  1240   142  0.91  15.43   0.99     0.98       4229.91|
| 13:  2.1161 -  2.0605  1258   136  0.90  16.80   0.99     0.98       3680.94|
| 14:  2.0605 -  2.0104   987   112  0.91  15.15   0.97     0.93       2653.92|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2653.92 max =        11210.26 mean =      6930.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.73|
|phase err.(test): min =        0.00 max =           87.86 mean =        14.16|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1648   ksol= 0.32   Bsol= 58.47   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,-0.37,0.66,-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: 5.188049                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1648   ksol= 0.32   Bsol= 58.47   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,-0.37,0.66,-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: 5.188049                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.7980 0.99   1380  154 0.1020 0.1359      5.4072      5.5538|
|  2:  4.7980 -  3.8282 0.99   1324  145 0.0882 0.1151      5.4655      5.6684|
|  3:  3.8282 -  3.3502 0.99   1287  143 0.1071 0.1523      5.5017      5.8491|
|  4:  3.3502 -  3.0465 0.99   1284  147 0.1241 0.1616      5.4869      5.6411|
|  5:  3.0465 -  2.8297 0.99   1292  140 0.1422 0.1879      5.3861      5.6199|
|  6:  2.8297 -  2.6638 0.99   1274  141 0.1286 0.1993       5.275      5.5053|
|  7:  2.6638 -  2.5310 0.99   1277  136 0.1347 0.1727      5.2289      5.4288|
|  8:  2.5310 -  2.4213 0.98   1254  148 0.1256 0.1780       5.132      5.3859|
|  9:  2.4213 -  2.3284 0.98   1255  137 0.1247 0.1783      5.0957      5.3335|
| 10:  2.3284 -  2.2483 1.00   1268  141 0.1208 0.1865      5.0164      5.3024|
| 11:  2.2483 -  2.1782 0.97   1250  137 0.1207 0.1782      4.9988       5.262|
| 12:  2.1782 -  2.1161 0.98   1240  142 0.1173 0.1869      4.9187      5.2721|
| 13:  2.1161 -  2.0605 1.00   1258  136 0.1224 0.1808      4.8445      5.1271|
| 14:  2.0605 -  2.0104 0.77    987  112 0.1156 0.1749      4.7126      4.9299|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2323 -  4.7980  1380   154  0.94   9.45   0.97     0.95       7694.36|
|  2:  4.7980 -  3.8282  1324   145  0.95   8.31   1.00     0.98       9643.42|
|  3:  3.8282 -  3.3502  1287   143  0.93  11.70   1.01     1.01      11180.34|
|  4:  3.3502 -  3.0465  1284   147  0.92  13.95   1.00     0.98      10918.86|
|  5:  3.0465 -  2.8297  1292   140  0.89  17.09   0.99     0.96       9290.85|
|  6:  2.8297 -  2.6638  1274   141  0.90  16.65   0.98     0.96       8067.52|
|  7:  2.6638 -  2.5310  1277   136  0.90  16.65   0.98     0.95       6985.17|
|  8:  2.5310 -  2.4213  1254   148  0.90  16.25   0.98     0.96       5981.70|
|  9:  2.4213 -  2.3284  1255   137  0.90  16.36   0.99     0.96       5636.79|
| 10:  2.3284 -  2.2483  1268   141  0.90  15.98   0.99     0.95       4712.83|
| 11:  2.2483 -  2.1782  1250   137  0.89  17.37   0.99     0.95       4879.17|
| 12:  2.1782 -  2.1161  1240   142  0.91  15.44   0.99     0.98       4235.33|
| 13:  2.1161 -  2.0605  1258   136  0.90  16.80   0.99     0.98       3683.05|
| 14:  2.0605 -  2.0104   987   112  0.91  15.15   0.97     0.93       2652.83|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2652.83 max =        11180.34 mean =      6928.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.73|
|phase err.(test): min =        0.00 max =           89.58 mean =        14.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.62    88.71   15.18    None  None   None       |
|    all(noH): 2823   0      3.62    88.71   15.18    None  None   None       |
|    Sol.    : 438    0      4.64    88.71   37.55    None  None   None       |
|    Mac.    : 2385   0      3.62    88.17   11.07    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:     3.624 -  12.133: 1763   |   5:    46.169 -  54.678:   99        |
|      1:    12.133 -  20.642:  511   |   6:    54.678 -  63.187:   42        |
|      2:    20.642 -  29.151:  155   |   7:    63.187 -  71.696:   17        |
|      3:    29.151 -  37.660:  123   |   8:    71.696 -  80.205:    5        |
|      4:    37.660 -  46.169:  101   |   9:    80.205 -  88.713:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 332         
Filter by distance & map next to the model:
   mapped sites are within: 0.288 - 4.756
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 321 from: 332
   mapped sites are within: 0.715 - 4.756

peak=   10.437 closest distance to " CG2 VAL A 230 " =    1.487
peak=    7.928 closest distance to " CG2 VAL A 296 " =    1.214
peak=    5.844 closest distance to " CG  LEU A   5 " =    1.267
peak=    5.725 closest distance to " O   HOH Z 111 " =    2.071
peak=    5.659 closest distance to " CD2 LEU A   5 " =    1.186
peak=    5.548 closest distance to " CB  GLN A 223 " =    1.404
peak=    5.265 closest distance to " CG  LEU A 228 " =    1.207
peak=    5.176 closest distance to " CG  ARG A 138 " =    1.029
peak=    5.006 closest distance to " CB  GLN A 183 " =    1.244
peak=    4.949 closest distance to " O   HOH Z 232 " =    2.261
peak=    4.908 closest distance to " CB  SER A  63 " =    1.279
peak=    4.816 closest distance to " O   HOH Z 369 " =    2.031
peak=    4.640 closest distance to " CD1AILE A 234 " =    1.034
peak=    4.610 closest distance to " NH1 ARG A 138 " =    1.055
peak=    4.530 closest distance to " O   HOH Z 368 " =    2.228
peak=    4.504 closest distance to " CB  VAL A 230 " =    1.258
peak=    4.474 closest distance to " O   HOH Z  54 " =    2.334
peak=    4.469 closest distance to " NE2 GLN A  11 " =    1.110
peak=    4.451 closest distance to " CB  ASP A 124 " =    0.742
peak=    4.444 closest distance to " CB  TRP A 266 " =    0.937
peak=    4.427 closest distance to " O   HOH Z 303 " =    2.131
peak=    4.393 closest distance to " CZ  PHE A 218 " =    1.078
peak=    4.372 closest distance to " CG  PRO A 243 " =    1.179
peak=    4.350 closest distance to " C   PRO A 198 " =    1.570
peak=    4.344 closest distance to " O   HOH Z 425 " =    1.480
