# Date 2008-01-16 Time 01:40:15 PST -0800 (1200476415.22 s)
#phil __OFF__

Command line arguments: "../515.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 = 15300
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 515

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.2261, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.97261
Completeness in resolution range: 0.946009
Completeness with d_max=infinity: 0.943139

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9726

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.97261
Completeness in resolution range: 0.946009
Completeness with d_max=infinity: 0.943139

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.2214 [2177/2201]  1957   220  10.1%
  bin  2:  4.2214 -  3.3630 [2083/2103]  1875   208  10.0%
  bin  3:  3.3630 -  2.9415 [2071/2090]  1866   205   9.9%
  bin  4:  2.9415 -  2.6742 [2022/2052]  1816   206  10.2%
  bin  5:  2.6742 -  2.4835 [2051/2070]  1851   200   9.8%
  bin  6:  2.4835 -  2.3376 [2009/2034]  1804   205  10.2%
  bin  7:  2.3376 -  2.2209 [2014/2042]  1816   198   9.8%
  bin  8:  2.2209 -  2.1245 [2003/2039]  1800   203  10.1%
  bin  9:  2.1245 -  2.0430 [1992/2034]  1798   194   9.7%
  bin 10:  2.0430 -  1.9726 [1167/2042]  1047   120  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_515/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:
        1.45 -     2.14: 12
        2.14 -     2.83: 943
        2.83 -     3.52: 4452
        3.52 -     4.21: 9302
        4.21 -     4.90: 13622
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.449 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.684 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.708 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  53 " - " O   HOH Z 102 "  1.892 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28326 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_515/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_515/model_refine_001.geo

CPU time processing inputs: 9.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.22605 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4889   r_free= 0.4727   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.288835                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7085 0.99   1414  154 0.4064 0.3882      6.6113      6.5702|
|  2:  4.7085 -  3.7565 0.99   1359  154 0.4086 0.4021      6.7924      6.7966|
|  3:  3.7565 -  3.2874 0.99   1330  146 0.4435 0.3865      6.6815      6.6363|
|  4:  3.2874 -  2.9894 0.99   1325  150 0.4875 0.4740      6.5524      6.5032|
|  5:  2.9894 -  2.7765 0.99   1310  147 0.5191 0.4729      6.3694      6.3859|
|  6:  2.7765 -  2.6138 0.99   1316  145 0.5247 0.5428      6.2872        6.22|
|  7:  2.6138 -  2.4835 0.99   1311  143 0.5242 0.5037       6.233      6.1934|
|  8:  2.4835 -  2.3758 0.98   1291  143 0.5424 0.4992      6.2008      6.1918|
|  9:  2.3758 -  2.2847 0.98   1288  144 0.5229 0.5540      6.1148      6.1946|
| 10:  2.2847 -  2.2061 1.00   1285  145 0.5459 0.5229       6.112      6.0924|
| 11:  2.2061 -  2.1373 0.98   1294  145 0.5212 0.5150      6.0312      6.0451|
| 12:  2.1373 -  2.0764 0.98   1277  141 0.5315 0.5119      5.9725      5.9633|
| 13:  2.0764 -  2.0218 0.96   1261  141 0.5309 0.5153      5.8765      5.8217|
| 14:  2.0218 -  1.9726 0.43    569   61 0.5454 0.5112      5.9027      5.8062|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7085  1414   154  0.69  35.08   0.79     0.74      75329.81|
|  2:  4.7085 -  3.7565  1359   154  0.71  34.54   0.87     0.79     104313.51|
|  3:  3.7565 -  3.2874  1330   146  0.61  43.22   0.84     0.73     110487.40|
|  4:  3.2874 -  2.9894  1325   150  0.51  50.84   0.77     0.61     100512.75|
|  5:  2.9894 -  2.7765  1310   147  0.40  60.05   0.74     0.48      84156.25|
|  6:  2.7765 -  2.6138  1316   145  0.35  63.99   0.71     0.40      76589.29|
|  7:  2.6138 -  2.4835  1311   143  0.29  68.23   0.72     0.34      72411.58|
|  8:  2.4835 -  2.3758  1291   143  0.28  68.70   0.71     0.34      65312.07|
|  9:  2.3758 -  2.2847  1288   144  0.28  69.01   0.72     0.34      60037.66|
| 10:  2.2847 -  2.2061  1285   145  0.30  67.66   0.73     0.36      52020.89|
| 11:  2.2061 -  2.1373  1294   145  0.28  68.73   0.76     0.37      50564.49|
| 12:  2.1373 -  2.0764  1277   141  0.29  68.07   0.74     0.37      44352.15|
| 13:  2.0764 -  2.0218  1261   141  0.28  68.85   0.71     0.36      39183.59|
| 14:  2.0218 -  1.9726   569    61  0.32  66.56   0.75     0.36      32448.94|
|alpha:            min =        0.34 max =            0.79 mean =         0.48|
|beta:             min =    32448.94 max =       110487.40 mean =     71061.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.99 mean =        58.92|
|phase err.(test): min =        0.00 max =           89.99 mean =        59.18|
|-----------------------------------------------------------------------------|

