# Date 2008-01-16 Time 00:45:51 PST -0800 (1200473151.21 s)
#phil __OFF__

Command line arguments: "../149.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7623
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 149

-------------------------------------------------------------------------------
  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: (68.845, 46.2261, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


================================== 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: (68.845, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7929 1.96071
Completeness in resolution range: 0.95757
Completeness with d_max=infinity: 0.954583

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7929
                             d_min =   1.9607

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: (68.845, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7929 1.96071
Completeness in resolution range: 0.95757
Completeness with d_max=infinity: 0.954583

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7934 -  4.1951 [2152/2176]  1933   219  10.2%
  bin  2:  4.1951 -  3.3424 [2062/2081]  1859   203   9.8%
  bin  3:  3.3424 -  2.9236 [2037/2056]  1834   203  10.0%
  bin  4:  2.9236 -  2.6580 [2014/2044]  1810   204  10.1%
  bin  5:  2.6580 -  2.4684 [2009/2028]  1809   200  10.0%
  bin  6:  2.4684 -  2.3235 [2003/2028]  1802   201  10.0%
  bin  7:  2.3235 -  2.2075 [1990/2018]  1795   195   9.8%
  bin  8:  2.2075 -  2.1117 [1971/2007]  1768   203  10.3%
  bin  9:  2.1117 -  2.0306 [1970/2012]  1779   191   9.7%
  bin 10:  2.0306 -  1.9607 [1381/2007]  1241   140  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_149/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:
        1.64 -     2.29: 34
        2.29 -     2.94: 1663
        2.94 -     3.60: 4623
        3.60 -     4.25: 9378
        4.25 -     4.90: 13095
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.639 3.040 -x+1,y-1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.743 3.120 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.763 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.784 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.787 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28788 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_149/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_149/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 = 68.845 46.22605 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4824   r_free= 0.4789   ksol= 0.00   Bsol= 0.00   scale= 0.801    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.282536                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6788 0.99   1398  153 0.3992 0.3882      6.5895      6.5837|
|  2:  4.6788 -  3.7334 0.99   1340  153 0.3906 0.4063       6.762      6.7938|
|  3:  3.7334 -  3.2673 0.99   1310  146 0.4373 0.4127      6.6728       6.669|
|  4:  3.2673 -  2.9712 0.99   1310  139 0.4711 0.4578      6.5392       6.513|
|  5:  2.9712 -  2.7597 0.99   1308  146 0.5038 0.4850      6.3698      6.3948|
|  6:  2.7597 -  2.5979 0.99   1291  148 0.5158 0.5508      6.2895      6.2275|
|  7:  2.5979 -  2.4684 0.99   1288  144 0.5149 0.5198      6.2478      6.1777|
|  8:  2.4684 -  2.3614 0.98   1281  140 0.5279 0.5029      6.1943      6.2114|
|  9:  2.3614 -  2.2708 0.98   1276  145 0.5184 0.5495      6.1052      6.1922|
| 10:  2.2708 -  2.1927 0.99   1277  139 0.5466 0.5449      6.1256      6.0739|
| 11:  2.1927 -  2.1244 0.98   1271  140 0.5445 0.5042      6.0475      6.0502|
| 12:  2.1244 -  2.0638 0.97   1258  140 0.5370 0.5126      5.9799      6.0501|
| 13:  2.0638 -  2.0096 1.00   1280  142 0.5336 0.4924      5.8921       5.808|
| 14:  2.0096 -  1.9607 0.57    742   84 0.5521 0.5566      5.9073      5.8049|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7934 -  4.6788  1398   153  0.66  37.50   0.80     0.71      82543.24|
|  2:  4.6788 -  3.7334  1340   153  0.69  35.95   0.89     0.77     109862.62|
|  3:  3.7334 -  3.2673  1310   146  0.59  44.38   0.87     0.72     115166.70|
|  4:  3.2673 -  2.9712  1310   139  0.50  51.65   0.81     0.60     102976.71|
|  5:  2.9712 -  2.7597  1308   146  0.39  60.47   0.74     0.47      87064.58|
|  6:  2.7597 -  2.5979  1291   148  0.33  64.94   0.72     0.39      78658.78|
|  7:  2.5979 -  2.4684  1288   144  0.26  70.38   0.76     0.31      74695.91|
|  8:  2.4684 -  2.3614  1281   140  0.25  71.16   0.73     0.30      67354.48|
|  9:  2.3614 -  2.2708  1276   145  0.27  69.99   0.74     0.33      60808.48|
| 10:  2.2708 -  2.1927  1277   139  0.32  66.05   0.75     0.39      51354.11|
| 11:  2.1927 -  2.1244  1271   140  0.32  65.74   0.75     0.41      48419.55|
| 12:  2.1244 -  2.0638  1258   140  0.31  66.94   0.76     0.40      43981.80|
| 13:  2.0638 -  2.0096  1280   142  0.29  68.26   0.75     0.37      38257.27|
| 14:  2.0096 -  1.9607   742    84  0.33  65.10   0.72     0.35      28982.96|
|alpha:            min =        0.30 max =            0.77 mean =         0.47|
|beta:             min =    28982.96 max =       115166.70 mean =     72422.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.98 mean =        59.46|
|phase err.(test): min =        0.00 max =           89.98 mean =        59.70|
|-----------------------------------------------------------------------------|