peak=    4.332 closest distance to " CB  ASN A 148 " =    1.368
peak=    4.331 closest distance to " O   HOH Z 298 " =    1.903
peak=    4.329 closest distance to " NH1AARG A 145 " =    1.213
peak=    4.324 closest distance to " CG  PRO A 198 " =    1.250
peak=    4.272 closest distance to " O   HOH Z 236 " =    1.951
peak=    4.260 closest distance to " CG  PRO A 213 " =    1.203
peak=    4.259 closest distance to " O   HOH Z 126 " =    1.996
peak=    4.238 closest distance to " O   HOH Z  78 " =    1.799
peak=    4.233 closest distance to " O   HOH Z 272 " =    1.910
peak=    4.221 closest distance to " O   HOH Z 234 " =    3.750
peak=    4.205 closest distance to " CG2 THR A 221 " =    1.015
peak=    4.199 closest distance to " CD2 LEU A 228 " =    1.182
peak=    4.184 closest distance to " CB  GLU A 128 " =    1.076
peak=    4.179 closest distance to " CB  LEU A 143 " =    1.184
peak=    4.152 closest distance to " O   HOH Z 427 " =    3.174
peak=    4.135 closest distance to " O   HOH Z 403 " =    1.730
peak=    4.129 closest distance to " O   HOH Z 261 " =    1.963
peak=    4.119 closest distance to " O   HOH Z 316 " =    3.155
peak=    4.105 closest distance to " O   HOH Z  15 " =    2.039
peak=    4.082 closest distance to " CB  ARG A 275 " =    0.909
peak=    4.064 closest distance to " ND2 ASN A 187 " =    1.500
peak=    4.046 closest distance to " CB BVAL A  41 " =    0.965
peak=    4.044 closest distance to " CB  GLU A 152 " =    1.140
peak=    4.030 closest distance to " CB  ASP A 140 " =    0.881
peak=    3.992 closest distance to " CB  ALA A   9 " =    1.622
peak=    3.987 closest distance to " CB  ASN A  39 " =    0.862
peak=    3.971 closest distance to " OD1 ASN A  69 " =    2.633
peak=    3.967 closest distance to " CB  GLU A 277 " =    3.704
peak=    3.951 closest distance to " O   HOH Z 158 " =    3.031
peak=    3.943 closest distance to " CB  LEU A 228 " =    1.180
peak=    3.937 closest distance to " CD1 LEU A 300 " =    1.202
peak=    3.930 closest distance to " ND2 ASN A 249 " =    1.915
peak=    3.916 closest distance to " O   HOH Z  88 " =    3.377
peak=    3.914 closest distance to " NH2 ARG A 156 " =    1.086
peak=    3.906 closest distance to " CB  ARG A 190 " =    1.670
peak=    3.896 closest distance to " O   HOH Z 411 " =    3.610
peak=    3.882 closest distance to " CD  ARG A 159 " =    0.784
peak=    3.870 closest distance to " O   MET A 105 " =    1.802
peak=    3.865 closest distance to " CD1 LEU A   5 " =    1.342
peak=    3.862 closest distance to " CB  ARG A  79 " =    1.491
peak=    3.850 closest distance to " O   SER A  87 " =    2.248
peak=    3.837 closest distance to " O   HOH Z 142 " =    1.591
peak=    3.831 closest distance to " CA  ALA A  51 " =    1.009
peak=    3.828 closest distance to " CB  VAL A 202 " =    1.624
peak=    3.827 closest distance to " O   HOH Z 184 " =    1.549
peak=    3.818 closest distance to " O   HOH Z 423 " =    1.711
peak=    3.816 closest distance to " CB  ASN A 142 " =    1.014
peak=    3.774 closest distance to " CB  SER A 212 " =    1.228
peak=    3.773 closest distance to " CB  ASN A 187 " =    1.099
peak=    3.761 closest distance to " CG1 VAL A 153 " =    0.953
peak=    3.748 closest distance to " CD  ARG A  66 " =    2.482
peak=    3.745 closest distance to " O   ALA A 158 " =    1.360
peak=    3.744 closest distance to " CA  ALA A  21 " =    1.223
peak=    3.739 closest distance to " CD  LYS A 166 " =    1.275
peak=    3.733 closest distance to " CG  MET A 185 " =    1.253
peak=    3.732 closest distance to " CB  VAL A 265 " =    1.319
peak=    3.723 closest distance to " O   HOH Z  61 " =    1.649
peak=    3.719 closest distance to " O   HOH Z 280 " =    2.988
peak=    3.719 closest distance to " O   HOH Z 214 " =    2.115
peak=    3.718 closest distance to " O   HOH Z 346 " =    1.534
peak=    3.713 closest distance to " CA  TYR A  30 " =    0.930
peak=    3.712 closest distance to " O   HOH Z 247 " =    1.442
peak=    3.703 closest distance to " O   HOH Z 112 " =    1.676
peak=    3.698 closest distance to " O   HOH Z 437 " =    1.793
peak=    3.693 closest distance to " CD ALYS A 290 " =    1.042
peak=    3.682 closest distance to " CB  GLU A  46 " =    0.967
peak=    3.678 closest distance to " ND1 HIS A  81 " =    1.679
peak=    3.675 closest distance to " CA  SER A  87 " =    0.931
peak=    3.672 closest distance to " O   HOH Z  19 " =    2.474
peak=    3.657 closest distance to " O   HOH Z  63 " =    1.912
peak=    3.656 closest distance to " CB  ALA A 104 " =    0.811
peak=    3.655 closest distance to " CA  LYS A 117 " =    1.220
peak=    3.654 closest distance to " CB  PRO A  54 " =    0.802
peak=    3.651 closest distance to " O   HOH Z 133 " =    1.774
peak=    3.650 closest distance to " CG BARG A 275 " =    1.500
peak=    3.646 closest distance to " CA  LEU A 282 " =    1.014
peak=    3.643 closest distance to " CB  VAL A 296 " =    1.057
peak=    3.634 closest distance to " CB  TRP A 150 " =    1.419
peak=    3.633 closest distance to " O   HOH Z 163 " =    1.717
peak=    3.631 closest distance to " CZ  PHE A 192 " =    0.986
peak=    3.631 closest distance to " O   HOH Z  80 " =    1.725
peak=    3.629 closest distance to " O   HOH Z 126 " =    1.652
peak=    3.606 closest distance to " O   HOH Z 193 " =    2.098
peak=    3.596 closest distance to " CB  SER A   3 " =    1.395
peak=    3.596 closest distance to " CA  THR A 264 " =    0.715
peak=    3.595 closest distance to " CB  ALA A 291 " =    1.379
peak=    3.582 closest distance to " O   HOH Z 133 " =    2.281
peak=    3.582 closest distance to " CG1 ILE A  49 " =    1.539
peak=    3.579 closest distance to " CD  ARG A 269 " =    0.943
peak=    3.579 closest distance to " CA  MET A  40 " =    1.194
peak=    3.574 closest distance to " CA  ALA A 295 " =    1.139
peak=    3.573 closest distance to " O   HOH Z 213 " =    1.889
peak=    3.572 closest distance to " CA  THR A 221 " =    0.883
peak=    3.571 closest distance to " O   HOH Z 109 " =    2.632
peak=    3.565 closest distance to " CG1BVAL A  72 " =    1.739
peak=    3.564 closest distance to " O   HOH Z 102 " =    1.380