============================== 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 = 16.086273             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.072   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.470903              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.503   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       32 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      690 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1513 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2633 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3922 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5087 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6582 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7703 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.711 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.977 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4955   r_free= 0.4756   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.290826                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4795   r_free= 0.4595   ksol= 0.33   Bsol= 0.00   scale= 1.004    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.92,9.37,11.46,0.00,0.00,0.00); trace/3= 9.25                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.281921                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.351393             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.413   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.273520              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.663   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4795      final r-factor (work) = 0.4035          |
| start r-factor (free) = 0.4595      final r-factor (free) = 0.4243          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 92.5188 = 12.35 * 0.50 * 6.2840 + 1.00 * 53.7105                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.4765 = 12.35 * 0.50 * 6.2074 + 1.00 * 0.1415                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4035      final r-factor (work) = 0.3611          |
| start r-factor (free) = 0.4243      final r-factor (free) = 0.4173          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9197 = 1.27 * 1.00 * 6.2074 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8246 = 1.27 * 1.00 * 6.1299 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.35   14.52    None  None   None       |
|    all(noH): 2823   0      0.00    87.35   14.52    None  None   None       |
|    Sol.    : 438    0      0.00    87.35   25.79    None  None   None       |
|    Mac.    : 2385   0      0.00    62.74   12.45    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 -   8.735: 1115   |   5:    43.675 -  52.410:   54        |
|      1:     8.735 -  17.470:  805   |   6:    52.410 -  61.145:   33        |
|      2:    17.470 -  26.205:  488   |   7:    61.145 -  69.880:    9        |
|      3:    26.205 -  34.940:  215   |   8:    69.880 -  78.616:    1        |
|      4:    34.940 -  43.675:  102   |   9:    78.616 -  87.351:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3611 r_free = 0.4173             target_work(ml) = 6.117         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3605 r_free = 0.4177             target_work(ml) = 6.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3605   r_free= 0.4177   ksol= 0.33   Bsol= 0.00   scale= 1.135    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.92,9.37,11.46,0.00,0.00,0.00); trace/3= 9.25                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.116880                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3565   r_free= 0.4120   ksol= 0.32   Bsol= 20.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,4.82,6.99,0.00,0.00,0.00); trace/3= 5.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.117556                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.010584              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.422   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.557011              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.215  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3565      final r-factor (work) = 0.2788          |
| start r-factor (free) = 0.4120      final r-factor (free) = 0.3391          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.6146 = 7.01 * 0.50 * 6.1259 + 1.00 * 0.1415                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.1615 = 7.01 * 0.50 * 6.0129 + 1.00 * 0.0846                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2788      final r-factor (work) = 0.2527          |
| start r-factor (free) = 0.3391      final r-factor (free) = 0.3187          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3673 = 0.56 * 1.00 * 6.0129 + 1.00 * 0.0180                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2854 = 0.56 * 1.00 * 5.8760 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.76   13.74    None  None   None       |
|    all(noH): 2823   0      0.00    92.76   13.74    None  None   None       |
|    Sol.    : 438    0      0.00    92.76   31.73    None  None   None       |
|    Mac.    : 2385   0      0.00    63.65   10.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.276: 1305   |   5:    46.380 -  55.656:   50        |
|      1:     9.276 -  18.552:  860   |   6:    55.656 -  64.932:   19        |
|      2:    18.552 -  27.828:  293   |   7:    64.932 -  74.208:    5        |
|      3:    27.828 -  37.104:  173   |   8:    74.208 -  83.484:    0        |
|      4:    37.104 -  46.380:  117   |   9:    83.484 -  92.760:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2527 r_free = 0.3187             target_work(ml) = 5.846         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2525 r_free = 0.3183             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2525   r_free= 0.3183   ksol= 0.32   Bsol= 20.00   scale= 1.066   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,4.82,6.99,0.00,0.00,0.00); trace/3= 5.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.846613                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2502   r_free= 0.3177   ksol= 0.34   Bsol= 51.08   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.61,4.58,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.846675                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.516843              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.204  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.423666              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.339  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2502      final r-factor (work) = 0.1760          |
| start r-factor (free) = 0.3177      final r-factor (free) = 0.2276          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2382 = 6.52 * 0.50 * 5.8782 + 1.00 * 0.0846                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7001 = 6.52 * 0.50 * 5.7143 + 1.00 * 0.0804                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1760      final r-factor (work) = 0.1566          |
| start r-factor (free) = 0.2276      final r-factor (free) = 0.2085          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4337 = 0.42 * 1.00 * 5.7143 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3389 = 0.42 * 1.00 * 5.4732 + 1.00 * 0.0201                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.01  13.51    None  None   None       |
|    all(noH): 2823   0      0.00    107.01  13.51    None  None   None       |
|    Sol.    : 438    0      0.90    92.26   35.00    None  None   None       |
|    Mac.    : 2385   0      0.00    107.01  9.57     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.701: 1713   |   5:    53.507 -  64.208:   30        |
|      1:    10.701 -  21.403:  581   |   6:    64.208 -  74.909:    7        |
|      2:    21.403 -  32.104:  190   |   7:    74.909 -  85.611:    2        |
|      3:    32.104 -  42.805:  188   |   8:    85.611 -  96.312:    1        |
|      4:    42.805 -  53.507:  110   |   9:    96.312 - 107.013:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1566 r_free = 0.2085             target_work(ml) = 5.427         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1563 r_free = 0.2083             target_work(ml) = 5.425         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1563   r_free= 0.2083   ksol= 0.34   Bsol= 51.08   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.61,4.58,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.425151                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1558   r_free= 0.2077   ksol= 0.33   Bsol= 52.05   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.99,1.42,3.48,0.00,0.00,0.00); trace/3= 1.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.424564                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.964670              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.811  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.261149              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.272   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1558      final r-factor (work) = 0.1325          |
| start r-factor (free) = 0.2077      final r-factor (free) = 0.1823          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2037 = 2.96 * 0.50 * 5.4799 + 1.00 * 0.0806                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0126 = 2.96 * 0.50 * 5.3629 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1325      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.1823      final r-factor (free) = 0.1762          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7857 = 1.26 * 1.00 * 5.3629 + 1.00 * 0.0223                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6607 = 1.26 * 1.00 * 5.2708 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.04   14.02    None  None   None       |