============================== 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 = 15.574080             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.214   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.526984              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.530   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       38 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      185 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      715 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1555 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2673 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4024 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5154 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6647 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7839 |
|-----------------------------------------------------------------------------|
|-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 |       53.019 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.196 |       2.609 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.474)------------------------------------------|
|    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 = 11.474)------------------------------------------|
|    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: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4894   r_free= 0.4795   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.283763                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4745   r_free= 0.4647   ksol= 0.36   Bsol= 2.47   scale= 1.013    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.15,9.85,8.54,0.00,0.00,0.00); trace/3= 8.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.274231                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.943778             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.828   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.431024              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.114   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4745      final r-factor (work) = 0.3959          |
| start r-factor (free) = 0.4647      final r-factor (free) = 0.4144          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.6794 = 12.94 * 0.50 * 6.2826 + 1.00 * 53.0192                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.2756 = 12.94 * 0.50 * 6.2012 + 1.00 * 0.1421                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3959      final r-factor (work) = 0.3512          |
| start r-factor (free) = 0.4144      final r-factor (free) = 0.4080          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8885 = 1.43 * 1.00 * 6.2012 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7690 = 1.43 * 1.00 * 6.1151 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.474)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    59.37   12.97    None  None   None       |
|    all(noH): 2823   0      0.00    59.37   12.97    None  None   None       |
|    Sol.    : 438    0      0.00    59.37   23.55    None  None   None       |
|    Mac.    : 2385   0      0.00    51.76   11.03    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.937:  847   |   5:    29.683 -  35.619:  122        |
|      1:     5.937 -  11.873:  706   |   6:    35.619 -  41.556:   66        |
|      2:    11.873 -  17.810:  525   |   7:    41.556 -  47.493:   32        |
|      3:    17.810 -  23.746:  310   |   8:    47.493 -  53.429:   14        |
|      4:    23.746 -  29.683:  194   |   9:    53.429 -  59.366:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3512 r_free = 0.4080             target_work(ml) = 6.100         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3508 r_free = 0.4074             target_work(ml) = 6.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3508   r_free= 0.4074   ksol= 0.36   Bsol= 2.47   scale= 1.123    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.15,9.85,8.54,0.00,0.00,0.00); trace/3= 8.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.098981                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3462   r_free= 0.4021   ksol= 0.34   Bsol= 24.44   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.38,5.16,4.85,0.00,0.00,0.00); trace/3= 4.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.097542                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.007884              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.056   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.661850              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.354  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3462      final r-factor (work) = 0.2618          |
| start r-factor (free) = 0.4021      final r-factor (free) = 0.3215          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.5545 = 7.01 * 0.50 * 6.1109 + 1.00 * 0.1421                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0595 = 7.01 * 0.50 * 5.9872 + 1.00 * 0.0809                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2618      final r-factor (work) = 0.2342          |
| start r-factor (free) = 0.3215      final r-factor (free) = 0.2957          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9810 = 0.66 * 1.00 * 5.9872 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8688 = 0.66 * 1.00 * 5.8237 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.474)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.59   13.23    None  None   None       |
|    all(noH): 2823   0      0.00    82.59   13.23    None  None   None       |
|    Sol.    : 438    0      0.59    82.59   32.26    None  None   None       |
|    Mac.    : 2385   0      0.00    70.52   9.73     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 -   8.259: 1322   |   5:    41.294 -  49.552:   77        |
|      1:     8.259 -  16.517:  770   |   6:    49.552 -  57.811:   48        |
|      2:    16.517 -  24.776:  283   |   7:    57.811 -  66.070:   15        |
|      3:    24.776 -  33.035:  178   |   8:    66.070 -  74.328:    6        |
|      4:    33.035 -  41.294:  123   |   9:    74.328 -  82.587:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2342 r_free = 0.2957             target_work(ml) = 5.783         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2340 r_free = 0.2954             target_work(ml) = 5.783         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2340   r_free= 0.2954   ksol= 0.34   Bsol= 24.44   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.38,5.16,4.85,0.00,0.00,0.00); trace/3= 4.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.782907                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2323   r_free= 0.2937   ksol= 0.34   Bsol= 41.49   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,3.19,3.69,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.779794                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.014721              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.030   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.290223              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.105  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2323      final r-factor (work) = 0.1676          |
| start r-factor (free) = 0.2937      final r-factor (free) = 0.2162          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7754 = 4.01 * 0.50 * 5.8258 + 1.00 * 0.0809                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4156 = 4.01 * 0.50 * 5.6537 + 1.00 * 0.0666                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1676      final r-factor (work) = 0.1516          |
| start r-factor (free) = 0.2162      final r-factor (free) = 0.2013          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6546 = 0.29 * 1.00 * 5.6537 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5854 = 0.29 * 1.00 * 5.4283 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.474)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.69   13.05    None  None   None       |
|    all(noH): 2823   0      0.00    81.69   13.05    None  None   None       |
|    Sol.    : 438    0      1.96    81.69   34.89    None  None   None       |
|    Mac.    : 2385   0      0.00    73.38   9.04     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 -   8.169: 1461   |   5:    40.844 -  49.013:  102        |
|      1:     8.169 -  16.338:  709   |   6:    49.013 -  57.181:   63        |
|      2:    16.338 -  24.506:  204   |   7:    57.181 -  65.350:   18        |
|      3:    24.506 -  32.675:  131   |   8:    65.350 -  73.519:    7        |
|      4:    32.675 -  40.844:  127   |   9:    73.519 -  81.688:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1516 r_free = 0.2013             target_work(ml) = 5.395         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1513 r_free = 0.2007             target_work(ml) = 5.393         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1513   r_free= 0.2007   ksol= 0.34   Bsol= 41.49   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,3.19,3.69,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.392983                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1506   r_free= 0.2003   ksol= 0.32   Bsol= 36.50   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,1.96,3.17,0.00,0.00,0.00); trace/3= 2.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.390098                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.924547              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.578  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.359925              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.471  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1506      final r-factor (work) = 0.1305          |
| start r-factor (free) = 0.2003      final r-factor (free) = 0.1758          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2946 = 1.92 * 0.50 * 5.4330 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1824 = 1.92 * 0.50 * 5.3284 + 1.00 * 0.0551                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1305      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1712          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9277 = 0.36 * 1.00 * 5.3284 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9026 = 0.36 * 1.00 * 5.2477 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.474)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.72   13.10    None  None   None       |