peak=    3.564 closest distance to " O   HOH Z 188 " =    3.079
peak=    3.558 closest distance to " O   HOH Z 197 " =    2.897
peak=    3.555 closest distance to " CA  ALA A 158 " =    1.104
peak=    3.553 closest distance to " CG2 ILE A 234 " =    0.905
peak=    3.551 closest distance to " O   ASP A 124 " =    1.154
peak=    3.549 closest distance to " OD2 ASP A 286 " =    2.896
peak=    3.549 closest distance to " CG BARG A 102 " =    1.825
peak=    3.547 closest distance to " OG  SER A  22 " =    2.917
peak=    3.547 closest distance to " CG  LEU A 167 " =    1.180
peak=    3.546 closest distance to " N   SER A 135 " =    1.473
peak=    3.544 closest distance to " O   HOH Z 313 " =    1.785
peak=    3.544 closest distance to " CG1 ILE A  33 " =    1.304
peak=    3.542 closest distance to " O   HOH Z 171 " =    3.920
peak=    3.541 closest distance to " O   HOH Z 193 " =    1.688
peak=    3.538 closest distance to " CA  ASP A 191 " =    0.743
peak=    3.536 closest distance to " O   HOH Z 227 " =    1.736
peak=    3.536 closest distance to " CD  ARG A 138 " =    1.200
peak=    3.534 closest distance to " O   HOH Z 406 " =    1.518
peak=    3.526 closest distance to " O   HOH Z 250 " =    1.303
peak=    3.516 closest distance to " O   HOH Z 290 " =    1.181
peak=    3.515 closest distance to " CB  ILE A 120 " =    1.377
peak=    3.514 closest distance to " CB  THR A  82 " =    1.387
peak=    3.511 closest distance to " CB  GLN A  88 " =    1.276
peak=    3.507 closest distance to " O   HOH Z 273 " =    2.702
peak=    3.504 closest distance to " O   HOH Z 285 " =    2.990
peak=    3.503 closest distance to " O   HOH Z 128 " =    2.267
peak=    3.501 closest distance to " O   HOH Z  48 " =    1.755
peak=    3.494 closest distance to " CB  SER A 216 " =    0.875
peak=    3.487 closest distance to " O   HOH Z 147 " =    1.680
peak=    3.483 closest distance to " O   HOH Z  62 " =    2.366
peak=    3.479 closest distance to " O   HOH Z 180 " =    2.097
peak=    3.466 closest distance to " CE  LYS A  76 " =    0.847
peak=    3.466 closest distance to " OG BSER A 164 " =    2.217
peak=    3.466 closest distance to " O   HOH Z 352 " =    1.860
peak=    3.460 closest distance to " N   VAL A 126 " =    1.417
peak=    3.456 closest distance to " O   HOH Z 422 " =    2.660
peak=    3.452 closest distance to " CA  ALA A 291 " =    0.927
peak=    3.451 closest distance to " O   HOH Z 313 " =    1.797
peak=    3.450 closest distance to " CB  TRP A 179 " =    1.440
peak=    3.447 closest distance to " NH1 ARG A  56 " =    0.984
peak=    3.445 closest distance to " O   HOH Z 132 " =    2.712
peak=    3.442 closest distance to " O   HOH Z 402 " =    1.536
peak=    3.442 closest distance to " CG  GLN A  88 " =    1.058
peak=    3.440 closest distance to " O   HOH Z  20 " =    1.860
peak=    3.437 closest distance to " O   HOH Z 134 " =    1.438
peak=    3.434 closest distance to " CA  ASP A 162 " =    0.994
peak=    3.433 closest distance to " CB  ALA A 248 " =    1.145
peak=    3.432 closest distance to " CB  MET A  40 " =    0.822
peak=    3.428 closest distance to " CB  THR A  31 " =    1.631
peak=    3.424 closest distance to " CB  VAL A 268 " =    0.896
peak=    3.421 closest distance to " O   HOH Z 141 " =    1.683
peak=    3.421 closest distance to " CD1 ILE A 106 " =    0.945
peak=    3.420 closest distance to " CA  ASP A 124 " =    0.771
peak=    3.420 closest distance to " O   HOH Z 135 " =    1.991
peak=    3.412 closest distance to " O   HOH Z 302 " =    1.930
peak=    3.412 closest distance to " O   HOH Z 295 " =    1.525
peak=    3.406 closest distance to " O   HOH Z 263 " =    1.582
peak=    3.403 closest distance to " CD  ARG A  66 " =    2.351
peak=    3.402 closest distance to " CB  ALA A 100 " =    1.294
peak=    3.401 closest distance to " OD1 ASN A 217 " =    1.561
peak=    3.387 closest distance to " O   TRP A 274 " =    1.843
peak=    3.374 closest distance to " CB  ALA A 161 " =    0.896
peak=    3.373 closest distance to " CB  GLN A  89 " =    1.144
peak=    3.372 closest distance to " CB  MET A  47 " =    1.047
peak=    3.371 closest distance to " NH2 ARG A  79 " =    1.393
peak=    3.366 closest distance to " CB  ALA A   1 " =    4.756
peak=    3.362 closest distance to " O   HOH Z  57 " =    1.341
peak=    3.361 closest distance to " OG BSER A 212 " =    2.398
peak=    3.359 closest distance to " CA  VAL A 112 " =    1.143
peak=    3.351 closest distance to " CB  GLN A 103 " =    0.983
peak=    3.350 closest distance to " CG2 THR A 220 " =    0.903
peak=    3.349 closest distance to " CG  GLU A  37 " =    0.857
peak=    3.348 closest distance to " CB  ALA A 248 " =    1.329
peak=    3.345 closest distance to " O   HOH Z  68 " =    2.081
peak=    3.345 closest distance to " O   HOH Z 305 " =    3.621
peak=    3.340 closest distance to " O   HOH Z 201 " =    3.070
peak=    3.340 closest distance to " CA  ARG A 195 " =    1.238
peak=    3.339 closest distance to " NH1 ARG A  14 " =    0.934
peak=    3.336 closest distance to " O   HOH Z 155 " =    3.382
peak=    3.333 closest distance to " O   HOH Z  44 " =    2.051
peak=    3.331 closest distance to " N   PHE A 130 " =    1.235
peak=    3.331 closest distance to " NH2BARG A 145 " =    2.086
peak=    3.329 closest distance to " CD2 TRP A 179 " =    1.338
peak=    3.326 closest distance to " CE1 TYR A 186 " =    1.300
peak=    3.325 closest distance to " CG2 THR A  42 " =    0.844
peak=    3.323 closest distance to " O   HOH Z 185 " =    1.944
peak=    3.323 closest distance to " O   HOH Z 116 " =    1.861
peak=    3.321 closest distance to " CB  MET A 113 " =    1.810
peak=    3.316 closest distance to " O   HOH Z 353 " =    2.719
peak=    3.315 closest distance to " O   HOH Z 368 " =    3.568
peak=    3.314 closest distance to " CG1 VAL A 174 " =    1.068
peak=    3.313 closest distance to " O   HOH Z 193 " =    2.024
peak=    3.312 closest distance to " O   GLN A 278 " =    1.555
peak=    3.311 closest distance to " O   HOH Z 172 " =    3.729
peak=    3.311 closest distance to " O   HOH Z 248 " =    1.800