|    all(noH): 2823   0      0.00    93.04   14.02    None  None   None       |
|    Sol.    : 438    0      2.65    93.04   39.15    None  None   None       |
|    Mac.    : 2385   0      0.00    77.22   9.40     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.304: 1587   |   5:    46.520 -  55.824:  103        |
|      1:     9.304 -  18.608:  646   |   6:    55.824 -  65.128:   57        |
|      2:    18.608 -  27.912:  176   |   7:    65.128 -  74.432:   28        |
|      3:    27.912 -  37.216:  114   |   8:    74.432 -  83.736:    4        |
|      4:    37.216 -  46.520:  106   |   9:    83.736 -  93.040:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1264 r_free = 0.1762             target_work(ml) = 5.255         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1263 r_free = 0.1761             target_work(ml) = 5.255         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1263   r_free= 0.1761   ksol= 0.33   Bsol= 52.05   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.99,1.42,3.48,0.00,0.00,0.00); trace/3= 1.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.254594                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1760   ksol= 0.32   Bsol= 54.60   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.98,1.21,3.29,0.00,0.00,0.00); trace/3= 1.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.253622                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.724810              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.171  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.042891              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.314  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1265      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1760      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8790 = 3.72 * 0.50 * 5.2706 + 1.00 * 0.0630                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7952 = 3.72 * 0.50 * 5.2188 + 1.00 * 0.0757                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6747 = 2.04 * 1.00 * 5.2188 + 1.00 * 0.0133                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5964 = 2.04 * 1.00 * 5.1802 + 1.00 * 0.0137                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.15   13.92    None  None   None       |
|    all(noH): 2823   0      0.00    95.15   13.92    None  None   None       |
|    Sol.    : 438    0      2.29    95.15   39.37    None  None   None       |
|    Mac.    : 2385   0      0.00    87.44   9.24     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.515: 1658   |   5:    47.573 -  57.088:   87        |
|      1:     9.515 -  19.029:  601   |   6:    57.088 -  66.602:   58        |
|      2:    19.029 -  28.544:  165   |   7:    66.602 -  76.117:   26        |
|      3:    28.544 -  38.058:  120   |   8:    76.117 -  85.631:   11        |
|      4:    38.058 -  47.573:   94   |   9:    85.631 -  95.146:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1137 r_free = 0.1636             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1137 r_free = 0.1635             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1635   ksol= 0.32   Bsol= 54.60   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.98,1.21,3.29,0.00,0.00,0.00); trace/3= 1.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.172977                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7085 0.99   1414  154 0.0964 0.1267      5.3828      5.5432|
|  2:  4.7085 -  3.7565 0.99   1359  154 0.0836 0.1126      5.4346      5.6377|
|  3:  3.7565 -  3.2874 0.99   1330  146 0.1088 0.1523      5.4913      5.8499|
|  4:  3.2874 -  2.9894 0.99   1325  150 0.1248 0.1831      5.4694      5.6659|
|  5:  2.9894 -  2.7765 0.99   1310  147 0.1309 0.1636      5.3415       5.564|
|  6:  2.7765 -  2.6138 0.99   1316  145 0.1237 0.2121      5.2268      5.5315|
|  7:  2.6138 -  2.4835 0.99   1311  143 0.1318 0.1674      5.2064      5.3638|
|  8:  2.4835 -  2.3758 0.98   1291  143 0.1214 0.1740      5.1283      5.3751|
|  9:  2.3758 -  2.2847 0.98   1288  144 0.1244 0.1941      5.0793      5.3734|
| 10:  2.2847 -  2.2061 1.00   1285  145 0.1176 0.1759      4.9991      5.2304|
| 11:  2.2061 -  2.1373 0.98   1294  145 0.1171 0.1892      4.9709       5.327|
| 12:  2.1373 -  2.0764 0.98   1277  141 0.1219 0.1777      4.9311      5.2104|
| 13:  2.0764 -  2.0218 0.96   1261  141 0.1072 0.1737      4.7706      4.9976|
| 14:  2.0218 -  1.9726 0.43    569   61 0.0876 0.1548      4.6032      4.8982|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7085  1414   154  0.94   9.64   0.98     0.95       7713.35|
|  2:  4.7085 -  3.7565  1359   154  0.95   8.18   1.02     1.00       9349.82|
|  3:  3.7565 -  3.2874  1330   146  0.93  11.75   1.03     1.03      10715.98|
|  4:  3.2874 -  2.9894  1325   150  0.91  14.21   1.01     0.99      10793.20|
|  5:  2.9894 -  2.7765  1310   147  0.90  16.11   1.00     0.99       8857.89|
|  6:  2.7765 -  2.6138  1316   145  0.89  16.94   0.98     0.95       7492.32|
|  7:  2.6138 -  2.4835  1311   143  0.90  16.68   0.99     0.95       6766.86|
|  8:  2.4835 -  2.3758  1291   143  0.90  16.64   0.99     0.97       6185.62|
|  9:  2.3758 -  2.2847  1288   144  0.90  16.63   0.99     0.95       5616.63|
| 10:  2.2847 -  2.2061  1285   145  0.89  16.82   1.00     0.96       4916.98|
| 11:  2.2061 -  2.1373  1294   145  0.89  17.60   0.99     0.95       4845.18|
| 12:  2.1373 -  2.0764  1277   141  0.90  16.94   1.00     0.99       4424.17|
| 13:  2.0764 -  2.0218  1261   141  0.90  16.68   0.99     0.96       3385.46|
| 14:  2.0218 -  1.9726   569    61  0.93  12.37   0.98     0.96       2362.07|
|alpha:            min =        0.95 max =            1.03 mean =         0.97|
|beta:             min =     2362.07 max =        10793.20 mean =      6895.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.83|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.24|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1635   ksol= 0.32   Bsol= 56.62   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.66,1.44,-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: 5.173049                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1635   ksol= 0.32   Bsol= 56.62   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.66,1.44,-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: 5.173049                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7085 0.99   1414  154 0.0965 0.1268      5.3836      5.5445|
|  2:  4.7085 -  3.7565 0.99   1359  154 0.0836 0.1127      5.4354      5.6381|
|  3:  3.7565 -  3.2874 0.99   1330  146 0.1088 0.1524      5.4917      5.8507|
|  4:  3.2874 -  2.9894 0.99   1325  150 0.1248 0.1831      5.4695       5.666|
|  5:  2.9894 -  2.7765 0.99   1310  147 0.1309 0.1636      5.3413      5.5634|
|  6:  2.7765 -  2.6138 0.99   1316  145 0.1237 0.2120      5.2267      5.5314|
|  7:  2.6138 -  2.4835 0.99   1311  143 0.1318 0.1677      5.2066       5.365|
|  8:  2.4835 -  2.3758 0.98   1291  143 0.1215 0.1739      5.1287      5.3746|
|  9:  2.3758 -  2.2847 0.98   1288  144 0.1243 0.1940      5.0794      5.3736|
| 10:  2.2847 -  2.2061 1.00   1285  145 0.1176 0.1761      4.9991      5.2307|
| 11:  2.2061 -  2.1373 0.98   1294  145 0.1172 0.1890      4.9708      5.3266|
| 12:  2.1373 -  2.0764 0.98   1277  141 0.1219 0.1774      4.9308      5.2098|
| 13:  2.0764 -  2.0218 0.96   1261  141 0.1071 0.1734      4.7698      4.9969|
| 14:  2.0218 -  1.9726 0.43    569   61 0.0877 0.1545      4.6024      4.8967|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7085  1414   154  0.94   9.65   0.98     0.95       7730.31|
|  2:  4.7085 -  3.7565  1359   154  0.95   8.20   1.02     1.00       9366.42|
|  3:  3.7565 -  3.2874  1330   146  0.93  11.76   1.04     1.03      10729.85|
|  4:  3.2874 -  2.9894  1325   150  0.91  14.22   1.02     1.00      10796.06|
|  5:  2.9894 -  2.7765  1310   147  0.90  16.11   1.01     0.99       8855.43|
|  6:  2.7765 -  2.6138  1316   145  0.89  16.94   0.99     0.96       7489.94|
|  7:  2.6138 -  2.4835  1311   143  0.90  16.69   0.99     0.96       6769.75|
|  8:  2.4835 -  2.3758  1291   143  0.90  16.65   1.00     0.98       6190.23|
|  9:  2.3758 -  2.2847  1288   144  0.90  16.64   1.00     0.96       5620.84|
| 10:  2.2847 -  2.2061  1285   145  0.89  16.82   1.01     0.97       4916.92|
| 11:  2.2061 -  2.1373  1294   145  0.89  17.60   1.00     0.96       4843.30|
| 12:  2.1373 -  2.0764  1277   141  0.90  16.93   1.01     1.00       4421.53|
| 13:  2.0764 -  2.0218  1261   141  0.90  16.66   1.00     0.98       3378.05|
| 14:  2.0218 -  1.9726   569    61  0.94  12.34   0.99     0.97       2353.85|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2353.85 max =        10796.06 mean =      6899.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.83|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.24|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.02    97.16   15.93    None  None   None       |
|    all(noH): 2823   0      2.02    97.16   15.93    None  None   None       |
|    Sol.    : 438    0      4.31    97.16   41.39    None  None   None       |
|    Mac.    : 2385   0      2.02    89.45   11.26    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.017 -  11.531: 1658   |   5:    49.590 -  59.104:   87        |
|      1:    11.531 -  21.046:  601   |   6:    59.104 -  68.619:   58        |
|      2:    21.046 -  30.561:  165   |   7:    68.619 -  78.134:   26        |
|      3:    30.561 -  40.075:  120   |   8:    78.134 -  87.648:   11        |
|      4:    40.075 -  49.590:   94   |   9:    87.648 -  97.163:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 312         
Filter by distance & map next to the model:
   mapped sites are within: 0.226 - 4.827
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 312
   mapped sites are within: 0.707 - 4.827