|    all(noH): 2823   0      0.00    81.72   13.10    None  None   None       |
|    Sol.    : 438    0      2.46    81.72   36.02    None  None   None       |
|    Mac.    : 2385   0      0.00    76.96   8.89     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 -   8.172: 1511   |   5:    40.859 -  49.030:  100        |
|      1:     8.172 -  16.344:  679   |   6:    49.030 -  57.202:   69        |
|      2:    16.344 -  24.515:  186   |   7:    57.202 -  65.374:   34        |
|      3:    24.515 -  32.687:  114   |   8:    65.374 -  73.545:    8        |
|      4:    32.687 -  40.859:  119   |   9:    73.545 -  81.717:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1264 r_free = 0.1712             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1263 r_free = 0.1711             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1263   r_free= 0.1711   ksol= 0.32   Bsol= 36.50   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,1.96,3.17,0.00,0.00,0.00); trace/3= 2.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.233071                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1263   r_free= 0.1710   ksol= 0.32   Bsol= 36.50   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.20,1.73,3.20,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.232413                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.502302              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.841  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.628385              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.639   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1263      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1710      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9964 = 1.50 * 0.50 * 5.2471 + 1.00 * 0.0551                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9672 = 1.50 * 0.50 * 5.2099 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.7053 = 2.63 * 1.00 * 5.2099 + 1.00 * 0.0115                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.6378 = 2.63 * 1.00 * 5.1809 + 1.00 * 0.0205                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.474)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.28   13.62    None  None   None       |
|    all(noH): 2823   0      0.00    94.28   13.62    None  None   None       |
|    Sol.    : 438    0      1.37    87.36   38.69    None  None   None       |
|    Mac.    : 2385   0      0.00    94.28   9.02     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 -   9.428: 1701   |   5:    47.142 -  56.570:   88        |
|      1:     9.428 -  18.857:  569   |   6:    56.570 -  65.998:   53        |
|      2:    18.857 -  28.285:  152   |   7:    65.998 -  75.427:   27        |
|      3:    28.285 -  37.713:  115   |   8:    75.427 -  84.855:   12        |
|      4:    37.713 -  47.142:  103   |   9:    84.855 -  94.283:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1180 r_free = 0.1633             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1633             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1633   ksol= 0.32   Bsol= 36.50   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.20,1.73,3.20,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.182466                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6788 0.99   1398  153 0.1046 0.1242      5.4098      5.5121|
|  2:  4.6788 -  3.7334 0.99   1340  153 0.0902 0.1150      5.4647      5.6403|
|  3:  3.7334 -  3.2673 0.99   1310  146 0.1112 0.1535      5.5099      5.8656|
|  4:  3.2673 -  2.9712 0.99   1310  139 0.1284 0.1719      5.4916      5.6394|
|  5:  2.9712 -  2.7597 0.99   1308  146 0.1371 0.1697      5.3648      5.5527|
|  6:  2.7597 -  2.5979 0.99   1291  148 0.1279 0.2097      5.2432      5.5386|
|  7:  2.5979 -  2.4684 0.99   1288  144 0.1310 0.1665      5.2056      5.3554|
|  8:  2.4684 -  2.3614 0.98   1281  140 0.1245 0.1702      5.1316      5.3673|
|  9:  2.3614 -  2.2708 0.98   1276  145 0.1267 0.1931      5.0755      5.3826|
| 10:  2.2708 -  2.1927 0.99   1277  139 0.1182 0.1697      4.9872      5.1639|
| 11:  2.1927 -  2.1244 0.98   1271  140 0.1196 0.1855      4.9801      5.3001|
| 12:  2.1244 -  2.0638 0.97   1258  140 0.1217 0.1761      4.9305      5.2614|
| 13:  2.0638 -  2.0096 1.00   1280  142 0.1158 0.1814      4.8221      5.0725|
| 14:  2.0096 -  1.9607 0.57    742   84 0.0993 0.1640      4.6567      4.9026|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7934 -  4.6788  1398   153  0.94   9.23   0.98     0.96       7283.87|
|  2:  4.6788 -  3.7334  1340   153  0.95   7.94   1.03     1.02       8991.71|
|  3:  3.7334 -  3.2673  1310   146  0.93  11.49   1.05     1.04      10622.71|
|  4:  3.2673 -  2.9712  1310   139  0.91  14.24   1.02     1.02      10954.40|
|  5:  2.9712 -  2.7597  1308   146  0.90  16.29   1.01     0.98       8887.45|
|  6:  2.7597 -  2.5979  1291   148  0.89  16.81   0.98     0.96       7560.18|
|  7:  2.5979 -  2.4684  1288   144  0.90  16.36   0.99     0.95       6594.20|
|  8:  2.4684 -  2.3614  1281   140  0.90  15.91   1.00     0.98       5951.48|
|  9:  2.3614 -  2.2708  1276   145  0.90  16.22   1.01     0.98       5452.19|
| 10:  2.2708 -  2.1927  1277   139  0.90  16.35   1.00     0.96       4602.35|
| 11:  2.1927 -  2.1244  1271   140  0.89  16.88   1.01     0.98       4809.82|
| 12:  2.1244 -  2.0638  1258   140  0.90  16.72   1.02     1.01       4381.81|
| 13:  2.0638 -  2.0096  1280   142  0.90  16.38   1.01     0.99       3581.06|
| 14:  2.0096 -  1.9607   742    84  0.92  13.75   0.99     0.96       2452.33|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2452.33 max =        10954.40 mean =      6742.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.57|
|phase err.(test): min =        0.00 max =           87.68 mean =        14.08|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1638   ksol= 0.32   Bsol= 43.42   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.35,1.18,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.182992                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1638   ksol= 0.32   Bsol= 43.42   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.35,1.18,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.182992                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6788 0.99   1398  153 0.1034 0.1260      5.4092      5.5187|
|  2:  4.6788 -  3.7334 0.99   1340  153 0.0914 0.1173      5.4799      5.6583|
|  3:  3.7334 -  3.2673 0.99   1310  146 0.1130 0.1525      5.5201      5.8635|
|  4:  3.2673 -  2.9712 0.99   1310  139 0.1280 0.1722      5.4903      5.6434|
|  5:  2.9712 -  2.7597 0.99   1308  146 0.1372 0.1688      5.3651      5.5473|
|  6:  2.7597 -  2.5979 0.99   1291  148 0.1278 0.2085      5.2401      5.5347|
|  7:  2.5979 -  2.4684 0.99   1288  144 0.1306 0.1673      5.2027      5.3572|
|  8:  2.4684 -  2.3614 0.98   1281  140 0.1244 0.1690      5.1282      5.3612|
|  9:  2.3614 -  2.2708 0.98   1276  145 0.1263 0.1929      5.0723       5.382|
| 10:  2.2708 -  2.1927 0.99   1277  139 0.1179 0.1687      4.9858      5.1621|
| 11:  2.1927 -  2.1244 0.98   1271  140 0.1194 0.1845      4.9789      5.2973|
| 12:  2.1244 -  2.0638 0.97   1258  140 0.1214 0.1767      4.9295      5.2636|
| 13:  2.0638 -  2.0096 1.00   1280  142 0.1157 0.1811      4.8214      5.0707|
| 14:  2.0096 -  1.9607 0.57    742   84 0.0994 0.1634      4.6557       4.902|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7934 -  4.6788  1398   153  0.94   9.34   0.98     0.96       7475.32|
|  2:  4.6788 -  3.7334  1340   153  0.95   8.21   1.03     1.02       9293.94|
|  3:  3.7334 -  3.2673  1310   146  0.93  11.77   1.05     1.04      10912.48|
|  4:  3.2673 -  2.9712  1310   139  0.91  14.24   1.03     1.02      10947.78|
|  5:  2.9712 -  2.7597  1308   146  0.90  16.29   1.01     0.98       8856.02|
|  6:  2.7597 -  2.5979  1291   148  0.89  16.75   0.99     0.96       7497.64|
|  7:  2.5979 -  2.4684  1288   144  0.90  16.31   1.00     0.96       6565.15|
|  8:  2.4684 -  2.3614  1281   140  0.90  15.85   1.01     0.98       5896.94|
|  9:  2.3614 -  2.2708  1276   145  0.90  16.15   1.01     0.98       5413.32|
| 10:  2.2708 -  2.1927  1277   139  0.90  16.29   1.00     0.96       4573.35|
| 11:  2.1927 -  2.1244  1271   140  0.89  16.86   1.01     0.98       4796.98|
| 12:  2.1244 -  2.0638  1258   140  0.90  16.71   1.02     1.01       4379.16|
| 13:  2.0638 -  2.0096  1280   142  0.90  16.37   1.01     0.99       3575.12|
| 14:  2.0096 -  1.9607   742    84  0.92  13.72   0.99     0.96       2440.98|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2440.98 max =        10947.78 mean =      6781.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        14.60|
|phase err.(test): min =        0.00 max =           89.03 mean =        14.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.474)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.11    96.40   15.73    None  None   None       |
|    all(noH): 2823   0      2.11    96.40   15.73    None  None   None       |
|    Sol.    : 438    0      3.49    89.47   40.81    None  None   None       |
|    Mac.    : 2385   0      2.11    96.40   11.13    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:     2.113 -  11.542: 1701   |   5:    49.255 -  58.683:   88        |
|      1:    11.542 -  20.970:  569   |   6:    58.683 -  68.112:   53        |
|      2:    20.970 -  30.398:  152   |   7:    68.112 -  77.540:   27        |
|      3:    30.398 -  39.827:  115   |   8:    77.540 -  86.968:   12        |
|      4:    39.827 -  49.255:  103   |   9:    86.968 -  96.397:    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)= 328         
Filter by distance & map next to the model:
   mapped sites are within: 0.447 - 4.522
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 328
   mapped sites are within: 0.714 - 4.522