peak=    3.309 closest distance to " CA  ILE A 106 " =    0.798
peak=    3.305 closest distance to " CG1 ILE A 151 " =    1.207
peak=    3.304 closest distance to " CD1 ILE A  33 " =    1.692
peak=    3.301 closest distance to " O   HOH Z 383 " =    2.153
peak=    3.298 closest distance to " CA  ALA A 154 " =    1.004
peak=    3.297 closest distance to " CB  LEU A 237 " =    0.811
peak=    3.297 closest distance to " C   TYR A 214 " =    1.543
peak=    3.294 closest distance to " O   HOH Z  21 " =    1.704
peak=    3.287 closest distance to " C   GLN A  88 " =    1.589
peak=    3.286 closest distance to " N   ARG A 190 " =    1.096
peak=    3.281 closest distance to " N   ASN A  39 " =    1.229
peak=    3.280 closest distance to " O   HOH Z 332 " =    1.549
peak=    3.278 closest distance to " CE2 TYR A  30 " =    0.907
peak=    3.278 closest distance to " O   HOH Z   4 " =    1.727
peak=    3.277 closest distance to " CA  ARG A  36 " =    1.180
peak=    3.277 closest distance to " CD2 LEU A 255 " =    1.584
peak=    3.271 closest distance to " O   HOH Z 156 " =    2.918
peak=    3.262 closest distance to " O   HOH Z 350 " =    1.668
peak=    3.261 closest distance to " O   HOH Z 355 " =    1.802
peak=    3.255 closest distance to " CA  GLY A 211 " =    1.341
peak=    3.255 closest distance to " CA  ASN A 215 " =    1.183
peak=    3.250 closest distance to " CZ3 TRP A  85 " =    1.122
peak=    3.249 closest distance to " O   HOH Z 344 " =    3.085
peak=    3.248 closest distance to " O   HOH Z  10 " =    1.839
peak=    3.246 closest distance to " CB  LEU A  83 " =    0.771
peak=    3.245 closest distance to " CE2 TYR A 186 " =    0.957
peak=    3.238 closest distance to " OE1 GLN A  11 " =    1.916
peak=    3.238 closest distance to " O   HOH Z 371 " =    3.119
peak=    3.235 closest distance to " CB  ASN A 110 " =    1.261
peak=    3.233 closest distance to " O   HOH Z 392 " =    1.325
peak=    3.232 closest distance to " O   HOH Z 435 " =    2.024
peak=    3.231 closest distance to " O   HOH Z 329 " =    3.922
peak=    3.230 closest distance to " O   HOH Z 130 " =    2.196
peak=    3.228 closest distance to " O   HOH Z 162 " =    2.092
peak=    3.228 closest distance to " CA  ASN A 127 " =    1.055
peak=    3.225 closest distance to " OG  SER A  28 " =    1.571
peak=    3.224 closest distance to " CB  THR A 157 " =    1.116
peak=    3.224 closest distance to " O   HOH Z 187 " =    2.304
peak=    3.223 closest distance to " CG  LEU A  25 " =    1.840
peak=    3.221 closest distance to " CG2 ILE A 120 " =    1.250
peak=    3.220 closest distance to " O   HOH Z 326 " =    2.202
peak=    3.219 closest distance to " O   HOH Z  58 " =    1.396
peak=    3.219 closest distance to " CA  TYR A 116 " =    1.469
peak=    3.218 closest distance to " O   HOH Z 410 " =    1.390
peak=    3.216 closest distance to " NZ  LYS A  48 " =    1.428
peak=    3.216 closest distance to " CB  GLU A 236 " =    1.060
peak=    3.213 closest distance to " CD2 LEU A 297 " =    0.917
peak=    3.213 closest distance to " O   HOH Z 148 " =    2.041
peak=    3.212 closest distance to " O   ARG A  56 " =    2.888
peak=    3.210 closest distance to " CB  PRO A 243 " =    1.527
peak=    3.208 closest distance to " O   HOH Z  43 " =    1.945
peak=    3.206 closest distance to " ND1 HIS A  86 " =    1.514
peak=    3.199 closest distance to " O   HOH Z 291 " =    1.651
peak=    3.199 closest distance to " CB  THR A 235 " =    1.127
peak=    3.199 closest distance to " O   HOH Z 128 " =    2.228
peak=    3.192 closest distance to " O   HOH Z 175 " =    3.583
peak=    3.191 closest distance to " CG  ARG A 269 " =    1.784
peak=    3.185 closest distance to " CB  SER A  26 " =    1.782
peak=    3.183 closest distance to " O   HOH Z  97 " =    2.081
peak=    3.181 closest distance to " CG  MET A 185 " =    1.013
peak=    3.181 closest distance to " CB  LYS A 117 " =    1.192
peak=    3.177 closest distance to " CB  SER A  62 " =    1.160
peak=    3.176 closest distance to " O   HOH Z  97 " =    2.578
peak=    3.174 closest distance to " OH  TYR A 214 " =    1.229
peak=    3.173 closest distance to " CB  HIS A 108 " =    0.790
peak=    3.171 closest distance to " N   TYR A  15 " =    0.766
peak=    3.168 closest distance to " CG  ARG A 159 " =    1.050
peak=    3.164 closest distance to " OE2 GLU A   2 " =    1.792
peak=    3.163 closest distance to " O   HOH Z 216 " =    3.049
peak=    3.160 closest distance to " CA  ASP A 140 " =    1.322
peak=    3.159 closest distance to " O   HOH Z 271 " =    2.503
peak=    3.159 closest distance to " N   ASN A 127 " =    1.224
peak=    3.159 closest distance to " O   HOH Z 171 " =    2.343
peak=    3.152 closest distance to " O   PRO A  90 " =    1.381
peak=    3.147 closest distance to " O   HOH Z 299 " =    4.356
peak=    3.146 closest distance to " O   HOH Z 166 " =    3.438
peak=    3.145 closest distance to " OG  SER A  62 " =    3.044
peak=    3.138 closest distance to " O   HOH Z 151 " =    1.757
peak=    3.134 closest distance to " CG2 ILE A  20 " =    1.460
peak=    3.132 closest distance to " NE  ARG A  79 " =    1.209
peak=    3.123 closest distance to " CZ3 TRP A 274 " =    4.675
peak=    3.117 closest distance to " O   ASN A 209 " =    1.439
peak=    3.117 closest distance to " OG  SER A 206 " =    1.157
peak=    3.107 closest distance to " O   HOH Z 298 " =    2.516
peak=    3.107 closest distance to " CA  ARG A 139 " =    1.100
peak=    3.103 closest distance to " CA  TRP A  92 " =    0.884
peak=    3.102 closest distance to " CB  ARG A 139 " =    0.858
peak=    3.099 closest distance to " CB  ALA A 227 " =    1.028
peak=    3.095 closest distance to " OG  SER A  62 " =    3.043
peak=    3.094 closest distance to " O   HOH Z  89 " =    1.881
peak=    3.091 closest distance to " CB  PRO A  54 " =    1.298
peak=    3.090 closest distance to " O   HOH Z  68 " =    1.579
peak=    3.090 closest distance to " O   HOH Z 420 " =    2.034
peak=    3.079 closest distance to " O   HOH Z 294 " =    1.545
peak=    3.078 closest distance to " CE  MET A 113 " =    1.826
peak=    3.071 closest distance to " CB  TYR A 116 " =    0.930