peak=   10.801 closest distance to " CB  VAL A 230 " =    1.425
peak=    9.496 closest distance to " CB  VAL A 296 " =    1.537
peak=    7.212 closest distance to " O   HOH Z 130 " =    1.244
peak=    6.075 closest distance to " NE2 GLN A  11 " =    1.207
peak=    5.915 closest distance to " CD2 LEU A   5 " =    1.229
peak=    5.664 closest distance to " CG  LEU A   5 " =    1.117
peak=    5.516 closest distance to " NH2 ARG A  56 " =    2.057
peak=    5.515 closest distance to " O   HOH Z 142 " =    2.065
peak=    5.413 closest distance to " CG  LEU A 228 " =    1.207
peak=    5.395 closest distance to " CG  PRO A  54 " =    1.335
peak=    5.083 closest distance to " O   HOH Z  65 " =    1.166
peak=    4.971 closest distance to " O   HOH Z 427 " =    2.554
peak=    4.970 closest distance to " O   HOH Z   9 " =    2.309
peak=    4.879 closest distance to " O   HOH Z 232 " =    2.258
peak=    4.726 closest distance to " CB  GLN A 223 " =    1.543
peak=    4.715 closest distance to " CB  GLN A 183 " =    1.253
peak=    4.567 closest distance to " CB  PRO A  54 " =    1.014
peak=    4.520 closest distance to " CB  ASN A 142 " =    1.045
peak=    4.516 closest distance to " O   HOH Z 369 " =    2.238
peak=    4.492 closest distance to " O   HOH Z 287 " =    1.864
peak=    4.433 closest distance to " CB  ASN A 148 " =    1.404
peak=    4.425 closest distance to " NH2AARG A 190 " =    1.912
peak=    4.356 closest distance to " O   HOH Z 425 " =    1.493
peak=    4.352 closest distance to " O   HOH Z 126 " =    2.096
peak=    4.342 closest distance to " O   SER A  87 " =    2.325
peak=    4.283 closest distance to " CB  VAL A 265 " =    1.296
peak=    4.273 closest distance to " O   PRO A 198 " =    1.579
peak=    4.269 closest distance to " O   HOH Z 417 " =    1.409
peak=    4.204 closest distance to " O   HOH Z 362 " =    2.284
peak=    4.193 closest distance to " O   HOH Z 423 " =    1.480
peak=    4.175 closest distance to " O   HOH Z 272 " =    1.748
peak=    4.162 closest distance to " O   HOH Z 380 " =    1.918
peak=    4.155 closest distance to " CB  ARG A 275 " =    0.968
peak=    4.146 closest distance to " ND2 ASN A 187 " =    1.701
peak=    4.134 closest distance to " CB  GLU A 277 " =    3.531
peak=    4.123 closest distance to " O   HOH Z  78 " =    1.585
peak=    4.115 closest distance to " CB  VAL A 230 " =    1.210
peak=    4.111 closest distance to " O   HOH Z 359 " =    1.487
peak=    4.108 closest distance to " O   HOH Z  30 " =    1.742
peak=    4.082 closest distance to " O   HOH Z   7 " =    1.267
peak=    4.081 closest distance to " CB  LYS A 117 " =    1.241
peak=    4.074 closest distance to " O   HOH Z 214 " =    2.361
peak=    4.064 closest distance to " O   HOH Z  61 " =    1.673
peak=    4.064 closest distance to " CB  ARG A 190 " =    1.418
peak=    4.051 closest distance to " O   HOH Z 303 " =    2.171
peak=    4.047 closest distance to " O   HOH Z 248 " =    1.470
peak=    4.021 closest distance to " O  BHOH Z 338 " =    2.407
peak=    4.004 closest distance to " O   HOH Z  69 " =    1.001
peak=    4.002 closest distance to " CB  TRP A 266 " =    1.120
peak=    3.992 closest distance to " CG AARG A 275 " =    1.201
peak=    3.987 closest distance to " O   HOH Z 346 " =    1.572
peak=    3.986 closest distance to " CG  PRO A 198 " =    1.251
peak=    3.984 closest distance to " CB  SER A  63 " =    1.212
peak=    3.981 closest distance to " CG  LYS A  76 " =    1.592
peak=    3.970 closest distance to " CG  PRO A 213 " =    1.181
peak=    3.965 closest distance to " O   HOH Z 234 " =    3.661
peak=    3.956 closest distance to " CH2 TRP A 266 " =    1.080
peak=    3.918 closest distance to " O   HOH Z 188 " =    3.062
peak=    3.913 closest distance to " CB AVAL A  41 " =    1.297
peak=    3.888 closest distance to " CB  GLN A  88 " =    1.306
peak=    3.885 closest distance to " CB  ASP A 124 " =    0.819
peak=    3.881 closest distance to " CE  LYS A  76 " =    0.864
peak=    3.874 closest distance to " O   HOH Z  59 " =    1.686
peak=    3.870 closest distance to " CG  LEU A 167 " =    1.253
peak=    3.869 closest distance to " O   HOH Z 130 " =    2.496
peak=    3.864 closest distance to " CG  PRO A 280 " =    0.866
peak=    3.852 closest distance to " O   HOH Z 403 " =    1.566
peak=    3.847 closest distance to " CA  TYR A  30 " =    1.028
peak=    3.831 closest distance to " CB  SER A  26 " =    1.740
peak=    3.821 closest distance to " CB  VAL A 202 " =    1.661
peak=    3.818 closest distance to " NH1AARG A 145 " =    1.160
peak=    3.815 closest distance to " O   HOH Z 203 " =    1.692
peak=    3.809 closest distance to " CA  ALA A 160 " =    0.925
peak=    3.800 closest distance to " CB  ASN A 215 " =    1.230
peak=    3.800 closest distance to " OG BSER A 164 " =    2.189
peak=    3.793 closest distance to " CZ  PHE A 218 " =    1.079
peak=    3.790 closest distance to " CG  GLN A  58 " =    0.950
peak=    3.785 closest distance to " O   HOH Z 406 " =    1.612
peak=    3.773 closest distance to " O   HOH Z 180 " =    2.134
peak=    3.770 closest distance to " CG  PRO A 243 " =    1.071
peak=    3.769 closest distance to " O   HOH Z 236 " =    1.460
peak=    3.768 closest distance to " O   HOH Z 437 " =    1.880
peak=    3.757 closest distance to " O   HOH Z 258 " =    1.945
peak=    3.756 closest distance to " O   HOH Z  10 " =    1.747
peak=    3.754 closest distance to " CD  ARG A 269 " =    0.996
peak=    3.751 closest distance to " CB  ASN A  39 " =    1.032
peak=    3.750 closest distance to " CA  LYS A 117 " =    1.244
peak=    3.750 closest distance to " O   HOH Z 411 " =    3.617
peak=    3.738 closest distance to " O   HOH Z 422 " =    2.653
peak=    3.731 closest distance to " O   HOH Z 365 " =    2.939
peak=    3.730 closest distance to " OD1 ASN A  69 " =    2.556
peak=    3.730 closest distance to " O   HOH Z 143 " =    1.403
peak=    3.722 closest distance to " O   HOH Z 371 " =    2.787
peak=    3.720 closest distance to " O   HOH Z 298 " =    1.655
peak=    3.715 closest distance to " CD2 LEU A 228 " =    1.293
peak=    3.711 closest distance to " O   HOH Z 368 " =    2.115
peak=    3.694 closest distance to " NZ  LYS A 117 " =    2.991
peak=    3.694 closest distance to " O   HOH Z   2 " =    1.654
peak=    3.679 closest distance to " ND2 ASN A 249 " =    0.883
peak=    3.676 closest distance to " O   HOH Z 286 " =    2.348
peak=    3.675 closest distance to " CD  ARG A 159 " =    0.707
peak=    3.674 closest distance to " CB  SER A 216 " =    0.894
peak=    3.670 closest distance to " O   HOH Z 419 " =    2.077
peak=    3.668 closest distance to " O   HOH Z  68 " =    2.208
peak=    3.666 closest distance to " CB  SER A   3 " =    1.436
peak=    3.664 closest distance to " CB  ARG A  79 " =    1.420
peak=    3.662 closest distance to " O   HOH Z   1 " =    1.689
peak=    3.655 closest distance to " O   HOH Z 196 " =    1.494
peak=    3.652 closest distance to " O   HOH Z 193 " =    1.366
peak=    3.651 closest distance to " CA  PHE A 283 " =    1.112
peak=    3.649 closest distance to " O   HOH Z  88 " =    3.197
peak=    3.645 closest distance to " O   HOH Z 126 " =    1.532
peak=    3.635 closest distance to " O   HOH Z 357 " =    2.101
peak=    3.620 closest distance to " CG2 ILE A  20 " =    1.634
peak=    3.609 closest distance to " O   HOH Z 193 " =    1.604
peak=    3.609 closest distance to " O   HOH Z  44 " =    1.689
peak=    3.606 closest distance to " CD2 TRP A 179 " =    1.232
peak=    3.606 closest distance to " O   HOH Z 405 " =    1.375
peak=    3.606 closest distance to " CB  ALA A  43 " =    0.868
peak=    3.605 closest distance to " CG2 ILE A 234 " =    1.054
peak=    3.603 closest distance to " CE3 TRP A 150 " =    1.111
peak=    3.601 closest distance to " OG BSER A  99 " =    2.178
peak=    3.592 closest distance to " O   HOH Z   3 " =    2.054
peak=    3.592 closest distance to " CB  TYR A 169 " =    0.806
peak=    3.583 closest distance to " OG  SER A  62 " =    2.809
peak=    3.574 closest distance to " O   HOH Z  76 " =    1.057
peak=    3.574 closest distance to " O   HOH Z 184 " =    1.456
peak=    3.574 closest distance to " CA  ASN A 127 " =    1.069
peak=    3.570 closest distance to " CA  MET A 105 " =    0.928
peak=    3.568 closest distance to " OG ASER A 258 " =    3.012
peak=    3.568 closest distance to " CB  GLU A 128 " =    1.052
peak=    3.568 closest distance to " O   HOH Z 361 " =    3.614
peak=    3.560 closest distance to " CG2 THR A 221 " =    1.112
peak=    3.558 closest distance to " O   HOH Z 158 " =    3.245
peak=    3.557 closest distance to " O   HOH Z 251 " =    1.526
peak=    3.555 closest distance to " O   PRO A 198 " =    1.232
peak=    3.553 closest distance to " CA  ARG A 195 " =    1.175
peak=    3.552 closest distance to " O   HOH Z  43 " =    1.895
peak=    3.551 closest distance to " O   HOH Z 112 " =    1.049
peak=    3.550 closest distance to " O   HOH Z  69 " =    2.043
peak=    3.545 closest distance to " O   HOH Z  80 " =    1.525
peak=    3.534 closest distance to " N   GLY A 133 " =    3.810
peak=    3.533 closest distance to " OE2 GLU A   2 " =    1.920
peak=    3.526 closest distance to " CB  GLN A  89 " =    1.294
peak=    3.524 closest distance to " O   HOH Z 329 " =    4.130
peak=    3.522 closest distance to " NH2AARG A 275 " =    3.539
peak=    3.520 closest distance to " O   HOH Z 427 " =    1.369
peak=    3.516 closest distance to " O   HOH Z 265 " =    1.746
peak=    3.514 closest distance to " O   HOH Z 303 " =    2.879
peak=    3.514 closest distance to " O   HOH Z 128 " =    2.141
peak=    3.508 closest distance to " O   HOH Z  85 " =    1.336
peak=    3.502 closest distance to " CG2 VAL A 257 " =    0.903
peak=    3.498 closest distance to " CB  ALA A 114 " =    1.492
peak=    3.496 closest distance to " NH2AARG A 145 " =    1.098
peak=    3.488 closest distance to " CB  ARG A  79 " =    0.911
