# Date 2008-01-16 Time 02:02:57 PST -0800 (1200477777.18 s)
#phil __OFF__

Command line arguments: "../671.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26284
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 671

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.1647, 84.2302, 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: 3.26, 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: (70.25, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95137
Completeness in resolution range: 0.935616
Completeness with d_max=infinity: 0.93281

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8895
                             d_min =   1.9514

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95137
Completeness in resolution range: 0.935616
Completeness with d_max=infinity: 0.93281

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8899 -  4.1761 [2206/2235]  1987   219   9.9%
  bin  2:  4.1761 -  3.3268 [2098/2121]  1889   209  10.0%
  bin  3:  3.3268 -  2.9099 [2078/2103]  1865   213  10.3%
  bin  4:  2.9099 -  2.6454 [2077/2093]  1875   202   9.7%
  bin  5:  2.6454 -  2.4567 [2039/2078]  1832   207  10.2%
  bin  6:  2.4567 -  2.3124 [2060/2092]  1858   202   9.8%
  bin  7:  2.3124 -  2.1970 [2012/2049]  1809   203  10.1%
  bin  8:  2.1970 -  2.1017 [2019/2061]  1818   201  10.0%
  bin  9:  2.1017 -  2.0209 [2015/2053]  1811   204  10.1%
  bin 10:  2.0209 -  1.9514 [ 985/2052]   886    99  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_671/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 20
        2.18 -     2.86: 1161
        2.86 -     3.54: 4473
        3.54 -     4.22: 9327
        4.22 -     4.90: 13637
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.495 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.560 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.789 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.810 3.120 -x,y-1/2,-z+1/2
  ... (remaining 28613 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_671/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_671/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 = 70.25 47.16465 84.23025 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: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4651   r_free= 0.4726   ksol= 0.00   Bsol= 0.00   scale= 0.808    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.268655                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6581 0.99   1425  161 0.3855 0.3780      6.5768      6.5897|
|  2:  4.6581 -  3.7162 0.99   1370  145 0.3797 0.3808      6.7507      6.7451|
|  3:  3.7162 -  3.2520 0.99   1345  157 0.4230 0.4252      6.6467      6.7262|
|  4:  3.2520 -  2.9572 0.99   1347  147 0.4334 0.4744      6.4936      6.4939|
|  5:  2.9572 -  2.7467 0.98   1319  148 0.4871 0.5076      6.3557      6.3567|
|  6:  2.7467 -  2.5856 0.99   1335  143 0.4828 0.5313      6.2513      6.2053|
|  7:  2.5856 -  2.4567 0.99   1307  149 0.5080 0.4494      6.2555      6.1504|
|  8:  2.4567 -  2.3502 0.99   1312  144 0.5184 0.5381       6.143      6.1855|
|  9:  2.3502 -  2.2601 0.99   1314  153 0.5171 0.4975      6.1226      6.1328|
| 10:  2.2601 -  2.1823 0.98   1309  141 0.5232 0.5184      6.0955      6.0985|
| 11:  2.1823 -  2.1143 0.98   1293  139 0.5199 0.5376      6.0234       6.025|
| 12:  2.1143 -  2.0540 1.00   1293  149 0.5185 0.5646      5.9466      5.9893|
| 13:  2.0540 -  2.0001 0.95   1262  142 0.5347 0.5188      5.8731      5.8287|
| 14:  2.0001 -  1.9514 0.30    399   41 0.5418 0.5915       5.844      5.7775|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6581  1425   161  0.70  33.91   0.81     0.73      68573.01|
|  2:  4.6581 -  3.7162  1370   145  0.70  34.91   0.89     0.78     101999.93|
|  3:  3.7162 -  3.2520  1345   157  0.60  44.08   0.85     0.72     113702.32|
|  4:  3.2520 -  2.9572  1347   147  0.51  51.32   0.83     0.62     102493.52|
|  5:  2.9572 -  2.7467  1319   148  0.42  58.48   0.75     0.52      85167.83|
|  6:  2.7467 -  2.5856  1335   143  0.41  58.64   0.75     0.49      68781.28|
|  7:  2.5856 -  2.4567  1307   149  0.42  58.14   0.76     0.47      60165.30|