peak=    3.070 closest distance to " O   HOH Z 271 " =    2.121
peak=    3.065 closest distance to " N   GLN A 278 " =    1.083
peak=    3.057 closest distance to " CA  MET A 105 " =    0.922
peak=    3.030 closest distance to " O   HOH Z 213 " =    2.833
peak=    3.029 closest distance to " O   TYR A 116 " =    1.182
peak=    3.027 closest distance to " CA  ALA A 299 " =    0.935
peak=    3.024 closest distance to " O   HOH Z  40 " =    1.649
peak=    3.016 closest distance to " O   HOH Z 359 " =    4.102
peak=    3.010 closest distance to " O   HOH Z 173 " =    1.626

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.646 - 5.423
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 206
   mapped sites are within: 0.759 - 5.423

peak=   -5.420 closest distance to " CG2 VAL A 230 " =    0.781
peak=   -4.242 closest distance to " O   HOH Z 266 " =    5.270
peak=   -4.214 closest distance to " CD  ARG A 156 " =    2.048
peak=   -4.156 closest distance to " O   HOH Z 290 " =    1.293
peak=   -4.119 closest distance to " O   SER A 271 " =    2.287
peak=   -4.074 closest distance to " O   HOH Z 231 " =    1.837
peak=   -4.040 closest distance to " CG1 VAL A 112 " =    2.612
peak=   -4.002 closest distance to " O   HOH Z 211 " =    1.351
peak=   -4.001 closest distance to " O   HOH Z  52 " =    1.665
peak=   -3.987 closest distance to " C   ALA A 158 " =    1.319
peak=   -3.977 closest distance to " NH2AARG A 275 " =    5.423
peak=   -3.965 closest distance to " OE1 GLN A 223 " =    2.203
peak=   -3.961 closest distance to " CG2 VAL A 296 " =    1.295
peak=   -3.959 closest distance to " CB  PRO A 243 " =    2.704
peak=   -3.931 closest distance to " CD  ARG A  14 " =    3.289
peak=   -3.920 closest distance to " CG2BVAL A  41 " =    2.653
peak=   -3.918 closest distance to " CE2 TYR A  30 " =    2.813
peak=   -3.908 closest distance to " O   HOH Z 241 " =    1.073
peak=   -3.903 closest distance to " O   HOH Z 196 " =    2.288
peak=   -3.899 closest distance to " O   HOH Z 231 " =    1.062
peak=   -3.870 closest distance to " OG  SER A  97 " =    2.241
peak=   -3.866 closest distance to " O   HOH Z 166 " =    1.938
peak=   -3.866 closest distance to " CG1 VAL A 250 " =    2.781
peak=   -3.850 closest distance to " O   HOH Z  10 " =    1.539
peak=   -3.829 closest distance to " CG  ARG A 138 " =    1.020
peak=   -3.828 closest distance to " O   ILE A 109 " =    2.637
peak=   -3.822 closest distance to " O   HOH Z  73 " =    2.122
peak=   -3.806 closest distance to " CD  GLN A  58 " =    0.993
peak=   -3.778 closest distance to " CG  ASP A 231 " =    0.759
peak=   -3.773 closest distance to " O   HOH Z 394 " =    1.513
peak=   -3.748 closest distance to " O   HOH Z  19 " =    2.387
peak=   -3.738 closest distance to " CG  LEU A 101 " =    2.514
peak=   -3.736 closest distance to " CA  GLY A 241 " =    3.107
peak=   -3.728 closest distance to " CB  ARG A  79 " =    2.643
peak=   -3.708 closest distance to " CA  GLY A 241 " =    2.315
peak=   -3.680 closest distance to " CA  ASP A 298 " =    1.087
peak=   -3.678 closest distance to " CD1 LEU A 101 " =    2.902
peak=   -3.671 closest distance to " CG  TRP A 266 " =    1.805
peak=   -3.658 closest distance to " OG  SER A  87 " =    1.610
peak=   -3.657 closest distance to " C   HIS A 108 " =    1.192
peak=   -3.650 closest distance to " O   HOH Z 351 " =    1.498
peak=   -3.642 closest distance to " CG1 VAL A 296 " =    1.483
peak=   -3.640 closest distance to " CD2 LEU A 300 " =    2.809
peak=   -3.639 closest distance to " OG BSER A 134 " =    1.243
peak=   -3.639 closest distance to " N   ALA A 226 " =    2.225
peak=   -3.633 closest distance to " CD1 PHE A  59 " =    1.928
peak=   -3.627 closest distance to " OE1 GLN A  88 " =    1.117
peak=   -3.622 closest distance to " CZ3 TRP A 179 " =    1.151
peak=   -3.621 closest distance to " O   HOH Z 377 " =    1.756
peak=   -3.616 closest distance to " N   ALA A  43 " =    2.676
peak=   -3.601 closest distance to " CD1 LEU A 228 " =    2.440
peak=   -3.589 closest distance to " O   HOH Z 128 " =    2.622
peak=   -3.584 closest distance to " O   HOH Z 435 " =    2.729
peak=   -3.578 closest distance to " C   ASN A 285 " =    2.519
peak=   -3.566 closest distance to " CD2 LEU A 167 " =    1.782
peak=   -3.564 closest distance to " O   VAL A 189 " =    2.656
peak=   -3.560 closest distance to " CG  ARG A 269 " =    2.391
peak=   -3.559 closest distance to " O   HOH Z 185 " =    2.371
peak=   -3.556 closest distance to " O   GLY A 211 " =    1.477
peak=   -3.546 closest distance to " CG1 VAL A 197 " =    2.373
peak=   -3.545 closest distance to " O   HOH Z 103 " =    1.851
peak=   -3.538 closest distance to " OD1 ASN A 148 " =    1.451
peak=   -3.537 closest distance to " O   HOH Z  38 " =    1.304
peak=   -3.531 closest distance to " CE BMET A  47 " =    1.826
peak=   -3.523 closest distance to " O   PRO A 163 " =    2.097
peak=   -3.521 closest distance to " O   HOH Z 184 " =    1.466
peak=   -3.521 closest distance to " CD  PRO A 213 " =    2.205
peak=   -3.518 closest distance to " O   HOH Z 389 " =    1.962
peak=   -3.516 closest distance to " OG ASER A 134 " =    1.455
peak=   -3.510 closest distance to " O   HOH Z 216 " =    1.611
peak=   -3.509 closest distance to " O   PRO A 198 " =    1.254
peak=   -3.507 closest distance to " CG  MET A 105 " =    0.997
peak=   -3.506 closest distance to " N   THR A  18 " =    1.271
peak=   -3.503 closest distance to " O   HOH Z 377 " =    1.090
peak=   -3.495 closest distance to " O   GLY A 203 " =    2.358
peak=   -3.485 closest distance to " CH2 TRP A 177 " =    2.270
peak=   -3.468 closest distance to " OG  SER A  26 " =    1.307
peak=   -3.467 closest distance to " CG1 VAL A 265 " =    2.464
peak=   -3.464 closest distance to " NH2 ARG A  66 " =    1.996
peak=   -3.459 closest distance to " CE3 TRP A  70 " =    1.789
peak=   -3.457 closest distance to " CB  PRO A 163 " =    2.515
peak=   -3.452 closest distance to " CZ2 TRP A  92 " =    2.845
peak=   -3.448 closest distance to " OXT GLY A 302 " =    3.084
peak=   -3.446 closest distance to " CD1 LEU A   5 " =    2.706