peak=    3.486 closest distance to " CB  GLU A 152 " =    1.145
peak=    3.478 closest distance to " CA  ARG A 102 " =    1.135
peak=    3.478 closest distance to " CD1 ILE A  33 " =    1.787
peak=    3.477 closest distance to " CB  ALA A 248 " =    1.044
peak=    3.471 closest distance to " O   HOH Z 290 " =    1.030
peak=    3.466 closest distance to " O   HOH Z 132 " =    2.955
peak=    3.463 closest distance to " O   HOH Z 216 " =    3.428
peak=    3.457 closest distance to " CA  VAL A 125 " =    1.168
peak=    3.457 closest distance to " CB  ASN A 110 " =    1.015
peak=    3.448 closest distance to " N   PHE A 130 " =    1.292
peak=    3.447 closest distance to " O   HOH Z 222 " =    2.249
peak=    3.446 closest distance to " O   HOH Z  92 " =    2.360
peak=    3.445 closest distance to " O   HOH Z  63 " =    1.282
peak=    3.444 closest distance to " CG  MET A 185 " =    1.174
peak=    3.441 closest distance to " O   HOH Z  40 " =    2.137
peak=    3.439 closest distance to " CA  TYR A 116 " =    1.359
peak=    3.439 closest distance to " CA  ALA A  51 " =    1.005
peak=    3.436 closest distance to " O   HOH Z 299 " =    4.248
peak=    3.436 closest distance to " CB  SER A 212 " =    1.271
peak=    3.435 closest distance to " CB  ASP A 140 " =    1.048
peak=    3.429 closest distance to " O   HOH Z 421 " =    2.262
peak=    3.427 closest distance to " CB  THR A 157 " =    1.144
peak=    3.425 closest distance to " O   HOH Z  49 " =    0.827
peak=    3.418 closest distance to " O   HOH Z 261 " =    1.834
peak=    3.418 closest distance to " O   HOH Z 323 " =    1.613
peak=    3.417 closest distance to " CB  TRP A 179 " =    1.451
peak=    3.415 closest distance to " O   HOH Z 261 " =    1.698
peak=    3.411 closest distance to " NE2 HIS A 207 " =    1.203
peak=    3.403 closest distance to " CA  ALA A 233 " =    1.094
peak=    3.399 closest distance to " N   ASN A 127 " =    1.316
peak=    3.397 closest distance to " CG  LEU A 281 " =    1.006
peak=    3.397 closest distance to " ND1 HIS A  86 " =    1.817
peak=    3.396 closest distance to " O   HOH Z 128 " =    1.803
peak=    3.396 closest distance to " O   HOH Z 325 " =    2.206
peak=    3.391 closest distance to " O   HOH Z 145 " =    1.497
peak=    3.381 closest distance to " CD  LYS A 166 " =    1.344
peak=    3.378 closest distance to " O   HOH Z  88 " =    3.123
peak=    3.374 closest distance to " O   HOH Z 193 " =    1.550
peak=    3.364 closest distance to " O   HOH Z 425 " =    2.152
peak=    3.363 closest distance to " O   HOH Z 122 " =    1.860
peak=    3.356 closest distance to " CB  SER A 273 " =    0.856
peak=    3.355 closest distance to " CB  PHE A 204 " =    1.090
peak=    3.354 closest distance to " NZ  LYS A  48 " =    1.163
peak=    3.352 closest distance to " O   HOH Z 281 " =    2.297
peak=    3.352 closest distance to " O   HOH Z   1 " =    1.823
peak=    3.351 closest distance to " N   ASN A  39 " =    1.238
peak=    3.343 closest distance to " O   HOH Z 284 " =    3.003
peak=    3.341 closest distance to " CA  ALA A 158 " =    1.329
peak=    3.337 closest distance to " O   HOH Z 153 " =    3.603
peak=    3.332 closest distance to " CB  THR A  52 " =    0.952
peak=    3.332 closest distance to " O   HOH Z 218 " =    1.549
peak=    3.332 closest distance to " N   GLN A 278 " =    1.463
peak=    3.331 closest distance to " N   ALA A 256 " =    1.019
peak=    3.325 closest distance to " CA  ALA A  21 " =    1.220
peak=    3.324 closest distance to " CB  TRP A 150 " =    1.294
peak=    3.324 closest distance to " O   HOH Z 389 " =    1.275
peak=    3.321 closest distance to " N   SER A 146 " =    1.808
peak=    3.318 closest distance to " CG1BVAL A  72 " =    1.029
peak=    3.316 closest distance to " CB  LEU A  83 " =    0.728
peak=    3.314 closest distance to " N   ASP A 162 " =    1.075
peak=    3.311 closest distance to " O   HOH Z 197 " =    3.101
peak=    3.306 closest distance to " O   HOH Z 109 " =    2.454
peak=    3.303 closest distance to " O   HOH Z 258 " =    1.039
peak=    3.302 closest distance to " O   HOH Z 343 " =    3.135
peak=    3.295 closest distance to " O   HOH Z 394 " =    3.639
peak=    3.292 closest distance to " CG1 ILE A 151 " =    1.137
peak=    3.284 closest distance to " CB  PRO A  90 " =    1.158
peak=    3.284 closest distance to " O   PHE A 192 " =    1.384
peak=    3.283 closest distance to " CA  SER A  87 " =    1.031
peak=    3.279 closest distance to " CB  THR A  31 " =    1.585
peak=    3.277 closest distance to " CD1 ILE A 199 " =    1.089
peak=    3.277 closest distance to " O   HOH Z 148 " =    2.283
peak=    3.270 closest distance to " CA  ARG A  36 " =    1.043
peak=    3.270 closest distance to " CB  LEU A 143 " =    1.116
peak=    3.270 closest distance to " CB  ARG A 138 " =    0.909
peak=    3.270 closest distance to " CD  ARG A 195 " =    3.532
peak=    3.268 closest distance to " C   ALA A 299 " =    0.971
peak=    3.258 closest distance to " CA  ASN A 217 " =    1.211
peak=    3.258 closest distance to " CE AMET A  47 " =    1.366
peak=    3.255 closest distance to " CA  ASN A 215 " =    1.057
peak=    3.253 closest distance to " O   HOH Z  20 " =    1.460
peak=    3.251 closest distance to " O   HOH Z 189 " =    2.922
peak=    3.250 closest distance to " CE1 TYR A 186 " =    1.281
peak=    3.247 closest distance to " CA  LEU A 101 " =    1.378
peak=    3.245 closest distance to " O   HOH Z   1 " =    1.912
peak=    3.244 closest distance to " NH1 ARG A 138 " =    1.084
peak=    3.243 closest distance to " CG1 ILE A  49 " =    1.489
peak=    3.242 closest distance to " CG BARG A 102 " =    1.820
peak=    3.241 closest distance to " O   ASP A 191 " =    1.620
peak=    3.238 closest distance to " CA  ALA A 291 " =    0.820
peak=    3.236 closest distance to " CA  ASP A 162 " =    0.988
peak=    3.236 closest distance to " CZ  PHE A  38 " =    1.149
peak=    3.235 closest distance to " O   HOH Z 423 " =    1.665
peak=    3.234 closest distance to " CB  GLU A  46 " =    0.979
peak=    3.233 closest distance to " O   HOH Z 327 " =    1.487
peak=    3.232 closest distance to " O   HOH Z  61 " =    1.546
peak=    3.230 closest distance to " CB  ALA A   1 " =    4.827
peak=    3.230 closest distance to " CB  SER A  97 " =    0.944
peak=    3.229 closest distance to " CA  ARG A 159 " =    1.163
peak=    3.228 closest distance to " O   HOH Z 124 " =    1.223
peak=    3.227 closest distance to " O   HOH Z  51 " =    1.351
peak=    3.226 closest distance to " O   HOH Z 394 " =    1.686
peak=    3.226 closest distance to " O   HOH Z  97 " =    2.025
peak=    3.225 closest distance to " O   HOH Z 146 " =    1.450
peak=    3.223 closest distance to " O   HOH Z 227 " =    1.905
peak=    3.220 closest distance to " OG  SER A  62 " =    2.979
peak=    3.220 closest distance to " O   HOH Z 116 " =    2.993
peak=    3.217 closest distance to " O   HOH Z 128 " =    2.073
peak=    3.215 closest distance to " O   ASP A 124 " =    1.199
peak=    3.212 closest distance to " OG1 THR A 264 " =    0.715
peak=    3.208 closest distance to " CB  LEU A 300 " =    0.887
peak=    3.208 closest distance to " O   HOH Z  40 " =    2.036
peak=    3.206 closest distance to " O   HOH Z 130 " =    1.980
peak=    3.205 closest distance to " CG  GLN A  88 " =    1.155
peak=    3.204 closest distance to " OG BSER A 212 " =    2.873
peak=    3.203 closest distance to " OE2 GLU A  53 " =    1.896
peak=    3.195 closest distance to " CG1 ILE A 120 " =    1.277
peak=    3.190 closest distance to " CE ALYS A 290 " =    1.150
peak=    3.190 closest distance to " CA  ARG A 139 " =    1.004
peak=    3.188 closest distance to " CD2 TYR A 186 " =    1.084
peak=    3.185 closest distance to " O   HOH Z 162 " =    3.459
peak=    3.179 closest distance to " O   HOH Z 403 " =    1.563
peak=    3.171 closest distance to " CB  ARG A 156 " =    1.081
peak=    3.170 closest distance to " O   HOH Z 217 " =    2.146
peak=    3.166 closest distance to " CE  LYS A  48 " =    1.135
peak=    3.165 closest distance to " O   HOH Z 260 " =    1.530
peak=    3.163 closest distance to " O   HOH Z 391 " =    2.905
peak=    3.156 closest distance to " N   SER A 135 " =    1.298
peak=    3.153 closest distance to " O   HOH Z  55 " =    2.026
peak=    3.152 closest distance to " O   THR A 220 " =    1.365
peak=    3.151 closest distance to " CA  TYR A  30 " =    1.064
peak=    3.149 closest distance to " CB  SER A  62 " =    1.078
peak=    3.145 closest distance to " O   HOH Z 119 " =    1.818
peak=    3.143 closest distance to " OE1 GLN A 240 " =    1.527
peak=    3.140 closest distance to " CG  GLN A 278 " =    1.215
peak=    3.138 closest distance to " O   HOH Z 305 " =    3.459
peak=    3.133 closest distance to " CD1 LEU A 300 " =    1.066
peak=    3.123 closest distance to " CB  ALA A   9 " =    1.581
peak=    3.123 closest distance to " NE  ARG A  56 " =    3.519
peak=    3.120 closest distance to " CA  LYS A 290 " =    1.250
peak=    3.119 closest distance to " O   HOH Z 213 " =    2.192
peak=    3.102 closest distance to " O   HOH Z 438 " =    3.092
peak=    3.094 closest distance to " O   HOH Z 272 " =    2.079
peak=    3.093 closest distance to " O   HOH Z  94 " =    2.599
peak=    3.082 closest distance to " CG  ARG A 159 " =    0.856
peak=    3.080 closest distance to " NH2BARG A 145 " =    2.059
peak=    3.079 closest distance to " O   TYR A 116 " =    1.239
peak=    3.079 closest distance to " CB  ASN A 187 " =    1.100
peak=    3.068 closest distance to " O   HOH Z  85 " =    2.056
peak=    3.062 closest distance to " CA  ASP A 149 " =    1.239
peak=    3.061 closest distance to " O   HOH Z 172 " =    2.967
peak=    3.050 closest distance to " CZ3 TRP A 177 " =    1.067
peak=    3.045 closest distance to " O   HOH Z 327 " =    1.964
peak=    3.025 closest distance to " CA  GLY A 136 " =    1.064
peak=    3.016 closest distance to " CB  ASP A 171 " =    1.158