|  8:  2.4567 -  2.3502  1312   144  0.39  60.47   0.72     0.47      55470.57|
|  9:  2.3502 -  2.2601  1314   153  0.37  62.36   0.74     0.44      52807.43|
| 10:  2.2601 -  2.1823  1309   141  0.32  65.73   0.78     0.40      51886.00|
| 11:  2.1823 -  2.1143  1293   139  0.28  68.93   0.77     0.35      48982.28|
| 12:  2.1143 -  2.0540  1293   149  0.24  72.00   0.76     0.32      47150.11|
| 13:  2.0540 -  2.0001  1262   142  0.25  71.32   0.74     0.33      39443.91|
| 14:  2.0001 -  1.9514   399    41  0.32  66.05   0.71     0.39      31113.58|
|alpha:            min =        0.32 max =            0.78 mean =         0.51|
|beta:             min =    31113.58 max =       113702.32 mean =     68509.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.83|
|phase err.(test): min =        0.00 max =           89.91 mean =        57.38|
|-----------------------------------------------------------------------------|

============================== 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 = 12.754341             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.836   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.191515              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.929   (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:       29 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      707 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1527 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2676 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3966 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5069 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6658 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7793 |
|-----------------------------------------------------------------------------|
|-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 |       53.320 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.030 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    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 = 11.664)------------------------------------------|
|    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: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4719   r_free= 0.4788   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.271255                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4567   r_free= 0.4626   ksol= 0.36   Bsol= 20.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.54,7.80,9.66,0.00,0.00,0.00); trace/3= 8.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.267289                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.466086             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.071   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.089074              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.547   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4567      final r-factor (work) = 0.3798          |
| start r-factor (free) = 0.4626      final r-factor (free) = 0.4067          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.1220 = 10.47 * 0.50 * 6.2682 + 1.00 * 53.3202                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.4678 = 10.47 * 0.50 * 6.1790 + 1.00 * 0.1329                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3798      final r-factor (work) = 0.3315          |
| start r-factor (free) = 0.4067      final r-factor (free) = 0.3836          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7437 = 1.09 * 1.00 * 6.1790 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6461 = 1.09 * 1.00 * 6.0882 + 1.00 * 0.0156                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.61   12.67    None  None   None       |
|    all(noH): 2823   0      0.00    70.61   12.67    None  None   None       |
|    Sol.    : 438    0      0.00    65.83   26.74    None  None   None       |
|    Mac.    : 2385   0      0.00    70.61   10.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.061: 1129   |   5:    35.307 -  42.368:   73        |
|      1:     7.061 -  14.123:  763   |   6:    42.368 -  49.429:   46        |