peak=   -3.445 closest distance to " OD2 ASP A  50 " =    2.256
peak=   -3.436 closest distance to " NH2 ARG A  79 " =    2.021
peak=   -3.429 closest distance to " CG1 VAL A 112 " =    3.056
peak=   -3.426 closest distance to " O   HOH Z 136 " =    0.864
peak=   -3.425 closest distance to " CD1 LEU A 101 " =    2.510
peak=   -3.425 closest distance to " O   HOH Z 353 " =    2.206
peak=   -3.424 closest distance to " CD1 TRP A 179 " =    0.993
peak=   -3.423 closest distance to " CG2 VAL A 112 " =    2.537
peak=   -3.422 closest distance to " SD BMET A  47 " =    0.971
peak=   -3.421 closest distance to " CD1 TYR A 247 " =    2.375
peak=   -3.417 closest distance to " O   HOH Z 292 " =    4.688
peak=   -3.415 closest distance to " O   HOH Z  11 " =    1.965
peak=   -3.412 closest distance to " O   HOH Z 177 " =    1.735
peak=   -3.405 closest distance to " CD2 TYR A 293 " =    2.059
peak=   -3.405 closest distance to " O   HOH Z  13 " =    1.438
peak=   -3.399 closest distance to " O   HOH Z 113 " =    1.818
peak=   -3.398 closest distance to " NE2 GLN A 103 " =    1.771
peak=   -3.397 closest distance to " CG  PRO A 163 " =    2.383
peak=   -3.396 closest distance to " N   PHE A  59 " =    2.176
peak=   -3.395 closest distance to " O   HOH Z  43 " =    1.662
peak=   -3.391 closest distance to " O   HOH Z 290 " =    0.782
peak=   -3.384 closest distance to " O   HOH Z 176 " =    0.842
peak=   -3.383 closest distance to " NE2 GLN A  88 " =    0.875
peak=   -3.375 closest distance to " O   SER A 276 " =    1.630
peak=   -3.375 closest distance to " O   HOH Z 118 " =    3.316
peak=   -3.371 closest distance to " CE3 TRP A 150 " =    2.228
peak=   -3.368 closest distance to " O   HOH Z 426 " =    1.737
peak=   -3.367 closest distance to " C   GLU A 236 " =    0.903
peak=   -3.366 closest distance to " O   HOH Z  44 " =    2.104
peak=   -3.362 closest distance to " OH  TYR A 172 " =    1.726
peak=   -3.351 closest distance to " OD1 ASN A 249 " =    2.279
peak=   -3.350 closest distance to " O   VAL A  67 " =    2.555
peak=   -3.342 closest distance to " N   ASN A  60 " =    1.265
peak=   -3.341 closest distance to " N   THR A 157 " =    1.549
peak=   -3.339 closest distance to " CG  HIS A  86 " =    1.114
peak=   -3.333 closest distance to " O   HOH Z 222 " =    1.495
peak=   -3.330 closest distance to " CB  VAL A 230 " =    1.050
peak=   -3.330 closest distance to " O   HOH Z  60 " =    2.161
peak=   -3.328 closest distance to " CA  GLY A 241 " =    2.851
peak=   -3.317 closest distance to " CG  GLU A 277 " =    1.202
peak=   -3.314 closest distance to " O   HOH Z 275 " =    1.487
peak=   -3.313 closest distance to " CB  PHE A 192 " =    1.946
peak=   -3.312 closest distance to " O   HOH Z 136 " =    2.385
peak=   -3.311 closest distance to " O   HOH Z 111 " =    2.161
peak=   -3.310 closest distance to " CD2 PHE A  61 " =    2.488
peak=   -3.310 closest distance to " O   HOH Z 109 " =    0.915
peak=   -3.304 closest distance to " ND2 ASN A  45 " =    1.194
peak=   -3.303 closest distance to " CB  ALA A  43 " =    2.599
peak=   -3.302 closest distance to " CD1 ILE A  33 " =    2.458
peak=   -3.301 closest distance to " O   HOH Z  17 " =    1.447
peak=   -3.300 closest distance to " O   HOH Z 407 " =    3.322
peak=   -3.297 closest distance to " O   HOH Z 295 " =    1.513
peak=   -3.293 closest distance to " O   HOH Z 166 " =    1.605
peak=   -3.290 closest distance to " ND2 ASN A  60 " =    1.294
peak=   -3.288 closest distance to " O   VAL A 125 " =    2.317
peak=   -3.285 closest distance to " OG BSER A 134 " =    1.981
peak=   -3.281 closest distance to " NH2 ARG A  79 " =    1.631
peak=   -3.280 closest distance to " C   ASP A 270 " =    1.511
peak=   -3.278 closest distance to " CB  ALA A 291 " =    2.210
peak=   -3.277 closest distance to " OG  SER A 206 " =    1.834
peak=   -3.275 closest distance to " O   HOH Z 183 " =    1.243
peak=   -3.274 closest distance to " OG1 THR A 178 " =    1.358
peak=   -3.274 closest distance to " ND2 ASN A  45 " =    1.598
peak=   -3.263 closest distance to " O   HOH Z  51 " =    1.371
peak=   -3.257 closest distance to " O   ASP A 270 " =    1.641
peak=   -3.257 closest distance to " CD  LYS A 289 " =    2.534
peak=   -3.255 closest distance to " CA  GLY A 133 " =    2.263
peak=   -3.250 closest distance to " CD  GLN A  88 " =    0.883
peak=   -3.250 closest distance to " CD1 TYR A 247 " =    2.821
peak=   -3.245 closest distance to " O   HOH Z 308 " =    1.658
peak=   -3.243 closest distance to " O   HOH Z 431 " =    1.792
peak=   -3.239 closest distance to " CB  ALA A 114 " =    2.484
peak=   -3.232 closest distance to " CA  ASN A 127 " =    1.100
peak=   -3.230 closest distance to " CD1 ILE A 151 " =    2.463
peak=   -3.223 closest distance to " O   HOH Z 368 " =    1.684
peak=   -3.221 closest distance to " O   HOH Z 359 " =    3.057
peak=   -3.212 closest distance to " O   HOH Z 106 " =    1.951
peak=   -3.211 closest distance to " O   HOH Z 396 " =    1.917
peak=   -3.205 closest distance to " C   LEU A 143 " =    1.135
peak=   -3.204 closest distance to " O   HOH Z 252 " =    3.988
peak=   -3.201 closest distance to " N   ALA A 248 " =    2.397
peak=   -3.199 closest distance to " N   SER A 212 " =    1.912
peak=   -3.199 closest distance to " CB  ALA A 291 " =    2.227
peak=   -3.193 closest distance to " CD2 PHE A  61 " =    1.908
peak=   -3.183 closest distance to " CB  PHE A 283 " =    2.932
peak=   -3.183 closest distance to " N   THR A  52 " =    1.682
peak=   -3.182 closest distance to " O   HOH Z 234 " =    4.515
peak=   -3.179 closest distance to " O   HOH Z 423 " =    2.038
peak=   -3.176 closest distance to " CB  TRP A  85 " =    2.522
peak=   -3.173 closest distance to " ND2 ASN A  60 " =    1.854
peak=   -3.168 closest distance to " O   LEU A 167 " =    1.475
peak=   -3.167 closest distance to " OD1 ASP A 171 " =    1.702
peak=   -3.158 closest distance to " CE  LYS A  76 " =    2.616
peak=   -3.155 closest distance to " NE2 GLN A 194 " =    1.885
peak=   -3.148 closest distance to " O   HOH Z 380 " =    1.362