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.780 - 5.556
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 217
   mapped sites are within: 0.780 - 5.556

peak=   -4.762 closest distance to " CD  ARG A  14 " =    3.085
peak=   -4.662 closest distance to " OG BSER A 134 " =    1.274
peak=   -4.567 closest distance to " CD  ARG A 156 " =    2.021
peak=   -4.336 closest distance to " CG2 VAL A 230 " =    0.818
peak=   -4.303 closest distance to " O   HOH Z 211 " =    1.019
peak=   -4.247 closest distance to " O   VAL A  67 " =    2.517
peak=   -4.223 closest distance to " O   HOH Z 266 " =    5.419
peak=   -4.182 closest distance to " CB  ALA A  43 " =    2.572
peak=   -4.158 closest distance to " CB  PRO A 243 " =    2.722
peak=   -4.158 closest distance to " O   HOH Z 131 " =    4.091
peak=   -4.085 closest distance to " O   HOH Z  69 " =    1.837
peak=   -4.072 closest distance to " CG  GLN A 223 " =    2.327
peak=   -4.031 closest distance to " O   HOH Z 231 " =    2.061
peak=   -4.018 closest distance to " CE BMET A  47 " =    1.254
peak=   -4.016 closest distance to " O   HOH Z 185 " =    2.109
peak=   -4.002 closest distance to " O   PRO A 198 " =    1.206
peak=   -3.977 closest distance to " C   HIS A 108 " =    1.295
peak=   -3.915 closest distance to " CD1 LEU A 255 " =    2.909
peak=   -3.912 closest distance to " CG2 VAL A 202 " =    2.675
peak=   -3.875 closest distance to " CD2 LEU A 237 " =    2.819
peak=   -3.864 closest distance to " CG  GLN A  58 " =    1.057
peak=   -3.861 closest distance to " CB  PHE A 192 " =    1.885
peak=   -3.846 closest distance to " OG  SER A  62 " =    4.430
peak=   -3.844 closest distance to " O   HOH Z 231 " =    1.013
peak=   -3.838 closest distance to " C   ILE A 239 " =    2.169
peak=   -3.803 closest distance to " O   HOH Z 357 " =    2.110
peak=   -3.774 closest distance to " CB  VAL A 230 " =    1.136
peak=   -3.773 closest distance to " OG  SER A  97 " =    2.253
peak=   -3.755 closest distance to " CD1 LEU A 101 " =    2.343
peak=   -3.753 closest distance to " CA  ASP A  27 " =    2.429
peak=   -3.727 closest distance to " CG1BVAL A  72 " =    2.233
peak=   -3.715 closest distance to " O   HOH Z 191 " =    5.556
peak=   -3.712 closest distance to " O   HOH Z 429 " =    1.979
peak=   -3.705 closest distance to " O   PRO A 163 " =    2.024
peak=   -3.696 closest distance to " CE2 TYR A  30 " =    2.678
peak=   -3.694 closest distance to " NH2 ARG A  79 " =    2.035
peak=   -3.690 closest distance to " OG  SER A  87 " =    1.382
peak=   -3.687 closest distance to " O   HOH Z 389 " =    1.522
peak=   -3.686 closest distance to " O   SER A  22 " =    2.499
peak=   -3.679 closest distance to " CB  ALA A 291 " =    2.206
peak=   -3.673 closest distance to " O   HOH Z 111 " =    1.759
peak=   -3.654 closest distance to " CA  GLY A 241 " =    2.401
peak=   -3.651 closest distance to " O   HOH Z  73 " =    2.351
peak=   -3.646 closest distance to " O   HOH Z  52 " =    1.344
peak=   -3.642 closest distance to " CG2 VAL A 296 " =    2.056
peak=   -3.641 closest distance to " CA  GLY A  35 " =    2.103
peak=   -3.635 closest distance to " O   PHE A 218 " =    1.474
peak=   -3.621 closest distance to " N   ALA A 226 " =    1.996
peak=   -3.619 closest distance to " O   HOH Z 193 " =    1.193
peak=   -3.616 closest distance to " O   HOH Z 394 " =    1.507
peak=   -3.611 closest distance to " CA  ASP A 298 " =    1.070
peak=   -3.609 closest distance to " CE2 PHE A 218 " =    2.446
peak=   -3.607 closest distance to " CZ2 TRP A  92 " =    2.824
peak=   -3.589 closest distance to " C   MET A 188 " =    1.412
peak=   -3.583 closest distance to " CZ2 TRP A 274 " =    0.930
peak=   -3.580 closest distance to " O   HOH Z 352 " =    1.425
peak=   -3.553 closest distance to " O   HOH Z 134 " =    4.228
peak=   -3.541 closest distance to " O   HOH Z 140 " =    1.418
peak=   -3.524 closest distance to " O   HOH Z 208 " =    2.158
peak=   -3.523 closest distance to " CD2 TYR A 293 " =    1.947
peak=   -3.517 closest distance to " O   HOH Z 359 " =    3.244
peak=   -3.514 closest distance to " O   HOH Z 292 " =    1.632
peak=   -3.512 closest distance to " CG2 THR A  18 " =    2.873
peak=   -3.512 closest distance to " CA  VAL A  67 " =    2.986
peak=   -3.509 closest distance to " CG1 VAL A 250 " =    2.665
peak=   -3.503 closest distance to " ND2 ASN A 249 " =    2.182
peak=   -3.490 closest distance to " N   THR A 157 " =    1.481
peak=   -3.489 closest distance to " CZ3 TRP A 179 " =    1.272
peak=   -3.488 closest distance to " O   HOH Z 351 " =    1.587
peak=   -3.472 closest distance to " CB  PRO A 163 " =    2.347
peak=   -3.466 closest distance to " O   PRO A 198 " =    1.439
peak=   -3.465 closest distance to " CG2 THR A  42 " =    1.880
peak=   -3.459 closest distance to " O   HOH Z  51 " =    0.780
peak=   -3.445 closest distance to " O   HOH Z  43 " =    1.884
peak=   -3.441 closest distance to " CD  LYS A 289 " =    2.380
peak=   -3.440 closest distance to " O   HOH Z 198 " =    1.914
peak=   -3.435 closest distance to " O   SER A 135 " =    1.476
peak=   -3.428 closest distance to " NE2 GLN A 278 " =    1.811
peak=   -3.427 closest distance to " O   GLY A  17 " =    1.131
peak=   -3.424 closest distance to " O   HOH Z 117 " =    1.931
peak=   -3.422 closest distance to " O   HOH Z 108 " =    1.548
peak=   -3.418 closest distance to " OE2 GLU A 152 " =    1.269
peak=   -3.415 closest distance to " O   HOH Z 389 " =    2.209
peak=   -3.414 closest distance to " CE3 TRP A 150 " =    2.225
peak=   -3.412 closest distance to " ND2 ASN A  45 " =    2.155
peak=   -3.408 closest distance to " O   HOH Z  39 " =    1.086
peak=   -3.407 closest distance to " N   PRO A 163 " =    1.719
peak=   -3.404 closest distance to " O   HOH Z 236 " =    1.375
peak=   -3.404 closest distance to " CG1 VAL A 112 " =    3.053
peak=   -3.399 closest distance to " CB  ASP A 132 " =    2.389
peak=   -3.397 closest distance to " CA  GLY A  98 " =    1.861
peak=   -3.396 closest distance to " O   HOH Z 364 " =    2.625
peak=   -3.387 closest distance to " CB  ALA A 161 " =    2.451
peak=   -3.376 closest distance to " O   ASP A  27 " =    1.784
peak=   -3.372 closest distance to " O   ARG A 145 " =    1.510
peak=   -3.370 closest distance to " ND2 ASN A 187 " =    1.453
peak=   -3.370 closest distance to " CG2AVAL A  72 " =    2.595
peak=   -3.366 closest distance to " OH  TYR A 172 " =    1.764
peak=   -3.365 closest distance to " O   HOH Z 345 " =    2.121
peak=   -3.364 closest distance to " OE1 GLU A 277 " =    2.206
peak=   -3.356 closest distance to " OXT GLY A 302 " =    3.160
peak=   -3.355 closest distance to " NE2 GLN A 194 " =    1.810
peak=   -3.352 closest distance to " CB  TRP A  85 " =    2.509
peak=   -3.350 closest distance to " O   HOH Z 313 " =    1.613
peak=   -3.342 closest distance to " O   HOH Z 253 " =    3.668
peak=   -3.341 closest distance to " O   HOH Z 371 " =    2.113
peak=   -3.333 closest distance to " O   HOH Z  11 " =    1.798