|      2:    14.123 -  21.184:  395   |   7:    49.429 -  56.491:   30        |
|      3:    21.184 -  28.245:  222   |   8:    56.491 -  63.552:   11        |
|      4:    28.245 -  35.307:  148   |   9:    63.552 -  70.613:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3315 r_free = 0.3836             target_work(ml) = 6.069         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3310 r_free = 0.3839             target_work(ml) = 6.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3310   r_free= 0.3839   ksol= 0.36   Bsol= 20.00   scale= 1.095   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.54,7.80,9.66,0.00,0.00,0.00); trace/3= 8.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.068664                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3277   r_free= 0.3818   ksol= 0.34   Bsol= 50.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,4.22,6.55,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.068682                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.447617              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.677   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.528249              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.673  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3277      final r-factor (work) = 0.2560          |
| start r-factor (free) = 0.3818      final r-factor (free) = 0.3144          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7068 = 5.45 * 0.50 * 6.0848 + 1.00 * 0.1329                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3226 = 5.45 * 0.50 * 5.9660 + 1.00 * 0.0725                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2560      final r-factor (work) = 0.2371          |
| start r-factor (free) = 0.3144      final r-factor (free) = 0.2951          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1678 = 0.53 * 1.00 * 5.9660 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0991 = 0.53 * 1.00 * 5.8299 + 1.00 * 0.0195                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.10   13.25    None  None   None       |
|    all(noH): 2823   0      0.00    93.10   13.25    None  None   None       |
|    Sol.    : 438    0      0.00    70.66   32.12    None  None   None       |
|    Mac.    : 2385   0      0.00    93.10   9.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.310: 1493   |   5:    46.550 -  55.860:   67        |
|      1:     9.310 -  18.620:  685   |   6:    55.860 -  65.170:   19        |
|      2:    18.620 -  27.930:  268   |   7:    65.170 -  74.480:    6        |
|      3:    27.930 -  37.240:  168   |   8:    74.480 -  83.790:    1        |
|      4:    37.240 -  46.550:  115   |   9:    83.790 -  93.100:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2371 r_free = 0.2951             target_work(ml) = 5.803         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2369 r_free = 0.2953             target_work(ml) = 5.802         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2369   r_free= 0.2953   ksol= 0.34   Bsol= 50.00   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,4.22,6.55,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.802287                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2356   r_free= 0.2929   ksol= 0.32   Bsol= 35.24   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.92,3.06,4.17,0.00,0.00,0.00); trace/3= 3.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.800560                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.814494              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.093  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.957109              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.622  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2356      final r-factor (work) = 0.1800          |
| start r-factor (free) = 0.2929      final r-factor (free) = 0.2366          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2779 = 2.81 * 0.50 * 5.8308 + 1.00 * 0.0725                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0690 = 2.81 * 0.50 * 5.6895 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1800      final r-factor (work) = 0.1647          |