peak=   10.464 closest distance to " CB  VAL A 230 " =    1.400
peak=   10.438 closest distance to " CB  VAL A 296 " =    1.554
peak=    7.861 closest distance to " O   HOH Z 130 " =    1.667
peak=    7.051 closest distance to " CG  ARG A 138 " =    1.120
peak=    6.465 closest distance to " CD2 LEU A   5 " =    1.239
peak=    6.030 closest distance to " CD1AILE A 234 " =    0.996
peak=    5.858 closest distance to " NE2 GLN A  11 " =    1.118
peak=    5.836 closest distance to " O   HOH Z 375 " =    1.202
peak=    5.745 closest distance to " O   HOH Z 236 " =    1.565
peak=    5.673 closest distance to " CG  PRO A  54 " =    1.391
peak=    5.587 closest distance to " CG  LEU A   5 " =    1.194
peak=    5.501 closest distance to " O   HOH Z   9 " =    1.656
peak=    5.435 closest distance to " O   HOH Z  65 " =    1.176
peak=    5.396 closest distance to " NH1 ARG A 138 " =    0.899
peak=    5.381 closest distance to " CB  ARG A 275 " =    1.060
peak=    5.373 closest distance to " O   HOH Z 142 " =    1.849
peak=    5.166 closest distance to " O   HOH Z 124 " =    1.440
peak=    5.165 closest distance to " CG  LEU A 228 " =    1.154
peak=    5.130 closest distance to " CB  VAL A 230 " =    1.151
peak=    5.129 closest distance to " O   HOH Z 423 " =    1.597
peak=    5.063 closest distance to " CB  PRO A  54 " =    1.018
peak=    5.059 closest distance to " O   HOH Z 232 " =    2.374
peak=    4.922 closest distance to " O   HOH Z 424 " =    1.238
peak=    4.921 closest distance to " O   HOH Z 427 " =    2.600
peak=    4.900 closest distance to " NH2 ARG A  56 " =    2.030
peak=    4.886 closest distance to " O   HOH Z 403 " =    1.815
peak=    4.813 closest distance to " O   HOH Z  78 " =    1.627
peak=    4.812 closest distance to " O   HOH Z 369 " =    2.350
peak=    4.760 closest distance to " O   HOH Z  85 " =    1.516
peak=    4.743 closest distance to " O   HOH Z 193 " =    1.592
peak=    4.678 closest distance to " O   HOH Z  69 " =    2.289
peak=    4.601 closest distance to " O   HOH Z 123 " =    1.188
peak=    4.569 closest distance to " CB  GLN A 183 " =    1.255
peak=    4.523 closest distance to " O   HOH Z 346 " =    1.627
peak=    4.517 closest distance to " O   HOH Z 380 " =    1.838
peak=    4.490 closest distance to " O   HOH Z 112 " =    1.240
peak=    4.482 closest distance to " O   HOH Z 126 " =    1.859
peak=    4.466 closest distance to " O   HOH Z 272 " =    1.873
peak=    4.454 closest distance to " O   HOH Z 417 " =    1.322
peak=    4.408 closest distance to " CB  GLN A 223 " =    1.531
peak=    4.405 closest distance to " CB BVAL A  41 " =    1.214
peak=    4.400 closest distance to " CG  PRO A 243 " =    1.134
peak=    4.395 closest distance to " CG  PRO A 198 " =    1.210
peak=    4.326 closest distance to " O   SER A  87 " =    2.364
peak=    4.289 closest distance to " O   HOH Z  39 " =    1.384
peak=    4.244 closest distance to " CB  SER A   3 " =    1.264
peak=    4.225 closest distance to " CG  PRO A 213 " =    1.303
peak=    4.223 closest distance to " O   HOH Z  68 " =    2.168
peak=    4.212 closest distance to " CB  ASN A 148 " =    1.333
peak=    4.188 closest distance to " O   HOH Z 366 " =    2.667
peak=    4.164 closest distance to " O   HOH Z 422 " =    2.443
peak=    4.160 closest distance to " O   HOH Z 425 " =    1.512
peak=    4.141 closest distance to " CB  VAL A 265 " =    1.309
peak=    4.132 closest distance to " OG ASER A 258 " =    3.007
peak=    4.122 closest distance to " CB  VAL A 202 " =    1.659
peak=    4.116 closest distance to " O   HOH Z 419 " =    2.058
peak=    4.103 closest distance to " O   HOH Z 406 " =    1.354
peak=    4.095 closest distance to " O   HOH Z 130 " =    1.863
peak=    4.086 closest distance to " O   HOH Z 143 " =    1.459
peak=    4.076 closest distance to " O   HOH Z  30 " =    1.849
peak=    4.064 closest distance to " CD  ARG A 269 " =    1.045
peak=    4.050 closest distance to " CB  SER A  26 " =    1.674
peak=    3.979 closest distance to " O   HOH Z 402 " =    1.386
peak=    3.977 closest distance to " CB  TRP A 266 " =    1.126
peak=    3.974 closest distance to " O   HOH Z 234 " =    3.632
peak=    3.964 closest distance to " CA  ASN A 127 " =    1.108
peak=    3.960 closest distance to " O   HOH Z   2 " =    1.876
peak=    3.942 closest distance to " O   HOH Z 368 " =    2.085
peak=    3.931 closest distance to " O   HOH Z 298 " =    1.608
peak=    3.926 closest distance to " CB  GLU A 277 " =    3.482
peak=    3.918 closest distance to " CG  LYS A  76 " =    1.553
peak=    3.898 closest distance to " O   HOH Z 362 " =    2.490
peak=    3.878 closest distance to " O   HOH Z  61 " =    1.644
peak=    3.869 closest distance to " CG2 VAL A 257 " =    0.862
peak=    3.855 closest distance to " O   HOH Z 425 " =    2.092
peak=    3.853 closest distance to " O   HOH Z  44 " =    1.858
peak=    3.850 closest distance to " CG  GLN A  11 " =    2.175
peak=    3.848 closest distance to " OE1 GLU A   2 " =    1.967
peak=    3.843 closest distance to " CA  TYR A  30 " =    0.985
peak=    3.838 closest distance to " NE1 TRP A 274 " =    0.952
peak=    3.818 closest distance to " O   HOH Z 359 " =    1.287
peak=    3.810 closest distance to " O   HOH Z  59 " =    1.570
peak=    3.801 closest distance to " CB  ARG A 138 " =    1.235
peak=    3.794 closest distance to " O   HOH Z 258 " =    2.084
peak=    3.789 closest distance to " NZ  LYS A 117 " =    2.997
peak=    3.783 closest distance to " O   PRO A 198 " =    1.379
peak=    3.780 closest distance to " CB  GLN A  88 " =    1.331
peak=    3.772 closest distance to " NH2AARG A 190 " =    1.877
peak=    3.768 closest distance to " O   HOH Z 193 " =    1.640
peak=    3.765 closest distance to " O   HOH Z  97 " =    2.236
peak=    3.763 closest distance to " O   HOH Z 344 " =    1.248
peak=    3.763 closest distance to " CB  THR A  31 " =    1.622
peak=    3.755 closest distance to " O   HOH Z 250 " =    1.454
peak=    3.750 closest distance to " ND2 ASN A 187 " =    1.651
peak=    3.747 closest distance to " CB  ARG A  79 " =    1.394
peak=    3.741 closest distance to " O   HOH Z 118 " =    1.750
peak=    3.738 closest distance to " CG AARG A 275 " =    1.062
peak=    3.728 closest distance to " OG BSER A 216 " =    0.878
peak=    3.728 closest distance to " CB  SER A  63 " =    1.225
peak=    3.723 closest distance to " O   HOH Z 411 " =    3.602
peak=    3.722 closest distance to " O   HOH Z 423 " =    1.757
peak=    3.712 closest distance to " O   HOH Z  40 " =    1.511
peak=    3.708 closest distance to " CG  LEU A 167 " =    1.256
peak=    3.708 closest distance to " CA  PHE A 283 " =    1.140
peak=    3.696 closest distance to " OG  SER A  97 " =    2.891
peak=    3.696 closest distance to " O   HOH Z 248 " =    1.167
peak=    3.691 closest distance to " O   HOH Z  55 " =    2.034
peak=    3.688 closest distance to " N   PHE A 130 " =    1.255
peak=    3.685 closest distance to " O   HOH Z 126 " =    1.496
peak=    3.684 closest distance to " CA  ASN A 215 " =    0.980
peak=    3.680 closest distance to " O   HOH Z  43 " =    1.849
peak=    3.677 closest distance to " O   HOH Z 272 " =    2.032
peak=    3.671 closest distance to " O   HOH Z 287 " =    1.654
peak=    3.669 closest distance to " O   HOH Z 371 " =    2.788
peak=    3.665 closest distance to " O   HOH Z 389 " =    1.320
peak=    3.660 closest distance to " O   HOH Z 261 " =    1.730
peak=    3.658 closest distance to " CB  ALA A 114 " =    1.484
peak=    3.646 closest distance to " O   HOH Z 203 " =    1.486
peak=    3.646 closest distance to " CB  ASN A 142 " =    1.081
peak=    3.646 closest distance to " O   HOH Z 337 " =    1.725
peak=    3.645 closest distance to " O   HOH Z 261 " =    1.998
peak=    3.639 closest distance to " CB  TYR A 169 " =    0.782
peak=    3.636 closest distance to " CB  ASN A  39 " =    0.965
peak=    3.636 closest distance to " O   HOH Z 128 " =    2.134
peak=    3.626 closest distance to " CB  HIS A 108 " =    0.902
peak=    3.626 closest distance to " O   HOH Z  78 " =    2.261
peak=    3.619 closest distance to " CE AMET A  47 " =    1.333
peak=    3.610 closest distance to " CB  TYR A  30 " =    1.699
peak=    3.606 closest distance to " CD  GLN A 194 " =    1.341
peak=    3.604 closest distance to " CB  ALA A 248 " =    1.373
peak=    3.603 closest distance to " O   HOH Z 158 " =    3.000
peak=    3.600 closest distance to " CG AARG A 275 " =    1.202
peak=    3.600 closest distance to " O   HOH Z 371 " =    1.721
peak=    3.599 closest distance to " O   HOH Z 222 " =    2.243
peak=    3.599 closest distance to " O   HOH Z  43 " =    0.986
peak=    3.598 closest distance to " CG  TRP A 179 " =    2.242
peak=    3.593 closest distance to " O   HOH Z 146 " =    1.607
peak=    3.587 closest distance to " O   HOH Z 352 " =    1.363
peak=    3.586 closest distance to " OG BSER A 210 " =    1.413
peak=    3.584 closest distance to " O   HOH Z   9 " =    1.794
peak=    3.580 closest distance to " O   HOH Z 290 " =    0.955
peak=    3.578 closest distance to " OH  TYR A 116 " =    1.067
peak=    3.578 closest distance to " CG  GLN A  88 " =    1.107
peak=    3.577 closest distance to " CB  ARG A 219 " =    0.977
peak=    3.574 closest distance to " O   HOH Z  69 " =    1.078
peak=    3.572 closest distance to " C   PRO A 198 " =    1.531
peak=    3.569 closest distance to " CB  SER A 273 " =    0.892
peak=    3.562 closest distance to " CB  TRP A 179 " =    1.231
peak=    3.557 closest distance to " CB  GLN A 278 " =    0.928
peak=    3.550 closest distance to " O   HOH Z  88 " =    2.862
peak=    3.542 closest distance to " CG BARG A 102 " =    1.879
peak=    3.542 closest distance to " O   HOH Z 145 " =    2.178
peak=    3.541 closest distance to " O   HOH Z 345 " =    3.190
peak=    3.540 closest distance to " CB  ASN A 110 " =    1.023
peak=    3.539 closest distance to " CG  MET A 113 " =    0.957
peak=    3.539 closest distance to " O   HOH Z  95 " =    1.070
peak=    3.536 closest distance to " CD2 LEU A 228 " =    1.218
peak=    3.529 closest distance to " NH2AARG A 145 " =    1.032
peak=    3.524 closest distance to " CD  ARG A 138 " =    0.996
peak=    3.521 closest distance to " OG BSER A 164 " =    2.129
peak=    3.517 closest distance to " O   HOH Z 357 " =    1.889
peak=    3.512 closest distance to " O  BHOH Z 338 " =    2.424