peak=   -3.146 closest distance to " C   LEU A 222 " =    0.799
peak=   -3.144 closest distance to " CE  MET A 105 " =    2.313
peak=   -3.144 closest distance to " N   SER A   3 " =    2.075
peak=   -3.143 closest distance to " CB  TYR A  15 " =    2.236
peak=   -3.143 closest distance to " C   GLY A  13 " =    0.926
peak=   -3.140 closest distance to " CB  ALA A  10 " =    2.273
peak=   -3.138 closest distance to " O   HOH Z 113 " =    2.000
peak=   -3.135 closest distance to " CG  ARG A  66 " =    2.306
peak=   -3.133 closest distance to " OD1 ASN A 173 " =    1.264
peak=   -3.128 closest distance to " C   MET A 188 " =    1.492
peak=   -3.119 closest distance to " O   HOH Z 429 " =    2.130
peak=   -3.118 closest distance to " O   HOH Z 193 " =    2.037
peak=   -3.114 closest distance to " CD  ARG A 139 " =    1.714
peak=   -3.112 closest distance to " N   LYS A 166 " =    2.004
peak=   -3.112 closest distance to " O   HOH Z 357 " =    2.169
peak=   -3.101 closest distance to " O   HOH Z 165 " =    1.855
peak=   -3.095 closest distance to " O   MET A  40 " =    2.873
peak=   -3.088 closest distance to " O   HOH Z  37 " =    2.218
peak=   -3.088 closest distance to " O   PRO A 198 " =    1.345
peak=   -3.072 closest distance to " O   HOH Z 313 " =    1.090
peak=   -3.063 closest distance to " N   SER A 276 " =    1.430
peak=   -3.051 closest distance to " CD1 ILE A 199 " =    2.675
peak=   -3.048 closest distance to " O   HOH Z 326 " =    4.983
peak=   -3.040 closest distance to " CD  GLN A  88 " =    0.850
peak=   -3.035 closest distance to " NE2 GLN A 240 " =    1.632

================= 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    :  0.4474 0.4334   6.248055e+00   6.223645e+00
   1_bss:  0.4406 0.4212   6.242774e+00   6.212303e+00
   1_xyz:  0.3334 0.3610   6.057265e+00   6.109011e+00
   1_adp:  0.2801 0.3199   5.919888e+00   6.029840e+00
   1_occ:  0.2794 0.3204   5.918740e+00   6.030590e+00
   2_bss:  0.2765 0.3163   5.918249e+00   6.027631e+00
   2_xyz:  0.1996 0.2466   5.634436e+00   5.797604e+00
   2_adp:  0.1837 0.2309   5.563395e+00   5.739751e+00
   2_occ:  0.1834 0.2310   5.563073e+00   5.739790e+00
   3_bss:  0.1824 0.2294   5.563387e+00   5.739534e+00
   3_xyz:  0.1403 0.1857   5.329395e+00   5.544633e+00
   3_adp:  0.1293 0.1776   5.271793e+00   5.504991e+00
   3_occ:  0.1293 0.1776   5.271783e+00   5.505157e+00
   4_bss:  0.1298 0.1773   5.272147e+00   5.503871e+00
   4_xyz:  0.1249 0.1740   5.244335e+00   5.480191e+00
   4_adp:  0.1241 0.1714   5.234076e+00   5.464940e+00
   4_occ:  0.1239 0.1712   5.233649e+00   5.464541e+00
   5_bss:  0.1239 0.1712   5.233335e+00   5.464486e+00
   5_xyz:  0.1169 0.1661   5.190068e+00   5.436415e+00
   5_adp:  0.1172 0.1648   5.188459e+00   5.430941e+00
   5_occ:  0.1172 0.1648   5.188035e+00   5.430671e+00
   5_bss:  0.1172 0.1648   5.188049e+00   5.430656e+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   9.431   7.841   8.116   0.000   0.000   0.000
   1_xyz:  0.300  20.000   9.431   7.841   8.116   0.000   0.000   0.000
   1_adp:  0.300  20.000   9.431   7.841   8.116   0.000   0.000   0.000
   1_occ:  0.300  20.000   9.431   7.841   8.116   0.000   0.000   0.000
   2_bss:  0.327  50.000   6.177   4.838   5.399   0.000   0.000   0.000
   2_xyz:  0.327  50.000   6.177   4.838   5.399   0.000   0.000   0.000
   2_adp:  0.327  50.000   6.177   4.838   5.399   0.000   0.000   0.000
   2_occ:  0.327  50.000   6.177   4.838   5.399   0.000   0.000   0.000
   3_bss:  0.324  50.000   4.071   3.595   4.460   0.000   0.000   0.000
   3_xyz:  0.324  50.000   4.071   3.595   4.460   0.000   0.000   0.000
   3_adp:  0.324  50.000   4.071   3.595   4.460   0.000   0.000   0.000
   3_occ:  0.324  50.000   4.071   3.595   4.460   0.000   0.000   0.000
   4_bss:  0.317  50.000   3.504   3.280   4.262   0.000   0.000   0.000
   4_xyz:  0.317  50.000   3.504   3.280   4.262   0.000   0.000   0.000
   4_adp:  0.317  50.000   3.504   3.280   4.262   0.000   0.000   0.000
   4_occ:  0.317  50.000   3.504   3.280   4.262   0.000   0.000   0.000
   5_bss:  0.323  58.565   3.367   3.262   4.257   0.000   0.000   0.000
   5_xyz:  0.323  58.565   3.367   3.262   4.257   0.000   0.000   0.000
   5_adp:  0.323  58.565   3.367   3.262   4.257   0.000   0.000   0.000
   5_occ:  0.323  58.565   3.367   3.262   4.257   0.000   0.000   0.000
   5_bss:  0.319  58.470  -0.287  -0.375   0.661  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.222 0.5315  0.5888    55398.381
   1_bss:  48.745 0.5361  0.7648    53234.120
   1_xyz:  40.542 0.6349  0.8804    37321.374
   1_adp:  34.261 0.7098  0.9680    28697.557
   1_occ:  34.298 0.7093  0.9668    28724.592
   2_bss:  34.116 0.7113  0.8730    28485.692
   2_xyz:  24.358 0.8182  0.9767    15678.146
   2_adp:  22.277 0.8401  0.9968    13677.133
   2_occ:  22.283 0.8400  0.9963    13680.144
   3_bss:  22.262 0.8403  0.9463    13682.725
   3_xyz:  17.315 0.8868  0.9758     8787.012
   3_adp:  16.415 0.8948  0.9763     8060.111
   3_occ:  16.420 0.8948  0.9762     8061.565
   4_bss:  16.409 0.8948  0.9629     8038.333
   4_xyz:  15.797 0.9004  0.9652     7598.755
   4_adp:  15.404 0.9040  0.9656     7411.224
   4_occ:  15.406 0.9040  0.9654     7406.953
   5_bss:  15.400 0.9040  0.9637     7406.812
   5_xyz:  14.854 0.9083  0.9663     7011.809
   5_adp:  14.675 0.9099  0.9653     6935.095
   5_occ:  14.671 0.9100  0.9652     6929.986
   5_bss:  14.673 0.9099  0.9650     6928.153
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4375e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4375e+01
   1_xyz:   1.607  0.013  0.106 18.032  0.006  4.113   1.3027e-01
   1_adp:   1.607  0.013  0.106 18.032  0.006  4.113   1.3027e-01
   1_occ:   1.607  0.013  0.106 18.032  0.006  4.113   1.3027e-01
   2_bss:   1.607  0.013  0.106 18.032  0.006  4.113   1.3027e-01
   2_xyz:   1.024  0.007  0.073 16.485  0.004  4.129   6.6286e-02
   2_adp:   1.024  0.007  0.073 16.485  0.004  4.129   6.6286e-02
   2_occ:   1.024  0.007  0.073 16.485  0.004  4.129   6.6286e-02
   3_bss:   1.024  0.007  0.073 16.485  0.004  4.129   6.6286e-02