| start r-factor (free) = 0.2366      final r-factor (free) = 0.2227          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4592 = 0.96 * 1.00 * 5.6895 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3029 = 0.96 * 1.00 * 5.5255 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.74   13.89    None  None   None       |
|    all(noH): 2823   0      0.00    83.74   13.89    None  None   None       |
|    Sol.    : 438    0      2.36    77.86   37.92    None  None   None       |
|    Mac.    : 2385   0      0.00    83.74   9.47     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 -   8.374: 1443   |   5:    41.870 -  50.245:  100        |
|      1:     8.374 -  16.748:  710   |   6:    50.245 -  58.619:   77        |
|      2:    16.748 -  25.122:  198   |   7:    58.619 -  66.993:   37        |
|      3:    25.122 -  33.496:  119   |   8:    66.993 -  75.367:   17        |
|      4:    33.496 -  41.870:  117   |   9:    75.367 -  83.741:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1647 r_free = 0.2227             target_work(ml) = 5.493         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1645 r_free = 0.2226             target_work(ml) = 5.493         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1645   r_free= 0.2226   ksol= 0.32   Bsol= 35.24   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.92,3.06,4.17,0.00,0.00,0.00); trace/3= 3.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.492664                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1643   r_free= 0.2221   ksol= 0.32   Bsol= 38.63   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.47,2.20,2.63,0.00,0.00,0.00); trace/3= 2.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.490082                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.139102              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.369   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.098454              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.420  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1643      final r-factor (work) = 0.1341          |
| start r-factor (free) = 0.2221      final r-factor (free) = 0.1834          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7419 = 3.14 * 0.50 * 5.5299 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5518 = 3.14 * 0.50 * 5.4096 + 1.00 * 0.0611                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1341      final r-factor (work) = 0.1267          |
| start r-factor (free) = 0.1834      final r-factor (free) = 0.1752          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9573 = 1.10 * 1.00 * 5.4096 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8121 = 1.10 * 1.00 * 5.2792 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.52   13.84    None  None   None       |
|    all(noH): 2823   0      0.00    97.52   13.84    None  None   None       |
|    Sol.    : 438    0      2.88    82.80   39.05    None  None   None       |
|    Mac.    : 2385   0      0.00    97.52   9.20     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 -   9.752: 1694   |   5:    48.759 -  58.510:   76        |
|      1:     9.752 -  19.503:  579   |   6:    58.510 -  68.262:   46        |
|      2:    19.503 -  29.255:  153   |   7:    68.262 -  78.014:   21        |
|      3:    29.255 -  39.007:  111   |   8:    78.014 -  87.765:    6        |
|      4:    39.007 -  48.759:  133   |   9:    87.765 -  97.517:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1267 r_free = 0.1752             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1266 r_free = 0.1751             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1751   ksol= 0.32   Bsol= 38.63   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.47,2.20,2.63,0.00,0.00,0.00); trace/3= 2.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.252583                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1757   ksol= 0.32   Bsol= 38.63   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.50,2.06,2.26,0.00,0.00,0.00); trace/3= 1.