peak=    3.506 closest distance to " O   HOH Z 181 " =    2.204
peak=    3.506 closest distance to " CB  VAL A 268 " =    0.878
peak=    3.500 closest distance to " CG2 ILE A 234 " =    0.770
peak=    3.497 closest distance to " O   HOH Z 435 " =    1.999
peak=    3.495 closest distance to " O   HOH Z 337 " =    3.558
peak=    3.490 closest distance to " CG  GLN A  58 " =    0.932
peak=    3.487 closest distance to " O   HOH Z 437 " =    1.976
peak=    3.480 closest distance to " CG2 ILE A  20 " =    1.711
peak=    3.473 closest distance to " CA  LYS A 117 " =    1.143
peak=    3.469 closest distance to " OE2 GLU A   2 " =    1.816
peak=    3.466 closest distance to " O   HOH Z 128 " =    2.102
peak=    3.458 closest distance to " ND2 ASN A 249 " =    0.910
peak=    3.454 closest distance to " CB  ARG A 139 " =    1.020
peak=    3.447 closest distance to " NZ  LYS A  48 " =    1.125
peak=    3.438 closest distance to " O   HOH Z 405 " =    1.279
peak=    3.437 closest distance to " CA  ALA A  51 " =    1.003
peak=    3.436 closest distance to " CG1 ILE A  33 " =    1.333
peak=    3.431 closest distance to " O   HOH Z  10 " =    1.705
peak=    3.430 closest distance to " NH1 ARG A  14 " =    1.210
peak=    3.426 closest distance to " CZ  PHE A 218 " =    1.177
peak=    3.421 closest distance to " CG  MET A 185 " =    1.268
peak=    3.416 closest distance to " O   HOH Z 117 " =    1.860
peak=    3.410 closest distance to " CA  LEU A 101 " =    1.351
peak=    3.406 closest distance to " O   HOH Z 427 " =    1.367
peak=    3.406 closest distance to " CB  ASN A 215 " =    1.060
peak=    3.401 closest distance to " CB  GLU A 128 " =    1.120
peak=    3.396 closest distance to " O   GLN A 194 " =    1.615
peak=    3.395 closest distance to " CB  PHE A 204 " =    0.994
peak=    3.392 closest distance to " NE  ARG A  56 " =    3.414
peak=    3.392 closest distance to " O   THR A 182 " =    1.519
peak=    3.391 closest distance to " CB  LYS A 117 " =    1.208
peak=    3.389 closest distance to " N   SER A 271 " =    0.970
peak=    3.389 closest distance to " CZ  PHE A  38 " =    1.248
peak=    3.389 closest distance to " O   HOH Z 152 " =    1.836
peak=    3.380 closest distance to " O   HOH Z 305 " =    3.295
peak=    3.378 closest distance to " CA  ARG A 195 " =    1.146
peak=    3.372 closest distance to " O   HOH Z 233 " =    1.972
peak=    3.370 closest distance to " O   HOH Z 213 " =    1.381
peak=    3.368 closest distance to " O   HOH Z  43 " =    1.097
peak=    3.366 closest distance to " O   HOH Z 194 " =    2.099
peak=    3.366 closest distance to " O   HOH Z  58 " =    1.617
peak=    3.366 closest distance to " CD2 TRP A 179 " =    1.374
peak=    3.366 closest distance to " CB  THR A  52 " =    1.012
peak=    3.365 closest distance to " O   HOH Z 106 " =    2.811
peak=    3.362 closest distance to " CA  ALA A 129 " =    1.485
peak=    3.360 closest distance to " CE1 TYR A 186 " =    1.285
peak=    3.359 closest distance to " CD1 ILE A  33 " =    1.803
peak=    3.355 closest distance to " CB  ALA A   9 " =    1.492
peak=    3.353 closest distance to " CB  ASN A 187 " =    1.195
peak=    3.351 closest distance to " O   HOH Z  88 " =    3.285
peak=    3.350 closest distance to " CE  LYS A 119 " =    1.247
peak=    3.349 closest distance to " N   ASP A 162 " =    1.110
peak=    3.346 closest distance to " O   HOH Z  51 " =    1.187
peak=    3.343 closest distance to " O   HOH Z 153 " =    3.702
peak=    3.340 closest distance to " O   HOH Z 344 " =    2.724
peak=    3.336 closest distance to " C   LYS A 290 " =    1.227
peak=    3.336 closest distance to " O   HOH Z 180 " =    2.138
peak=    3.333 closest distance to " CB  LEU A 300 " =    0.898
peak=    3.332 closest distance to " CB  GLU A 152 " =    1.277
peak=    3.330 closest distance to " O   HOH Z  47 " =    1.484
peak=    3.330 closest distance to " N   GLN A 278 " =    1.384
peak=    3.328 closest distance to " OG  SER A  62 " =    2.562
peak=    3.325 closest distance to " O   HOH Z   4 " =    1.339
peak=    3.325 closest distance to " O   HOH Z  26 " =    1.309
peak=    3.324 closest distance to " O   HOH Z 368 " =    3.504
peak=    3.321 closest distance to " CB  ARG A 190 " =    1.717
peak=    3.318 closest distance to " CA  MET A 105 " =    0.974
peak=    3.316 closest distance to " O   HOH Z 291 " =    1.452
peak=    3.313 closest distance to " O   HOH Z 327 " =    1.824
peak=    3.311 closest distance to " CB  SER A 276 " =    1.205
peak=    3.308 closest distance to " O   HOH Z 303 " =    1.658
peak=    3.294 closest distance to " O   HOH Z 119 " =    1.535
peak=    3.292 closest distance to " CG  LEU A 281 " =    1.021
peak=    3.292 closest distance to " O   HOH Z  61 " =    1.495
peak=    3.290 closest distance to " OG  SER A  62 " =    2.882
peak=    3.284 closest distance to " O   HOH Z 407 " =    1.187
peak=    3.280 closest distance to " CG2 ILE A 120 " =    1.301
peak=    3.280 closest distance to " O   HOH Z 214 " =    2.484
peak=    3.277 closest distance to " O   HOH Z  40 " =    1.276
peak=    3.276 closest distance to " CB  ARG A  79 " =    0.873
peak=    3.276 closest distance to " O   HOH Z  80 " =    1.568
peak=    3.275 closest distance to " O   HOH Z 116 " =    2.764
peak=    3.270 closest distance to " O   ASP A 191 " =    1.694
peak=    3.269 closest distance to " OD1 ASN A  69 " =    2.486
peak=    3.268 closest distance to " CA  LEU A 282 " =    1.204
peak=    3.268 closest distance to " CA  VAL A 125 " =    1.086
peak=    3.258 closest distance to " O   HOH Z 172 " =    3.124
peak=    3.258 closest distance to " O   HOH Z 148 " =    2.375
peak=    3.256 closest distance to " CA  ASN A 217 " =    1.179
peak=    3.253 closest distance to " NH1BARG A 145 " =    1.573
peak=    3.250 closest distance to " CA  ARG A  36 " =    0.967
peak=    3.249 closest distance to " O  BHOH Z  74 " =    1.160
peak=    3.247 closest distance to " O   ASP A 124 " =    1.088
peak=    3.245 closest distance to " CA  ILE A 234 " =    1.057
peak=    3.244 closest distance to " O   HOH Z 365 " =    1.837
peak=    3.244 closest distance to " CG2 THR A 221 " =    1.223
peak=    3.242 closest distance to " O   HOH Z  59 " =    2.061
peak=    3.242 closest distance to " CG1BVAL A  72 " =    1.449
peak=    3.232 closest distance to " NH2BARG A 145 " =    2.295
peak=    3.232 closest distance to " N   ALA A 256 " =    0.974
peak=    3.232 closest distance to " O   HOH Z 347 " =    0.890
peak=    3.227 closest distance to " O   HOH Z 109 " =    2.388
peak=    3.221 closest distance to " O   HOH Z 193 " =    1.717
peak=    3.212 closest distance to " CB  LEU A 255 " =    0.736
peak=    3.210 closest distance to " CD2 TYR A 186 " =    1.039
peak=    3.209 closest distance to " O   HOH Z 392 " =    3.012
peak=    3.205 closest distance to " OG BSER A 164 " =    2.571
peak=    3.199 closest distance to " O   HOH Z   1 " =    4.522
peak=    3.194 closest distance to " CA  ARG A 139 " =    0.855
peak=    3.191 closest distance to " O   HOH Z 162 " =    1.506
peak=    3.191 closest distance to " NZ  LYS A 119 " =    2.645
peak=    3.189 closest distance to " O   HOH Z 392 " =    1.139
peak=    3.188 closest distance to " CG1 VAL A 126 " =    1.201
peak=    3.188 closest distance to " O   HOH Z   1 " =    1.592
peak=    3.186 closest distance to " CA  ASP A 124 " =    0.714
peak=    3.186 closest distance to " O   HOH Z  48 " =    1.508
peak=    3.185 closest distance to " O   HOH Z 322 " =    1.895
peak=    3.181 closest distance to " C   PHE A  59 " =    0.875
peak=    3.177 closest distance to " O   HOH Z 438 " =    2.338
peak=    3.175 closest distance to " CB  ALA A 291 " =    1.267
peak=    3.173 closest distance to " OG BSER A 134 " =    2.915
peak=    3.171 closest distance to " CB  SER A  62 " =    1.230
peak=    3.170 closest distance to " CA  SER A  87 " =    0.999
peak=    3.169 closest distance to " O   HOH Z 128 " =    1.855
peak=    3.167 closest distance to " O   HOH Z 366 " =    2.191
peak=    3.164 closest distance to " CA  ALA A 160 " =    0.848
peak=    3.164 closest distance to " CB  PRO A  90 " =    1.192
peak=    3.161 closest distance to " N   GLU A   2 " =    1.417
peak=    3.157 closest distance to " O   HOH Z 392 " =    1.775
peak=    3.156 closest distance to " O   HOH Z 125 " =    1.345
peak=    3.153 closest distance to " N   SER A 135 " =    1.323
peak=    3.151 closest distance to " O   HOH Z 273 " =    3.025
peak=    3.147 closest distance to " O   HOH Z 105 " =    1.667
peak=    3.138 closest distance to " O   HOH Z   6 " =    1.467
peak=    3.137 closest distance to " O   HOH Z  85 " =    1.723
peak=    3.136 closest distance to " CG  LYS A 289 " =    1.298
peak=    3.135 closest distance to " O   HOH Z  83 " =    1.272
peak=    3.135 closest distance to " O   HOH Z 244 " =    1.671
peak=    3.127 closest distance to " O   HOH Z 323 " =    1.472
peak=    3.124 closest distance to " CG1 ILE A 120 " =    1.189
peak=    3.117 closest distance to " CE3 TRP A 274 " =    1.259
peak=    3.112 closest distance to " NE2 GLN A  73 " =    1.388
peak=    3.106 closest distance to " CH2 TRP A 266 " =    1.068
peak=    3.102 closest distance to " O   HOH Z 189 " =    3.836
peak=    3.099 closest distance to " O   HOH Z 356 " =    1.272
peak=    3.097 closest distance to " O   ASN A  74 " =    1.493
peak=    3.096 closest distance to " OE2 GLU A  53 " =    1.956
peak=    3.094 closest distance to " CG1 VAL A 153 " =    0.893
peak=    3.094 closest distance to " OG ASER A 212 " =    1.731
peak=    3.093 closest distance to " NH2BARG A 190 " =    1.535
peak=    3.091 closest distance to " O   HOH Z 329 " =    3.960
peak=    3.090 closest distance to " O   HOH Z  71 " =    1.185
peak=    3.087 closest distance to " CE ALYS A 290 " =    1.080
peak=    3.081 closest distance to " O   HOH Z 435 " =    1.782
peak=    3.078 closest distance to " CE  MET A  40 " =    1.051
peak=    3.076 closest distance to " O   HOH Z  73 " =    3.709
peak=    3.066 closest distance to " O   HOH Z 334 " =    1.387
peak=    3.048 closest distance to " O   HOH Z 145 " =    1.552
peak=    3.034 closest distance to " CG1 ILE A 120 " =    1.349
peak=    3.028 closest distance to " O   HOH Z 154 " =    2.254
peak=    3.016 closest distance to " CG1 ILE A 151 " =    1.113