peak=   -3.332 closest distance to " N   ASP A 171 " =    2.584
peak=   -3.330 closest distance to " CB  ALA A   7 " =    2.110
peak=   -3.329 closest distance to " O   VAL A 189 " =    2.590
peak=   -3.329 closest distance to " O   ILE A  49 " =    1.681
peak=   -3.325 closest distance to " O   GLN A 144 " =    1.401
peak=   -3.325 closest distance to " CB  ASN A  39 " =    2.242
peak=   -3.321 closest distance to " O   HOH Z 384 " =    2.246
peak=   -3.314 closest distance to " O   HOH Z 426 " =    1.695
peak=   -3.311 closest distance to " CD1 LEU A 297 " =    2.211
peak=   -3.311 closest distance to " CE  MET A 105 " =    2.409
peak=   -3.310 closest distance to " CZ  TYR A 186 " =    2.359
peak=   -3.306 closest distance to " O   HOH Z 346 " =    1.692
peak=   -3.305 closest distance to " CG  LEU A   5 " =    0.953
peak=   -3.304 closest distance to " ND2 ASN A 252 " =    1.991
peak=   -3.303 closest distance to " O   SER A 276 " =    1.552
peak=   -3.301 closest distance to " O   HOH Z 427 " =    1.588
peak=   -3.300 closest distance to " N   VAL A  72 " =    1.504
peak=   -3.299 closest distance to " NH2AARG A 275 " =    5.294
peak=   -3.297 closest distance to " O   HOH Z 103 " =    1.730
peak=   -3.296 closest distance to " O   HOH Z 165 " =    2.045
peak=   -3.295 closest distance to " CB  PRO A  90 " =    1.779
peak=   -3.295 closest distance to " O   HOH Z  65 " =    1.372
peak=   -3.290 closest distance to " NE2 GLN A  11 " =    1.900
peak=   -3.287 closest distance to " O   SER A 271 " =    2.110
peak=   -3.286 closest distance to " O   HOH Z 102 " =    1.491
peak=   -3.285 closest distance to " O   HOH Z  20 " =    1.499
peak=   -3.285 closest distance to " NH2 ARG A 219 " =    1.716
peak=   -3.285 closest distance to " CG1 VAL A 112 " =    2.573
peak=   -3.278 closest distance to " O   HOH Z 243 " =    2.027
peak=   -3.273 closest distance to " O   HOH Z 318 " =    1.943
peak=   -3.271 closest distance to " CD2 LEU A   5 " =    1.153
peak=   -3.270 closest distance to " O   TRP A  70 " =    1.426
peak=   -3.270 closest distance to " N   ALA A  43 " =    2.644
peak=   -3.269 closest distance to " CB  ALA A 129 " =    2.492
peak=   -3.262 closest distance to " CA  GLY A 203 " =    2.491
peak=   -3.257 closest distance to " O   HOH Z 116 " =    1.859
peak=   -3.254 closest distance to " CZ  PHE A  38 " =    2.467
peak=   -3.251 closest distance to " O   HOH Z   9 " =    3.378
peak=   -3.251 closest distance to " CB  ALA A 114 " =    2.426
peak=   -3.250 closest distance to " CG  TRP A 266 " =    1.953
peak=   -3.250 closest distance to " N   SER A 141 " =    1.897
peak=   -3.250 closest distance to " C   LEU A 222 " =    0.939
peak=   -3.248 closest distance to " OD2 ASP A 191 " =    1.289
peak=   -3.245 closest distance to " O   HOH Z 426 " =    2.372
peak=   -3.243 closest distance to " CD2 HIS A 207 " =    2.189
peak=   -3.242 closest distance to " O   HOH Z  44 " =    2.258
peak=   -3.236 closest distance to " O   PRO A 243 " =    2.452
peak=   -3.232 closest distance to " CD2 PHE A 225 " =    1.129
peak=   -3.231 closest distance to " O   HOH Z 295 " =    1.661
peak=   -3.230 closest distance to " CG  PHE A 283 " =    2.600
peak=   -3.228 closest distance to " O   HOH Z  68 " =    1.312
peak=   -3.223 closest distance to " CB  ALA A 248 " =    2.304
peak=   -3.217 closest distance to " OD1 ASP A 191 " =    1.789
peak=   -3.217 closest distance to " O   HOH Z 166 " =    2.167
peak=   -3.216 closest distance to " OG ASER A 134 " =    1.204
peak=   -3.213 closest distance to " O   HOH Z 189 " =    2.345
peak=   -3.212 closest distance to " O   HOH Z 275 " =    1.489
peak=   -3.208 closest distance to " O   HOH Z 421 " =    3.044
peak=   -3.204 closest distance to " O   HOH Z 111 " =    4.642
peak=   -3.202 closest distance to " O   HOH Z  90 " =    2.469
peak=   -3.199 closest distance to " O   HOH Z 285 " =    2.147
peak=   -3.199 closest distance to " O   HOH Z 114 " =    3.037
peak=   -3.196 closest distance to " ND2 ASN A  69 " =    1.822
peak=   -3.193 closest distance to " O   ALA A  84 " =    1.664
peak=   -3.189 closest distance to " O   HOH Z 166 " =    1.520
peak=   -3.188 closest distance to " ND2 ASN A  45 " =    1.245
peak=   -3.185 closest distance to " O   HOH Z 232 " =    2.210
peak=   -3.185 closest distance to " O   HOH Z   1 " =    1.444
peak=   -3.180 closest distance to " NE2 GLN A 278 " =    1.851
peak=   -3.179 closest distance to " N   VAL A 125 " =    1.007
peak=   -3.175 closest distance to " CE1 PHE A 218 " =    2.619
peak=   -3.172 closest distance to " N   VAL A 232 " =    2.045
peak=   -3.166 closest distance to " O   HOH Z  89 " =    2.938
peak=   -3.163 closest distance to " O   SER A 210 " =    1.836
peak=   -3.160 closest distance to " C   ARG A 269 " =    1.363
peak=   -3.157 closest distance to " CG  ASN A 301 " =    1.941
peak=   -3.156 closest distance to " O   HOH Z 407 " =    2.943
peak=   -3.156 closest distance to " CE1 TYR A 247 " =    2.726
peak=   -3.154 closest distance to " C   ASN A 285 " =    2.131
peak=   -3.150 closest distance to " O   ALA A  51 " =    1.204
peak=   -3.136 closest distance to " O   ALA A  10 " =    1.766
peak=   -3.135 closest distance to " CE  LYS A  76 " =    2.703
peak=   -3.134 closest distance to " O   ALA A 227 " =    1.538
peak=   -3.132 closest distance to " CB  SER A 210 " =    1.152
peak=   -3.131 closest distance to " CD  PRO A 213 " =    2.063
peak=   -3.129 closest distance to " O   ALA A 161 " =    1.733
peak=   -3.123 closest distance to " CG  MET A 105 " =    0.969
peak=   -3.122 closest distance to " CB  ASP A 171 " =    2.260
peak=   -3.122 closest distance to " CA  GLY A 133 " =    2.283
peak=   -3.121 closest distance to " O   HOH Z 100 " =    1.247
peak=   -3.121 closest distance to " CG  GLN A  88 " =    0.807
peak=   -3.119 closest distance to " CB  ALA A 244 " =    2.092
peak=   -3.119 closest distance to " CA  GLY A 133 " =    1.925
peak=   -3.113 closest distance to " O   HOH Z 412 " =    4.235
peak=   -3.107 closest distance to " O   LYS A 289 " =    3.037
peak=   -3.105 closest distance to " CA  GLY A 241 " =    3.118
peak=   -3.105 closest distance to " ND2 ASN A 173 " =    1.699
peak=   -3.100 closest distance to " O   HOH Z  60 " =    1.946
peak=   -3.095 closest distance to " O   HOH Z 368 " =    1.649
peak=   -3.093 closest distance to " N   SER A 276 " =    1.429
peak=   -3.091 closest distance to " C   HIS A 207 " =    1.251
peak=   -3.083 closest distance to " O   HOH Z 281 " =    2.560
peak=   -3.081 closest distance to " CG  LEU A 228 " =    0.968
peak=   -3.079 closest distance to " O   HOH Z 262 " =    2.454
peak=   -3.071 closest distance to " CD1 LEU A 228 " =    2.299
peak=   -3.071 closest distance to " CD1 PHE A  61 " =    2.799
peak=   -3.048 closest distance to " OE1 GLN A  88 " =    1.291
peak=   -3.045 closest distance to " O   TYR A 186 " =    1.721
peak=   -3.016 closest distance to " ND2 ASN A  60 " =    1.150