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.254988                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.768243              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.709  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.467474              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.617  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1757      final r-factor (free) = 0.1664          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3692 = 2.77 * 0.50 * 5.2799 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2933 = 2.77 * 0.50 * 5.2231 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1664      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4547 = 0.47 * 1.00 * 5.2231 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4380 = 0.47 * 1.00 * 5.1898 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.09  13.36    None  None   None       |
|    all(noH): 2823   0      0.00    101.09  13.36    None  None   None       |
|    Sol.    : 438    0      2.31    83.21   37.26    None  None   None       |
|    Mac.    : 2385   0      0.00    101.09  8.97     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.109: 1776   |   5:    50.544 -  60.652:   68        |
|      1:    10.109 -  20.217:  536   |   6:    60.652 -  70.761:   29        |
|      2:    20.217 -  30.326:  153   |   7:    70.761 -  80.870:   14        |
|      3:    30.326 -  40.435:  131   |   8:    80.870 -  90.978:    2        |
|      4:    40.435 -  50.544:  110   |   9:    90.978 - 101.087:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1640             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1150 r_free = 0.1639             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1639   ksol= 0.32   Bsol= 38.63   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.50,2.06,2.26,0.00,0.00,0.00); trace/3= 1.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180974                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6581 0.99   1425  161 0.0969 0.1274      5.3711      5.5402|
|  2:  4.6581 -  3.7162 0.99   1370  145 0.0876 0.1172      5.4429      5.6753|
|  3:  3.7162 -  3.2520 0.99   1345  157 0.1083 0.1599      5.4918      5.8524|
|  4:  3.2520 -  2.9572 0.99   1347  147 0.1265 0.1524      5.4763      5.6148|
|  5:  2.9572 -  2.7467 0.98   1319  148 0.1333 0.1767      5.3406      5.4995|
|  6:  2.7467 -  2.5856 0.99   1335  143 0.1297 0.2112      5.2628      5.5717|
|  7:  2.5856 -  2.4567 0.99   1307  149 0.1269 0.1781       5.204      5.4281|
|  8:  2.4567 -  2.3502 0.99   1312  144 0.1217 0.1699      5.0974      5.3153|
|  9:  2.3502 -  2.2601 0.99   1314  153 0.1186 0.1892       5.047       5.319|
| 10:  2.2601 -  2.1823 0.98   1309  141 0.1161 0.1844      5.0111      5.2818|
| 11:  2.1823 -  2.1143 0.98   1293  139 0.1197 0.1872      4.9734      5.3023|
| 12:  2.1143 -  2.0540 1.00   1293  149 0.1172 0.1791      4.9036      5.1184|
| 13:  2.0540 -  2.0001 0.95   1262  142 0.1212 0.1797      4.8124      5.0291|
| 14:  2.0001 -  1.9514 0.30    399   41 0.1081 0.1854      4.6919      5.0296|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6581  1425   161  0.94   8.84   0.98     0.96       7088.33|
|  2:  4.6581 -  3.7162  1370   145  0.95   8.17   1.02     1.00       8988.88|
|  3:  3.7162 -  3.2520  1345   157  0.93  11.87   1.04     1.04      10984.97|
|  4:  3.2520 -  2.9572  1347   147  0.91  14.41   1.02     1.00      10797.92|
|  5:  2.9572 -  2.7467  1319   148  0.89  17.08   0.99     0.96       8863.03|
|  6:  2.7467 -  2.5856  1335   143  0.89  17.12   0.99     0.97       8024.00|
|  7:  2.5856 -  2.4567  1307   149  0.90  16.50   0.99     0.96       6849.12|
|  8:  2.4567 -  2.3502  1312   144  0.90  16.69   1.00     0.97       5891.41|
|  9:  2.3502 -  2.2601  1314   153  0.90  16.72   1.01     0.99       5396.88|
| 10:  2.2601 -  2.1823  1309   141  0.90  16.22   1.01     0.98       4996.65|
| 11:  2.1823 -  2.1143  1293   139  0.89  17.30   1.00     0.96       4769.50|
| 12:  2.1143 -  2.0540  1293   149  0.90  16.20   1.01     1.00       4229.27|