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.792 - 5.889
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 197
   mapped sites are within: 0.792 - 5.889

peak=   -4.593 closest distance to " CD  ARG A 156 " =    1.971
peak=   -4.584 closest distance to " OG BSER A 134 " =    1.187
peak=   -4.229 closest distance to " CD  ARG A 138 " =    1.227
peak=   -4.201 closest distance to " O   PRO A 198 " =    1.159
peak=   -4.183 closest distance to " CB  ALA A  43 " =    2.404
peak=   -4.084 closest distance to " C   HIS A 108 " =    1.206
peak=   -4.067 closest distance to " CD1 LEU A 255 " =    2.764
peak=   -4.041 closest distance to " O   HOH Z 429 " =    1.948
peak=   -4.032 closest distance to " SG  CYS A 254 " =    3.369
peak=   -4.026 closest distance to " OD2 ASP A 191 " =    1.267
peak=   -3.978 closest distance to " CG  GLN A  58 " =    0.972
peak=   -3.960 closest distance to " CG2 VAL A 230 " =    0.809
peak=   -3.934 closest distance to " CG2 ILE A  20 " =    2.838
peak=   -3.924 closest distance to " CG  ARG A 138 " =    0.921
peak=   -3.921 closest distance to " CG  GLN A 223 " =    1.995
peak=   -3.920 closest distance to " O   HOH Z  11 " =    1.835
peak=   -3.919 closest distance to " O   HOH Z 266 " =    5.100
peak=   -3.918 closest distance to " O   VAL A  67 " =    2.445
peak=   -3.888 closest distance to " O   HOH Z 185 " =    1.938
peak=   -3.878 closest distance to " O   HOH Z  69 " =    1.937
peak=   -3.851 closest distance to " O   ALA A 292 " =    2.122
peak=   -3.842 closest distance to " CG  PHE A 283 " =    2.558
peak=   -3.819 closest distance to " O   SER A  22 " =    2.364
peak=   -3.757 closest distance to " O   HOH Z 131 " =    4.069
peak=   -3.724 closest distance to " OD1 ASN A  39 " =    2.123
peak=   -3.721 closest distance to " CB  PHE A 192 " =    1.889
peak=   -3.710 closest distance to " O   HOH Z 211 " =    1.494
peak=   -3.704 closest distance to " O   HOH Z 423 " =    2.548
peak=   -3.680 closest distance to " O   SER A 135 " =    1.357
peak=   -3.664 closest distance to " CD  LYS A 289 " =    2.421
peak=   -3.663 closest distance to " O   HOH Z 406 " =    0.967
peak=   -3.642 closest distance to " ND2 ASN A 187 " =    1.543
peak=   -3.631 closest distance to " OXT GLY A 302 " =    3.007
peak=   -3.629 closest distance to " OG  SER A   3 " =    1.450
peak=   -3.626 closest distance to " CD  GLN A  88 " =    1.040
peak=   -3.624 closest distance to " O   HOH Z 387 " =    2.380
peak=   -3.619 closest distance to " CD  GLN A 278 " =    1.934
peak=   -3.619 closest distance to " O   HOH Z  15 " =    1.419
peak=   -3.618 closest distance to " CB  VAL A 230 " =    0.916
peak=   -3.617 closest distance to " NH2 ARG A  79 " =    1.994
peak=   -3.615 closest distance to " CB  ALA A 244 " =    2.187
peak=   -3.615 closest distance to " O   HOH Z 359 " =    1.718
peak=   -3.603 closest distance to " CE BMET A  47 " =    1.068
peak=   -3.590 closest distance to " O   PRO A 163 " =    1.948
peak=   -3.585 closest distance to " O   HOH Z 427 " =    1.719
peak=   -3.579 closest distance to " O   HOH Z 100 " =    1.061
peak=   -3.577 closest distance to " O   ALA A 180 " =    1.132
peak=   -3.564 closest distance to " O   HOH Z 130 " =    1.923
peak=   -3.561 closest distance to " N   ALA A 248 " =    1.594
peak=   -3.555 closest distance to " ND2 ASN A 252 " =    1.937
peak=   -3.548 closest distance to " O   HOH Z 313 " =    1.575
peak=   -3.545 closest distance to " N   ASP A 286 " =    2.134
peak=   -3.543 closest distance to " CZ2 TRP A 274 " =    0.899
peak=   -3.541 closest distance to " O   GLN A 240 " =    2.000
peak=   -3.521 closest distance to " O   SER A 271 " =    2.111
peak=   -3.512 closest distance to " CB  ALA A 114 " =    2.383
peak=   -3.511 closest distance to " CG2 VAL A 202 " =    2.603
peak=   -3.510 closest distance to " O   SER A  95 " =    1.509
peak=   -3.509 closest distance to " CE2 TYR A  30 " =    2.813
peak=   -3.507 closest distance to " CB  ASN A  39 " =    2.251
peak=   -3.501 closest distance to " O   HOH Z 238 " =    1.029
peak=   -3.493 closest distance to " CE  MET A 105 " =    2.421
peak=   -3.491 closest distance to " C   LEU A 222 " =    1.321
peak=   -3.485 closest distance to " CD2 TYR A 293 " =    1.952
peak=   -3.483 closest distance to " O   HOH Z 351 " =    1.517
peak=   -3.480 closest distance to " CB  GLN A  55 " =    1.148
peak=   -3.479 closest distance to " CA  GLY A 133 " =    1.913
peak=   -3.477 closest distance to " O   HOH Z 231 " =    2.068
peak=   -3.477 closest distance to " O   ARG A 219 " =    1.752
peak=   -3.473 closest distance to " N   ALA A 226 " =    1.888
peak=   -3.462 closest distance to " O   HOH Z 430 " =    1.943
peak=   -3.456 closest distance to " CG  TRP A 266 " =    1.914
peak=   -3.440 closest distance to " O   HOH Z 372 " =    2.135
peak=   -3.440 closest distance to " O   HOH Z 165 " =    2.052
peak=   -3.437 closest distance to " O   HOH Z 407 " =    2.452
peak=   -3.435 closest distance to " N   GLN A  58 " =    1.239
peak=   -3.430 closest distance to " O   HOH Z 286 " =    1.605
peak=   -3.430 closest distance to " CD2 LEU A   5 " =    1.109
peak=   -3.429 closest distance to " O   HOH Z  97 " =    1.286
peak=   -3.425 closest distance to " O   HOH Z 102 " =    1.628
peak=   -3.423 closest distance to " CB  SER A 210 " =    1.134
peak=   -3.415 closest distance to " CB  ASP A  27 " =    2.275
peak=   -3.414 closest distance to " O   HOH Z 377 " =    1.181
peak=   -3.413 closest distance to " O   HOH Z 193 " =    1.513
peak=   -3.410 closest distance to " C   MET A 188 " =    1.515
peak=   -3.410 closest distance to " O   HOH Z 412 " =    5.889
peak=   -3.409 closest distance to " C   GLN A 205 " =    1.781
peak=   -3.409 closest distance to " OG  SER A  87 " =    1.298
peak=   -3.403 closest distance to " O   ALA A   8 " =    1.829
peak=   -3.396 closest distance to " O   TRP A 179 " =    1.491
peak=   -3.395 closest distance to " O   ILE A  49 " =    1.678
peak=   -3.394 closest distance to " N   PRO A 163 " =    1.695
peak=   -3.388 closest distance to " O   HOH Z 166 " =    1.726
peak=   -3.388 closest distance to " O   HOH Z 137 " =    1.662
peak=   -3.385 closest distance to " CA  ASN A 127 " =    1.376
peak=   -3.384 closest distance to " CG  PRO A 243 " =    1.480
peak=   -3.384 closest distance to " O   HOH Z 111 " =    4.506