================= 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    :  0.4889 0.4727   6.288835e+00   6.269726e+00
   1_bss:  0.4795 0.4595   6.281921e+00   6.259532e+00
   1_xyz:  0.4035 0.4243   6.184726e+00   6.205262e+00
   1_adp:  0.3611 0.4173   6.117476e+00   6.193804e+00
   1_occ:  0.3605 0.4177   6.116880e+00   6.194625e+00
   2_bss:  0.3565 0.4120   6.117556e+00   6.193245e+00
   2_xyz:  0.2788 0.3391   5.914315e+00   6.053526e+00
   2_adp:  0.2527 0.3187   5.846496e+00   6.001622e+00
   2_occ:  0.2525 0.3183   5.846613e+00   6.001774e+00
   3_bss:  0.2502 0.3177   5.846675e+00   6.002828e+00
   3_xyz:  0.1760 0.2276   5.528673e+00   5.731742e+00
   3_adp:  0.1566 0.2085   5.426560e+00   5.645613e+00
   3_occ:  0.1563 0.2083   5.425151e+00   5.645091e+00
   4_bss:  0.1558 0.2077   5.424564e+00   5.644717e+00
   4_xyz:  0.1325 0.1823   5.293697e+00   5.524523e+00
   4_adp:  0.1264 0.1762   5.254950e+00   5.489231e+00
   4_occ:  0.1263 0.1761   5.254594e+00   5.488748e+00
   5_bss:  0.1265 0.1760   5.253622e+00   5.487079e+00
   5_xyz:  0.1159 0.1657   5.187726e+00   5.436048e+00
   5_adp:  0.1137 0.1636   5.173417e+00   5.423821e+00
   5_occ:  0.1137 0.1635   5.172977e+00   5.423273e+00
   5_bss:  0.1136 0.1635   5.173049e+00   5.423333e+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:  0.333   0.000   6.921   9.372  11.460   0.000   0.000   0.000
   1_xyz:  0.333   0.000   6.921   9.372  11.460   0.000   0.000   0.000
   1_adp:  0.333   0.000   6.921   9.372  11.460   0.000   0.000   0.000
   1_occ:  0.333   0.000   6.921   9.372  11.460   0.000   0.000   0.000
   2_bss:  0.318  20.000   3.204   4.815   6.987   0.000   0.000   0.000
   2_xyz:  0.318  20.000   3.204   4.815   6.987   0.000   0.000   0.000
   2_adp:  0.318  20.000   3.204   4.815   6.987   0.000   0.000   0.000
   2_occ:  0.318  20.000   3.204   4.815   6.987   0.000   0.000   0.000
   3_bss:  0.336  51.079   1.797   2.612   4.583   0.000   0.000   0.000
   3_xyz:  0.336  51.079   1.797   2.612   4.583   0.000   0.000   0.000
   3_adp:  0.336  51.079   1.797   2.612   4.583   0.000   0.000   0.000
   3_occ:  0.336  51.079   1.797   2.612   4.583   0.000   0.000   0.000
   4_bss:  0.328  52.050   0.995   1.419   3.480   0.000   0.000   0.000
   4_xyz:  0.328  52.050   0.995   1.419   3.480   0.000   0.000   0.000
   4_adp:  0.328  52.050   0.995   1.419   3.480   0.000   0.000   0.000
   4_occ:  0.328  52.050   0.995   1.419   3.480   0.000   0.000   0.000
   5_bss:  0.323  54.600   0.977   1.207   3.295   0.000   0.000   0.000
   5_xyz:  0.323  54.600   0.977   1.207   3.295   0.000   0.000   0.000
   5_adp:  0.323  54.600   0.977   1.207   3.295   0.000   0.000   0.000
   5_occ:  0.323  54.600   0.977   1.207   3.295   0.000   0.000   0.000
   5_bss:  0.323  56.617  -0.775  -0.661   1.436  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.947 0.4067  0.4791    71066.999
   1_bss:  58.385 0.4128  0.6325    68664.564
   1_xyz:  49.425 0.5259  0.7860    52482.311
   1_adp:  47.180 0.5541  0.8965    50146.171
   1_occ:  47.323 0.5523  0.8924    50326.318
   2_bss:  46.879 0.5578  0.7819    49696.698
   2_xyz:  36.392 0.6835  0.9332    30899.069
   2_adp:  32.767 0.7264  0.9650    26590.898
   2_occ:  32.806 0.7260  0.9639    26611.146
   3_bss:  32.738 0.7268  0.9003    26667.436
   3_xyz:  22.475 0.8369  0.9983    13456.453
   3_adp:  19.912 0.8627  1.0093    11198.566
   3_occ:  19.899 0.8627  1.0092    11164.349
   4_bss:  19.842 0.8632  0.9726    11125.875
   4_xyz:  16.978 0.8897  0.9810     8609.799
   4_adp:  16.254 0.8962  0.9736     8006.329
   4_occ:  16.248 0.8962  0.9735     7994.045
   5_bss:  16.215 0.8965  0.9687     7961.037
   5_xyz:  15.097 0.9059  0.9767     7097.129
   5_adp:  14.782 0.9087  0.9720     6906.054
   5_occ:  14.772 0.9088  0.9720     6896.395
   5_bss:  14.774 0.9088  0.9787     6899.666
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3711e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3711e+01
   1_xyz:   1.707  0.013  0.106 18.277  0.006  4.108   1.4149e-01
   1_adp:   1.707  0.013  0.106 18.277  0.006  4.108   1.4149e-01
   1_occ:   1.707  0.013  0.106 18.277  0.006  4.108   1.4149e-01
   2_bss:   1.707  0.013  0.106 18.277  0.006  4.108   1.4149e-01
   2_xyz:   1.177  0.008  0.084 16.240  0.005  4.109   8.4604e-02
   2_adp:   1.177  0.008  0.084 16.240  0.005  4.109   8.4604e-02
   2_occ:   1.177  0.008  0.084 16.240  0.005  4.109   8.4604e-02
   3_bss:   1.177  0.008  0.084 16.240  0.005  4.109   8.4604e-02
   3_xyz:   1.170  0.009  0.086 16.085  0.004  4.127   8.0449e-02
   3_adp:   1.170  0.009  0.086 16.085  0.004  4.127   8.0449e-02
   3_occ:   1.170  0.009  0.086 16.085  0.004  4.127   8.0449e-02
   4_bss:   1.170  0.009  0.086 16.085  0.004  4.127   8.0449e-02
   4_xyz:   0.994  0.007  0.074 15.550  0.004  4.119   6.2961e-02
   4_adp:   0.994  0.007  0.074 15.550  0.004  4.119   6.2961e-02
   4_occ:   0.994  0.007  0.074 15.550  0.004  4.119   6.2961e-02
   5_bss:   0.994  0.007  0.074 15.550  0.004  4.119   6.2961e-02
   5_xyz:   1.122  0.010  0.085 15.567  0.004  4.126   7.5747e-02
   5_adp:   1.122  0.010  0.085 15.567  0.004  4.126   7.5747e-02
   5_occ:   1.122  0.010  0.085 15.567  0.004  4.126   7.5747e-02
   5_bss:   1.122  0.010  0.085 15.567  0.004  4.126   7.5747e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9617e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9617e+00
   1_xyz:  13.626  0.171  0.416 84.840  0.033  2.112   9.8921e-02
   1_adp:  13.626  0.171  0.416 84.840  0.033  2.112   9.8921e-02
   1_occ:  13.626  0.171  0.416 84.840  0.033  2.112   9.8921e-02
   2_bss:  13.626  0.171  0.416 84.840  0.033  2.112   9.8921e-02
   2_xyz:   6.186  0.066  0.287 86.817  0.028  2.193   5.9575e-02
   2_adp:   6.186  0.066  0.287 86.817  0.028  2.193   5.9575e-02
   2_occ:   6.186  0.066  0.287 86.817  0.028  2.193   5.9575e-02
   3_bss:   6.186  0.066  0.287 86.817  0.028  2.193   5.9575e-02
   3_xyz:   7.513  0.047  0.379 89.032  0.030  2.196   6.0681e-02
   3_adp:   7.513  0.047  0.379 89.032  0.030  2.196   6.0681e-02
   3_occ:   7.513  0.047  0.379 89.032  0.030  2.196   6.0681e-02
   4_bss:   7.513  0.047  0.379 89.032  0.030  2.196   6.0681e-02
   4_xyz:   6.285  0.042  0.302 80.851  0.036  2.355   4.4216e-02
   4_adp:   6.285  0.042  0.302 80.851  0.036  2.355   4.4216e-02
   4_occ:   6.285  0.042  0.302 80.851  0.036  2.355   4.4216e-02
   5_bss:   6.285  0.042  0.302 80.851  0.036  2.355   4.4216e-02
   5_xyz:   6.539  0.054  0.333 83.147  0.038  2.292   6.6194e-02
   5_adp:   6.539  0.054  0.333 83.147  0.038  2.292   6.6194e-02
   5_occ:   6.539  0.054  0.333 83.147  0.038  2.292   6.6194e-02
   5_bss:   6.539  0.054  0.333 83.147  0.038  2.292   6.6194e-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:  87.35   0.00  14.52  62.74   0.00  12.45  87.35   0.00  25.79
   1_occ:  87.35   0.00  14.52  62.74   0.00  12.45  87.35   0.00  25.79
   2_bss:  87.35   0.00  14.52  62.74   0.00  12.45  87.35   0.00  25.79
   2_xyz:  87.35   0.00  14.52  62.74   0.00  12.45  87.35   0.00  25.79
   2_adp:  92.76   0.00  13.74  63.65   0.00  10.44  92.76   0.00  31.73
   2_occ:  92.76   0.00  13.74  63.65   0.00  10.44  92.76   0.00  31.73
   3_bss:  92.76   0.00  13.74  63.65   0.00  10.44  92.76   0.00  31.73
   3_xyz:  92.76   0.00  13.74  63.65   0.00  10.44  92.76   0.00  31.73
   3_adp: 107.01   0.00  13.51 107.01   0.00   9.57  92.26   0.90  35.00
   3_occ: 107.01   0.00  13.51 107.01   0.00   9.57  92.26   0.90  35.00
   4_bss: 107.01   0.00  13.51 107.01   0.00   9.57  92.26   0.90  35.00
   4_xyz: 107.01   0.00  13.51 107.01   0.00   9.57  92.26   0.90  35.00
   4_adp:  93.04   0.00  14.02  77.22   0.00   9.40  93.04   2.65  39.15
   4_occ:  93.04   0.00  14.02  77.22   0.00   9.40  93.04   2.65  39.15
   5_bss:  93.04   0.00  14.02  77.22   0.00   9.40  93.04   2.65  39.15
   5_xyz:  93.04   0.00  14.02  77.22   0.00   9.40  93.04   2.65  39.15
   5_adp:  95.15   0.00  13.92  87.44   0.00   9.24  95.15   2.29  39.37
   5_occ:  95.15   0.00  13.92  87.44   0.00   9.24  95.15   2.29  39.37
   5_bss:  97.16   2.02  15.93  89.45   2.02  11.26  97.16   4.31  41.39
------------------------------------------------------------------------
 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:    1.286    0.015    0.409
   1_adp:    1.286    0.015    0.409
   1_occ:    1.286    0.015    0.409
   2_bss:    1.286    0.015    0.409
   2_xyz:    1.799    0.029    0.576
   2_adp:    1.799    0.029    0.576
   2_occ:    1.799    0.029    0.576
   3_bss:    1.799    0.029    0.576
   3_xyz:    1.539    0.056    0.710
   3_adp:    1.539    0.056    0.710
   3_occ:    1.539    0.056    0.710
   4_bss:    1.539    0.056    0.710
   4_xyz:    1.670    0.041    0.736
   4_adp:    1.670    0.041    0.736
   4_occ:    1.670    0.041    0.736
   5_bss:    1.670    0.041    0.736
   5_xyz:    1.848    0.035    0.760
   5_adp:    1.848    0.035    0.760
   5_occ:    1.848    0.035    0.760
   5_bss:    1.848    0.035    0.760
------------------------------------------------------------------------

CPU time actual refinement: 340.19


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_515/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_515/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_515/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_515/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_515/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 340.04 
  Macro-tasks:
    bulk solvent and scale       = 45.82  
    individual site refinement   = 145.56 
    weights calculation          = 31.76  
    collect and process          = 6.41   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 229.66 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 103.05 
    alpha_beta                      = 8.10   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 115.26 
    fmodel                         = 7.61   
    r_factors                      = 0.17   
    phase_errors                   = 10.46  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 248.36 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.722 micro seconds
Total CPU time: 5.89 minutes
from_scatterers_fft:    643 calls, 102.63 s
gradients_fft:          588 calls, 101.43 s

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

# Date 2008-01-16 Time 01:46:08 PST -0800 (1200476768.36 s)
Start R-work = 0.4889, R-free = 0.4727 (no bulk solvent and anisotropic scale)
Final R-work = 0.1314, R-free = 0.1796 (no bulk solvent and anisotropic scale)

Start R-work = 0.4795, R-free = 0.4595
Final R-work = 0.1136, R-free = 0.1635