| 13:  2.0540 -  2.0001  1262   142  0.89  17.32   1.01     1.00       3543.31|
| 14:  2.0001 -  1.9514   399    41  0.89  16.51   1.00     0.97       2817.46|
|alpha:            min =        0.96 max =            1.04 mean =         0.98|
|beta:             min =     2817.46 max =        10984.97 mean =      6902.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.92|
|phase err.(test): min =        0.00 max =           89.51 mean =        14.43|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1639   ksol= 0.32   Bsol= 40.57   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,0.12,0.32,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180974                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1639   ksol= 0.32   Bsol= 40.57   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,0.12,0.32,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180974                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6581 0.99   1425  161 0.0969 0.1274      5.3711      5.5402|
|  2:  4.6581 -  3.7162 0.99   1370  145 0.0876 0.1172      5.4429      5.6753|
|  3:  3.7162 -  3.2520 0.99   1345  157 0.1083 0.1599      5.4918      5.8524|
|  4:  3.2520 -  2.9572 0.99   1347  147 0.1265 0.1524      5.4763      5.6148|
|  5:  2.9572 -  2.7467 0.98   1319  148 0.1333 0.1767      5.3406      5.4995|
|  6:  2.7467 -  2.5856 0.99   1335  143 0.1297 0.2112      5.2628      5.5717|
|  7:  2.5856 -  2.4567 0.99   1307  149 0.1269 0.1781       5.204      5.4281|
|  8:  2.4567 -  2.3502 0.99   1312  144 0.1217 0.1699      5.0974      5.3153|
|  9:  2.3502 -  2.2601 0.99   1314  153 0.1186 0.1892       5.047       5.319|
| 10:  2.2601 -  2.1823 0.98   1309  141 0.1161 0.1844      5.0111      5.2818|
| 11:  2.1823 -  2.1143 0.98   1293  139 0.1197 0.1872      4.9734      5.3023|
| 12:  2.1143 -  2.0540 1.00   1293  149 0.1172 0.1791      4.9036      5.1184|
| 13:  2.0540 -  2.0001 0.95   1262  142 0.1212 0.1797      4.8124      5.0291|
| 14:  2.0001 -  1.9514 0.30    399   41 0.1081 0.1854      4.6919      5.0296|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6581  1425   161  0.94   8.84   0.98     0.96       7088.33|
|  2:  4.6581 -  3.7162  1370   145  0.95   8.17   1.02     1.00       8988.88|
|  3:  3.7162 -  3.2520  1345   157  0.93  11.87   1.04     1.04      10984.97|
|  4:  3.2520 -  2.9572  1347   147  0.91  14.41   1.02     1.00      10797.92|
|  5:  2.9572 -  2.7467  1319   148  0.89  17.08   0.99     0.96       8863.03|
|  6:  2.7467 -  2.5856  1335   143  0.89  17.12   0.99     0.97       8024.00|
|  7:  2.5856 -  2.4567  1307   149  0.90  16.50   0.99     0.96       6849.12|
|  8:  2.4567 -  2.3502  1312   144  0.90  16.69   1.00     0.97       5891.41|
|  9:  2.3502 -  2.2601  1314   153  0.90  16.72   1.01     0.99       5396.88|
| 10:  2.2601 -  2.1823  1309   141  0.90  16.22   1.01     0.98       4996.65|
| 11:  2.1823 -  2.1143  1293   139  0.89  17.30   1.00     0.96       4769.50|
| 12:  2.1143 -  2.0540  1293   149  0.90  16.20   1.01     1.00       4229.27|
| 13:  2.0540 -  2.0001  1262   142  0.89  17.32   1.01     1.00       3543.31|
| 14:  2.0001 -  1.9514   399    41  0.89  16.51   1.00     0.97       2817.46|
|alpha:            min =        0.96 max =            1.04 mean =         0.98|
|beta:             min =     2817.46 max =        10984.97 mean =      6902.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.92|
|phase err.(test): min =        0.00 max =           89.51 mean =        14.43|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.94    103.03  15.30    None  None   None       |
|    all(noH): 2823   0      1.94    103.03  15.30    None  None   None       |
|    Sol.    : 438    0      4.25    85.15   39.20    None  None   None       |
|    Mac.    : 2385   0      1.94    103.03  10.91    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:     1.940 -  12.049: 1776   |   5:    52.483 -  62.592:   68        |
|      1:    12.049 -  22.157:  536   |   6:    62.592 -  72.701:   29        |
|      2:    22.157 -  32.266:  153   |   7:    72.701 -  82.810:   14        |