peak=   -3.374 closest distance to " O   HOH Z   9 " =    1.522
peak=   -3.368 closest distance to " CA  GLY A  23 " =    1.787
peak=   -3.364 closest distance to " CB  ALA A   7 " =    2.024
peak=   -3.364 closest distance to " O   HOH Z 191 " =    5.539
peak=   -3.361 closest distance to " N   THR A 157 " =    1.400
peak=   -3.351 closest distance to " O   HOH Z 388 " =    2.229
peak=   -3.350 closest distance to " N   PHE A  59 " =    2.281
peak=   -3.345 closest distance to " ND2 ASN A 173 " =    1.487
peak=   -3.343 closest distance to " N   VAL A  72 " =    1.735
peak=   -3.337 closest distance to " OE2 GLU A 152 " =    1.277
peak=   -3.337 closest distance to " O   HOH Z 281 " =    2.784
peak=   -3.333 closest distance to " CG1 VAL A 112 " =    2.983
peak=   -3.331 closest distance to " O   HOH Z 389 " =    1.507
peak=   -3.329 closest distance to " O   HOH Z 193 " =    2.062
peak=   -3.329 closest distance to " CZ  PHE A  59 " =    1.377
peak=   -3.326 closest distance to " O   HOH Z 359 " =    3.291
peak=   -3.325 closest distance to " O   PRO A 243 " =    2.528
peak=   -3.323 closest distance to " O   PRO A 198 " =    1.268
peak=   -3.321 closest distance to " O   HOH Z 235 " =    1.152
peak=   -3.319 closest distance to " O   HOH Z 216 " =    1.445
peak=   -3.319 closest distance to " CD1 LEU A 101 " =    2.132
peak=   -3.318 closest distance to " CB  CYS A 201 " =    2.587
peak=   -3.315 closest distance to " OG  SER A  63 " =    1.163
peak=   -3.314 closest distance to " N   HIS A 115 " =    2.125
peak=   -3.313 closest distance to " O   HOH Z 290 " =    1.100
peak=   -3.312 closest distance to " O   HOH Z 392 " =    0.859
peak=   -3.308 closest distance to " CG1 VAL A 230 " =    1.895
peak=   -3.306 closest distance to " O   HOH Z  16 " =    2.339
peak=   -3.304 closest distance to " N   ALA A   1 " =    1.519
peak=   -3.294 closest distance to " OG  SER A  97 " =    2.185
peak=   -3.292 closest distance to " OG  SER A 206 " =    1.506
peak=   -3.292 closest distance to " N   ALA A 244 " =    1.404
peak=   -3.283 closest distance to " CA  GLY A  35 " =    2.004
peak=   -3.281 closest distance to " CB  PRO A 163 " =    2.383
peak=   -3.280 closest distance to " O   ALA A 227 " =    1.399
peak=   -3.279 closest distance to " O   HOH Z 134 " =    3.318
peak=   -3.275 closest distance to " CA  GLY A 203 " =    2.344
peak=   -3.272 closest distance to " OD2 ASP A 171 " =    2.166
peak=   -3.269 closest distance to " O   HOH Z 114 " =    3.151
peak=   -3.268 closest distance to " O   HOH Z 139 " =    3.145
peak=   -3.262 closest distance to " O   HOH Z 389 " =    2.128
peak=   -3.249 closest distance to " OE1 GLN A  88 " =    1.140
peak=   -3.249 closest distance to " O   MET A  40 " =    2.748
peak=   -3.236 closest distance to " CZ  TYR A 169 " =    1.791
peak=   -3.236 closest distance to " O   PHE A 218 " =    1.478
peak=   -3.234 closest distance to " O   HOH Z 256 " =    1.408
peak=   -3.231 closest distance to " OD1 ASN A 301 " =    1.967
peak=   -3.229 closest distance to " CA  GLY A 241 " =    2.216
peak=   -3.228 closest distance to " O   SER A 210 " =    1.804
peak=   -3.224 closest distance to " CB  ALA A 131 " =    1.967
peak=   -3.222 closest distance to " NE2 GLN A  94 " =    1.715
peak=   -3.221 closest distance to " N   MET A 188 " =    1.927
peak=   -3.212 closest distance to " CZ  PHE A 130 " =    0.873
peak=   -3.212 closest distance to " O   HOH Z 414 " =    2.327
peak=   -3.210 closest distance to " O   HOH Z 426 " =    1.731
peak=   -3.205 closest distance to " CB  ASP A 132 " =    2.383
peak=   -3.200 closest distance to " O   ALA A 161 " =    1.702
peak=   -3.191 closest distance to " O   HOH Z 346 " =    1.719
peak=   -3.190 closest distance to " O   ALA A  10 " =    1.765
peak=   -3.189 closest distance to " CE  LYS A  76 " =    2.794
peak=   -3.188 closest distance to " O   HOH Z 377 " =    2.146
peak=   -3.186 closest distance to " O   GLU A 152 " =    1.523
peak=   -3.183 closest distance to " O   HOH Z 298 " =    3.774
peak=   -3.180 closest distance to " O   HOH Z 198 " =    1.669
peak=   -3.177 closest distance to " ND2 ASN A 285 " =    2.023
peak=   -3.176 closest distance to " O   HOH Z 134 " =    3.954
peak=   -3.168 closest distance to " CB  ALA A 291 " =    2.159
peak=   -3.163 closest distance to " CB  PRO A  90 " =    1.568
peak=   -3.162 closest distance to " O   GLY A  80 " =    2.362
peak=   -3.160 closest distance to " OE1 GLU A 277 " =    2.153
peak=   -3.157 closest distance to " OG  SER A  62 " =    4.170
peak=   -3.156 closest distance to " O   VAL A 125 " =    2.079
peak=   -3.154 closest distance to " O   ALA A  51 " =    1.122
peak=   -3.153 closest distance to " O   ARG A  24 " =    1.913
peak=   -3.149 closest distance to " CD2 HIS A 207 " =    2.244
peak=   -3.145 closest distance to " O   HOH Z 364 " =    2.535
peak=   -3.144 closest distance to " O   HOH Z 352 " =    1.616
peak=   -3.143 closest distance to " O   LEU A 297 " =    0.792
peak=   -3.143 closest distance to " O   SER A 273 " =    1.498
peak=   -3.138 closest distance to " O   ASN A 187 " =    1.418
peak=   -3.125 closest distance to " CG  GLU A 152 " =    1.516
peak=   -3.123 closest distance to " O   ARG A 145 " =    1.562
peak=   -3.122 closest distance to " CE3 TRP A 179 " =    1.317
peak=   -3.121 closest distance to " O   HOH Z 345 " =    1.996
peak=   -3.120 closest distance to " O   HOH Z 350 " =    1.861
peak=   -3.116 closest distance to " C   LEU A 222 " =    0.851
peak=   -3.108 closest distance to " CB  ALA A  51 " =    1.857
peak=   -3.103 closest distance to " O   HOH Z 414 " =    1.924
peak=   -3.099 closest distance to " CG2 THR A 178 " =    2.121
peak=   -3.097 closest distance to " NE2 GLN A 278 " =    1.619
peak=   -3.096 closest distance to " CD1 ILE A 199 " =    2.440
peak=   -3.083 closest distance to " O   HOH Z 288 " =    1.300
peak=   -3.082 closest distance to " O   HOH Z 208 " =    1.942
peak=   -3.082 closest distance to " OE1 GLN A 183 " =    1.551
peak=   -3.072 closest distance to " CZ3 TRP A 123 " =    1.792
peak=   -3.069 closest distance to " CB  ALA A  64 " =    2.663
peak=   -3.065 closest distance to " CG  LEU A 228 " =    1.042
peak=   -3.053 closest distance to " O   TRP A  70 " =    1.390
peak=   -3.044 closest distance to " OD1 ASP A 200 " =    1.447
peak=   -3.027 closest distance to " O   HOH Z 414 " =    1.949