   3_xyz:   1.083  0.008  0.084 16.098  0.004  4.116   7.2665e-02
   3_adp:   1.083  0.008  0.084 16.098  0.004  4.116   7.2665e-02
   3_occ:   1.083  0.008  0.084 16.098  0.004  4.116   7.2665e-02
   4_bss:   1.083  0.008  0.084 16.098  0.004  4.116   7.2665e-02
   4_xyz:   0.966  0.007  0.077 15.834  0.003  4.120   6.0321e-02
   4_adp:   0.966  0.007  0.077 15.834  0.003  4.120   6.0321e-02
   4_occ:   0.966  0.007  0.077 15.834  0.003  4.120   6.0321e-02
   5_bss:   0.966  0.007  0.077 15.834  0.003  4.120   6.0321e-02
   5_xyz:   1.116  0.010  0.088 15.841  0.004  4.125   7.5219e-02
   5_adp:   1.116  0.010  0.088 15.841  0.004  4.125   7.5219e-02
   5_occ:   1.116  0.010  0.088 15.841  0.004  4.125   7.5219e-02
   5_bss:   1.116  0.010  0.088 15.841  0.004  4.125   7.5219e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0507e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0507e+00
   1_xyz:  13.217  0.150  0.425 85.729  0.038  2.246   9.9548e-02
   1_adp:  13.217  0.150  0.425 85.729  0.038  2.246   9.9548e-02
   1_occ:  13.217  0.150  0.425 85.729  0.038  2.246   9.9548e-02
   2_bss:  13.217  0.150  0.425 85.729  0.038  2.246   9.9548e-02
   2_xyz:   6.453  0.069  0.227 89.697  0.037  2.308   4.5000e-02
   2_adp:   6.453  0.069  0.227 89.697  0.037  2.308   4.5000e-02
   2_occ:   6.453  0.069  0.227 89.697  0.037  2.308   4.5000e-02
   3_bss:   6.453  0.069  0.227 89.697  0.037  2.308   4.5000e-02
   3_xyz:   8.155  0.058  0.436 80.780  0.039  2.371   8.3207e-02
   3_adp:   8.155  0.058  0.436 80.780  0.039  2.371   8.3207e-02
   3_occ:   8.155  0.058  0.436 80.780  0.039  2.371   8.3207e-02
   4_bss:   8.155  0.058  0.436 80.780  0.039  2.371   8.3207e-02
   4_xyz:   7.997  0.047  0.386 82.740  0.037  2.414   3.8157e-02
   4_adp:   7.997  0.047  0.386 82.740  0.037  2.414   3.8157e-02
   4_occ:   7.997  0.047  0.386 82.740  0.037  2.414   3.8157e-02
   5_bss:   7.997  0.047  0.386 82.740  0.037  2.414   3.8157e-02
   5_xyz:   8.035  0.070  0.533 82.782  0.038  2.332   4.7317e-02
   5_adp:   8.035  0.070  0.533 82.782  0.038  2.332   4.7317e-02
   5_occ:   8.035  0.070  0.533 82.782  0.038  2.332   4.7317e-02
   5_bss:   8.035  0.070  0.533 82.782  0.038  2.332   4.7317e-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:  73.35   0.00  10.57  59.96   0.00   7.70  73.35   0.00  26.20
   1_occ:  73.35   0.00  10.57  59.96   0.00   7.70  73.35   0.00  26.20
   2_bss:  73.35   0.00  10.57  59.96   0.00   7.70  73.35   0.00  26.20
   2_xyz:  73.35   0.00  10.57  59.96   0.00   7.70  73.35   0.00  26.20
   2_adp:  74.66   0.00  11.16  74.66   0.00   7.53  73.54   0.00  30.92
   2_occ:  74.66   0.00  11.16  74.66   0.00   7.53  73.54   0.00  30.92
   3_bss:  74.66   0.00  11.16  74.66   0.00   7.53  73.54   0.00  30.92
   3_xyz:  74.66   0.00  11.16  74.66   0.00   7.53  73.54   0.00  30.92
   3_adp:  89.54   0.00  12.44  85.28   0.00   7.79  89.54   0.00  37.74
   3_occ:  89.54   0.00  12.44  85.28   0.00   7.79  89.54   0.00  37.74
   4_bss:  89.54   0.00  12.44  85.28   0.00   7.79  89.54   0.00  37.74
   4_xyz:  89.54   0.00  12.44  85.28   0.00   7.79  89.54   0.00  37.74
   4_adp:  88.68   0.00  12.13  86.68   0.00   7.68  88.68   0.54  36.34
   4_occ:  88.68   0.00  12.13  86.68   0.00   7.68  88.68   0.54  36.34
   5_bss:  88.68   0.00  12.13  86.68   0.00   7.68  88.68   0.54  36.34
   5_xyz:  88.68   0.00  12.13  86.68   0.00   7.68  88.68   0.54  36.34
   5_adp:  85.09   0.00  11.56  84.55   0.00   7.45  85.09   1.01  33.92
   5_occ:  85.09   0.00  11.56  84.55   0.00   7.45  85.09   1.01  33.92
   5_bss:  88.71   3.62  15.18  88.17   3.62  11.07  88.71   4.64  37.55
------------------------------------------------------------------------
 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:    1.212    0.008    0.409
   1_adp:    1.212    0.008    0.409
   1_occ:    1.212    0.008    0.409
   2_bss:    1.212    0.008    0.409
   2_xyz:    1.576    0.040    0.520
   2_adp:    1.576    0.040    0.520
   2_occ:    1.576    0.040    0.520
   3_bss:    1.576    0.040    0.520
   3_xyz:    1.516    0.031    0.585
   3_adp:    1.516    0.031    0.585
   3_occ:    1.516    0.031    0.585
   4_bss:    1.516    0.031    0.585
   4_xyz:    1.635    0.060    0.599
   4_adp:    1.635    0.060    0.599
   4_occ:    1.635    0.060    0.599
   5_bss:    1.635    0.060    0.599
   5_xyz:    1.668    0.065    0.613
   5_adp:    1.668    0.065    0.613
   5_occ:    1.668    0.065    0.613
   5_bss:    1.668    0.065    0.613
------------------------------------------------------------------------

CPU time actual refinement: 335.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1161/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_1161/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1161/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1161/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1161/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.52 
  Macro-tasks:
    bulk solvent and scale       = 42.03  
    individual site refinement   = 139.89 
    weights calculation          = 31.46  
    collect and process          = 6.59   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 220.11 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 102.05 
    alpha_beta                      = 8.29   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 114.03 
    fmodel                         = 7.60   
    r_factors                      = 0.32   
    phase_errors                   = 10.85  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 246.32 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.677 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    663 calls, 101.71 s
gradients_fft:          608 calls, 100.22 s

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

# Date 2008-01-16 Time 03:20:44 PST -0800 (1200482444.51 s)
Start R-work = 0.4474, R-free = 0.4334 (no bulk solvent and anisotropic scale)
Final R-work = 0.1336, R-free = 0.1798 (no bulk solvent and anisotropic scale)

Start R-work = 0.4406, R-free = 0.4212
Final R-work = 0.1172, R-free = 0.1648