|      3:    32.266 -  42.375:  131   |   8:    82.810 -  92.918:    2        |
|      4:    42.375 -  52.483:  110   |   9:    92.918 - 103.027:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 350         
Filter by distance & map next to the model:
   mapped sites are within: 0.435 - 5.857
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 348 from: 350
   mapped sites are within: 0.771 - 5.857

peak=   10.350 closest distance to " CB  VAL A 230 " =    1.440
peak=    9.008 closest distance to " CG2 VAL A 296 " =    1.290
peak=    6.395 closest distance to " NH2 ARG A  56 " =    2.167
peak=    6.391 closest distance to " O   HOH Z 279 " =    1.259
peak=    6.141 closest distance to " CG  LEU A   5 " =    1.321
peak=    6.119 closest distance to " O   HOH Z 278 " =    1.462
peak=    5.494 closest distance to " CD2 LEU A   5 " =    1.160
peak=    5.341 closest distance to " O   HOH Z 132 " =    1.596
peak=    5.260 closest distance to " O   HOH Z 142 " =    1.751
peak=    5.254 closest distance to " CD1AILE A 234 " =    1.070
peak=    5.167 closest distance to " O   HOH Z 124 " =    1.465
peak=    5.022 closest distance to " O   HOH Z 202 " =    1.312
peak=    4.960 closest distance to " NE2 GLN A  11 " =    1.133
peak=    4.947 closest distance to " CB  GLN A 223 " =    1.410
peak=    4.872 closest distance to " O   HOH Z  48 " =    1.705
peak=    4.818 closest distance to " CG  LEU A 228 " =    1.211
peak=    4.789 closest distance to " CB  SER A  63 " =    1.270
peak=    4.782 closest distance to " O   HOH Z  97 " =    1.928
peak=    4.751 closest distance to " CG  ARG A 138 " =    0.971
peak=    4.748 closest distance to " CG  PRO A  54 " =    1.187
peak=    4.727 closest distance to " CB  GLN A 183 " =    1.327
peak=    4.695 closest distance to " O   HOH Z 411 " =    3.785
peak=    4.687 closest distance to " O   HOH Z 247 " =    1.313
peak=    4.670 closest distance to " O   HOH Z 120 " =    1.043
peak=    4.648 closest distance to " O   HOH Z 193 " =    1.712
peak=    4.593 closest distance to " O   HOH Z 277 " =    1.058
peak=    4.592 closest distance to " CG  PRO A 213 " =    1.207
peak=    4.588 closest distance to " CB  ARG A 275 " =    0.881
peak=    4.567 closest distance to " O   HOH Z 199 " =    1.028
peak=    4.538 closest distance to " CB  PRO A  54 " =    0.834
peak=    4.507 closest distance to " O   HOH Z 316 " =    2.373
peak=    4.503 closest distance to " O   HOH Z  59 " =    2.217
peak=    4.502 closest distance to " O   HOH Z 427 " =    2.867
peak=    4.486 closest distance to " CB  ASN A 187 " =    1.945
peak=    4.471 closest distance to " CB  SER A   3 " =    1.400
peak=    4.432 closest distance to " CB  VAL A 230 " =    1.227
peak=    4.390 closest distance to " O   HOH Z 272 " =    1.925
peak=    4.368 closest distance to " O   HOH Z 128 " =    2.087
peak=    4.361 closest distance to " CG  PRO A 198 " =    1.245
peak=    4.359 closest distance to " O   SER A  87 " =    2.276
peak=    4.358 closest distance to " O   HOH Z 263 " =    1.401
peak=    4.353 closest distance to " CB  TRP A 179 " =    1.266
peak=    4.330 closest distance to " CB  GLU A 152 " =    1.132
peak=    4.310 closest distance to " O   PRO A 198 " =    1.537
peak=    4.300 closest distance to " CB  ASN A 148 " =    1.388
peak=    4.294 closest distance to " O   HOH Z 232 " =    2.163
peak=    4.292 closest distance to " O   HOH Z  78 " =    1.754
peak=    4.285 closest distance to " CD2 LEU A 228 " =    1.236
peak=    4.276 closest distance to " O   HOH Z 260 " =    1.271
peak=    4.272 closest distance to " O   HOH Z 134 " =    1.545
peak=    4.262 closest distance to " CA  ALA A  21 " =    1.193
peak=    4.234 closest distance to " O   HOH Z 371 " =    3.272
peak=    4.214 closest distance to " O   HOH Z 108 " =    1.411
peak=    4.174 closest distance to " O   HOH Z 368 " =    2.121
peak=    4.158 closest distance to " O   HOH Z 234 " =    3.813
peak=    4.129 closest distance to " CB  TYR A 169 " =    1.002
peak=    4.115 closest distance to " CG1BVAL A  72 " =    1.562
peak=    4.114 closest distance to " O   HOH Z 192 " =    1.333
peak=    4.093 closest distance to " OD1 ASN A  69 " =    2.626