================= 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    :  0.4824 0.4789   6.282536e+00   6.272979e+00
   1_bss:  0.4745 0.4647   6.274231e+00   6.261201e+00
   1_xyz:  0.3959 0.4144   6.170975e+00   6.199444e+00
   1_adp:  0.3512 0.4080   6.099674e+00   6.181578e+00
   1_occ:  0.3508 0.4074   6.098981e+00   6.182087e+00
   2_bss:  0.3462 0.4021   6.097542e+00   6.179758e+00
   2_xyz:  0.2618 0.3215   5.872241e+00   6.017130e+00
   2_adp:  0.2342 0.2957   5.783446e+00   5.948485e+00
   2_occ:  0.2340 0.2954   5.782907e+00   5.947896e+00
   3_bss:  0.2323 0.2937   5.779794e+00   5.943423e+00
   3_xyz:  0.1676 0.2162   5.477786e+00   5.674884e+00
   3_adp:  0.1516 0.2013   5.394669e+00   5.605282e+00
   3_occ:  0.1513 0.2007   5.392983e+00   5.603277e+00
   4_bss:  0.1506 0.2003   5.390098e+00   5.600707e+00
   4_xyz:  0.1305 0.1758   5.262698e+00   5.480076e+00
   4_adp:  0.1264 0.1712   5.233977e+00   5.453036e+00
   4_occ:  0.1263 0.1711   5.233071e+00   5.451894e+00
   5_bss:  0.1263 0.1710   5.232413e+00   5.451246e+00
   5_xyz:  0.1200 0.1628   5.189611e+00   5.414415e+00
   5_adp:  0.1180 0.1633   5.182808e+00   5.415697e+00
   5_occ:  0.1179 0.1633   5.182466e+00   5.415286e+00
   5_bss:  0.1180 0.1638   5.182992e+00   5.415968e+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:  0.360   2.470   8.149   9.854   8.542   0.000   0.000   0.000
   1_xyz:  0.360   2.470   8.149   9.854   8.542   0.000   0.000   0.000
   1_adp:  0.360   2.470   8.149   9.854   8.542   0.000   0.000   0.000
   1_occ:  0.360   2.470   8.149   9.854   8.542   0.000   0.000   0.000
   2_bss:  0.345  24.444   4.382   5.161   4.852   0.000   0.000   0.000
   2_xyz:  0.345  24.444   4.382   5.161   4.852   0.000   0.000   0.000
   2_adp:  0.345  24.444   4.382   5.161   4.852   0.000   0.000   0.000
   2_occ:  0.345  24.444   4.382   5.161   4.852   0.000   0.000   0.000
   3_bss:  0.341  41.494   2.343   3.189   3.690   0.000   0.000   0.000
   3_xyz:  0.341  41.494   2.343   3.189   3.690   0.000   0.000   0.000
   3_adp:  0.341  41.494   2.343   3.189   3.690   0.000   0.000   0.000
   3_occ:  0.341  41.494   2.343   3.189   3.690   0.000   0.000   0.000
   4_bss:  0.325  36.496   1.326   1.965   3.173   0.000   0.000   0.000
   4_xyz:  0.325  36.496   1.326   1.965   3.173   0.000   0.000   0.000
   4_adp:  0.325  36.496   1.326   1.965   3.173   0.000   0.000   0.000
   4_occ:  0.325  36.496   1.326   1.965   3.173   0.000   0.000   0.000
   5_bss:  0.318  36.496   1.201   1.730   3.202   0.000   0.000   0.000
   5_xyz:  0.318  36.496   1.201   1.730   3.202   0.000   0.000   0.000
   5_adp:  0.318  36.496   1.201   1.730   3.202   0.000   0.000   0.000
   5_occ:  0.318  36.496   1.201   1.730   3.202   0.000   0.000   0.000
   5_bss:  0.318  43.425  -0.829  -0.347   1.176   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.481 0.4004  0.4722    72422.133
   1_bss:  59.295 0.4009  0.6098    69220.468
   1_xyz:  48.695 0.5354  0.7996    51450.953
   1_adp:  45.812 0.5717  0.8984    48059.125
   1_occ:  45.869 0.5709  0.8958    48056.557
   2_bss:  45.377 0.5769  0.7877    47356.401
   2_xyz:  34.091 0.7112  0.9530    28323.756
   2_adp:  30.185 0.7561  0.9888    23254.209
   2_occ:  30.156 0.7564  0.9888    23215.095
   3_bss:  29.882 0.7593  0.9322    22873.442
   3_xyz:  20.723 0.8544  1.0059    11846.169
   3_adp:  18.838 0.8730  1.0135    10274.328
   3_occ:  18.792 0.8734  1.0136    10217.942
   4_bss:  18.705 0.8741  0.9798    10109.135
   4_xyz:  15.960 0.8988  0.9908     7762.438
   4_adp:  15.352 0.9041  0.9897     7391.704
   4_occ:  15.330 0.9043  0.9898     7369.229
   5_bss:  15.317 0.9044  0.9858     7354.506
   5_xyz:  14.525 0.9109  0.9889     6753.769
   5_adp:  14.529 0.9109  0.9846     6748.082
   5_occ:  14.526 0.9109  0.9845     6741.421
   5_bss:  14.551 0.9108  0.9865     6780.717
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3019e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3019e+01
   1_xyz:   1.702  0.013  0.106 18.103  0.006  4.105   1.4209e-01
   1_adp:   1.702  0.013  0.106 18.103  0.006  4.105   1.4209e-01
   1_occ:   1.702  0.013  0.106 18.103  0.006  4.105   1.4209e-01
   2_bss:   1.702  0.013  0.106 18.103  0.006  4.105   1.4209e-01
   2_xyz:   1.137  0.008  0.082 15.954  0.005  4.119   8.0859e-02
   2_adp:   1.137  0.008  0.082 15.954  0.005  4.119   8.0859e-02
   2_occ:   1.137  0.008  0.082 15.954  0.005  4.119   8.0859e-02
   3_bss:   1.137  0.008  0.082 15.954  0.005  4.119   8.0859e-02
   3_xyz:   1.035  0.007  0.073 15.723  0.004  4.110   6.6622e-02
   3_adp:   1.035  0.007  0.073 15.723  0.004  4.110   6.6622e-02
   3_occ:   1.035  0.007  0.073 15.723  0.004  4.110   6.6622e-02
   4_bss:   1.035  0.007  0.073 15.723  0.004  4.110   6.6622e-02
   4_xyz:   0.928  0.005  0.068 15.535  0.003  4.114   5.5093e-02
   4_adp:   0.928  0.005  0.068 15.535  0.003  4.114   5.5093e-02
   4_occ:   0.928  0.005  0.068 15.535  0.003  4.114   5.5093e-02
   5_bss:   0.928  0.005  0.068 15.535  0.003  4.114   5.5093e-02
   5_xyz:   0.922  0.005  0.068 15.510  0.003  4.108   5.3795e-02
   5_adp:   0.922  0.005  0.068 15.510  0.003  4.108   5.3795e-02
   5_occ:   0.922  0.005  0.068 15.510  0.003  4.108   5.3795e-02
   5_bss:   0.922  0.005  0.068 15.510  0.003  4.108   5.3795e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8673e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8673e+00
   1_xyz:  14.656  0.160  0.460 87.583  0.032  2.191   9.7573e-02
   1_adp:  14.656  0.160  0.460 87.583  0.032  2.191   9.7573e-02
   1_occ:  14.656  0.160  0.460 87.583  0.032  2.191   9.7573e-02
   2_bss:  14.656  0.160  0.460 87.583  0.032  2.191   9.7573e-02
   2_xyz:   7.304  0.084  0.304 84.141  0.036  2.148   8.0355e-02
   2_adp:   7.304  0.084  0.304 84.141  0.036  2.148   8.0355e-02
   2_occ:   7.304  0.084  0.304 84.141  0.036  2.148   8.0355e-02
   3_bss:   7.304  0.084  0.304 84.141  0.036  2.148   8.0355e-02
   3_xyz:   7.420  0.044  0.272 87.347  0.031  2.301   7.8364e-02
   3_adp:   7.420  0.044  0.272 87.347  0.031  2.301   7.8364e-02
   3_occ:   7.420  0.044  0.272 87.347  0.031  2.301   7.8364e-02
   4_bss:   7.420  0.044  0.272 87.347  0.031  2.301   7.8364e-02
   4_xyz:   7.030  0.042  0.222 84.229  0.030  2.373   4.3391e-02
   4_adp:   7.030  0.042  0.222 84.229  0.030  2.373   4.3391e-02
   4_occ:   7.030  0.042  0.222 84.229  0.030  2.373   4.3391e-02
   5_bss:   7.030  0.042  0.222 84.229  0.030  2.373   4.3391e-02
   5_xyz:   7.161  0.043  0.257 85.153  0.030  2.343   2.8581e-02
   5_adp:   7.161  0.043  0.257 85.153  0.030  2.343   2.8581e-02
   5_occ:   7.161  0.043  0.257 85.153  0.030  2.343   2.8581e-02
   5_bss:   7.161  0.043  0.257 85.153  0.030  2.343   2.8581e-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:  59.37   0.00  12.97  51.76   0.00  11.03  59.37   0.00  23.55
   1_occ:  59.37   0.00  12.97  51.76   0.00  11.03  59.37   0.00  23.55
   2_bss:  59.37   0.00  12.97  51.76   0.00  11.03  59.37   0.00  23.55
   2_xyz:  59.37   0.00  12.97  51.76   0.00  11.03  59.37   0.00  23.55
   2_adp:  82.59   0.00  13.23  70.52   0.00   9.73  82.59   0.59  32.26
   2_occ:  82.59   0.00  13.23  70.52   0.00   9.73  82.59   0.59  32.26
   3_bss:  82.59   0.00  13.23  70.52   0.00   9.73  82.59   0.59  32.26
   3_xyz:  82.59   0.00  13.23  70.52   0.00   9.73  82.59   0.59  32.26
   3_adp:  81.69   0.00  13.05  73.38   0.00   9.04  81.69   1.96  34.89
   3_occ:  81.69   0.00  13.05  73.38   0.00   9.04  81.69   1.96  34.89
   4_bss:  81.69   0.00  13.05  73.38   0.00   9.04  81.69   1.96  34.89
   4_xyz:  81.69   0.00  13.05  73.38   0.00   9.04  81.69   1.96  34.89
   4_adp:  81.72   0.00  13.10  76.96   0.00   8.89  81.72   2.46  36.02
   4_occ:  81.72   0.00  13.10  76.96   0.00   8.89  81.72   2.46  36.02
   5_bss:  81.72   0.00  13.10  76.96   0.00   8.89  81.72   2.46  36.02
   5_xyz:  81.72   0.00  13.10  76.96   0.00   8.89  81.72   2.46  36.02
   5_adp:  94.28   0.00  13.62  94.28   0.00   9.02  87.36   1.37  38.69
   5_occ:  94.28   0.00  13.62  94.28   0.00   9.02  87.36   1.37  38.69
   5_bss:  96.40   2.11  15.73  96.40   2.11  11.13  89.47   3.49  40.81
------------------------------------------------------------------------
 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:    1.264    0.020    0.412
   1_adp:    1.264    0.020    0.412
   1_occ:    1.264    0.020    0.412
   2_bss:    1.264    0.020    0.412
   2_xyz:    1.533    0.042    0.580
   2_adp:    1.533    0.042    0.580
   2_occ:    1.533    0.042    0.580
   3_bss:    1.533    0.042    0.580
   3_xyz:    1.572    0.053    0.677
   3_adp:    1.572    0.053    0.677
   3_occ:    1.572    0.053    0.677
   4_bss:    1.572    0.053    0.677
   4_xyz:    1.560    0.027    0.710
   4_adp:    1.560    0.027    0.710
   4_occ:    1.560    0.027    0.710
   5_bss:    1.560    0.027    0.710
   5_xyz:    1.736    0.025    0.729
   5_adp:    1.736    0.025    0.729
   5_occ:    1.736    0.025    0.729
   5_bss:    1.736    0.025    0.729
------------------------------------------------------------------------

CPU time actual refinement: 349.32


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_149/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_149/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_149/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_149/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_149/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.16 
  Macro-tasks:
    bulk solvent and scale       = 45.30  
    individual site refinement   = 143.63 
    weights calculation          = 31.81  
    collect and process          = 6.45   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 227.30 
  Micro-tasks:
    mask                            = 2.34   
    f_calc                          = 107.32 
    alpha_beta                      = 8.40   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 118.48 
    fmodel                         = 8.24   
    r_factors                      = 0.35   
    phase_errors                   = 10.48  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 257.00 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.852 micro seconds
Total CPU time: 6.05 minutes
from_scatterers_fft:    675 calls, 106.93 s
gradients_fft:          620 calls, 104.77 s

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

# Date 2008-01-16 Time 00:51:52 PST -0800 (1200473512.80 s)
Start R-work = 0.4824, R-free = 0.4789 (no bulk solvent and anisotropic scale)
Final R-work = 0.1347, R-free = 0.1785 (no bulk solvent and anisotropic scale)

Start R-work = 0.4745, R-free = 0.4647
Final R-work = 0.1180, R-free = 0.1638