peak=    4.073 closest distance to " O   HOH Z 303 " =    2.118
peak=    4.055 closest distance to " O   HOH Z 389 " =    1.786
peak=    4.043 closest distance to " OE1 GLU A   2 " =    2.085
peak=    4.028 closest distance to " O   HOH Z 326 " =    1.464
peak=    4.021 closest distance to " OD2 ASP A 286 " =    2.674
peak=    4.018 closest distance to " O   HOH Z  37 " =    1.178
peak=    4.017 closest distance to " NH1 ARG A 138 " =    1.156
peak=    4.016 closest distance to " O   HOH Z 423 " =    1.852
peak=    4.012 closest distance to " O   HOH Z  93 " =    2.510
peak=    4.006 closest distance to " O   HOH Z 236 " =    1.616
peak=    3.999 closest distance to " O   HOH Z 334 " =    3.005
peak=    3.989 closest distance to " O   HOH Z 214 " =    2.317
peak=    3.988 closest distance to " O   HOH Z 344 " =    2.674
peak=    3.954 closest distance to " CB  GLU A 277 " =    3.560
peak=    3.944 closest distance to " CA  VAL A  41 " =    0.894
peak=    3.938 closest distance to " O   HOH Z 133 " =    1.630
peak=    3.925 closest distance to " O   HOH Z 136 " =    1.311
peak=    3.924 closest distance to " O   HOH Z 295 " =    1.598
peak=    3.911 closest distance to " O   HOH Z 276 " =    1.379
peak=    3.908 closest distance to " O   HOH Z  20 " =    1.564
peak=    3.903 closest distance to " CB  VAL A 265 " =    1.257
peak=    3.899 closest distance to " O   MET A 105 " =    1.799
peak=    3.896 closest distance to " O   HOH Z  44 " =    2.522
peak=    3.880 closest distance to " O   HOH Z 369 " =    1.949
peak=    3.864 closest distance to " O   HOH Z 203 " =    1.576
peak=    3.844 closest distance to " O   HOH Z 298 " =    1.964
peak=    3.843 closest distance to " CB  VAL A 296 " =    1.056
peak=    3.837 closest distance to " O   HOH Z 193 " =    2.057
peak=    3.837 closest distance to " O   HOH Z   3 " =    1.568
peak=    3.831 closest distance to " CG2 THR A 221 " =    1.008
peak=    3.829 closest distance to " O   HOH Z 180 " =    2.130
peak=    3.816 closest distance to " O   HOH Z  80 " =    1.700
peak=    3.811 closest distance to " CG  ARG A  66 " =    2.815
peak=    3.811 closest distance to " CB  LEU A 228 " =    1.416
peak=    3.810 closest distance to " CB  GLN A  88 " =    1.282
peak=    3.809 closest distance to " O   HOH Z  15 " =    2.384
peak=    3.804 closest distance to " O   HOH Z 227 " =    1.756
peak=    3.801 closest distance to " CG  ARG A 138 " =    1.075
peak=    3.793 closest distance to " CA  ASP A 191 " =    0.934
peak=    3.788 closest distance to " CA  TYR A  30 " =    1.048
peak=    3.786 closest distance to " CB  GLU A 128 " =    1.105
peak=    3.785 closest distance to " CD  GLN A  58 " =    5.857
peak=    3.772 closest distance to " O   HOH Z 346 " =    1.486
peak=    3.770 closest distance to " O   HOH Z  88 " =    3.214
peak=    3.764 closest distance to " CD  LYS A 119 " =    1.774
peak=    3.763 closest distance to " OG  SER A  22 " =    2.839
peak=    3.757 closest distance to " O   HOH Z 112 " =    1.552
peak=    3.750 closest distance to " CB  VAL A 202 " =    1.643
peak=    3.748 closest distance to " NH1 ARG A  14 " =    1.064
peak=    3.748 closest distance to " O   HOH Z 345 " =    3.133
peak=    3.741 closest distance to " O   HOH Z  63 " =    1.145
peak=    3.740 closest distance to " O   HOH Z 189 " =    2.473
peak=    3.736 closest distance to " CA  ALA A 295 " =    1.079
peak=    3.735 closest distance to " O   HOH Z 118 " =    1.503
peak=    3.734 closest distance to " O   HOH Z 280 " =    1.528
peak=    3.723 closest distance to " O   TRP A 274 " =    1.883
peak=    3.705 closest distance to " CD1 ILE A  33 " =    1.624
peak=    3.701 closest distance to " O   HOH Z 374 " =    2.946
peak=    3.698 closest distance to " O   HOH Z 215 " =    1.579
peak=    3.694 closest distance to " O   HOH Z  61 " =    1.543
peak=    3.692 closest distance to " O   HOH Z 426 " =    1.414
peak=    3.687 closest distance to " CB  SER A  62 " =    1.256
peak=    3.681 closest distance to " CB  ARG A 139 " =    0.940
peak=    3.679 closest distance to " O   HOH Z 209 " =    2.311
peak=    3.668 closest distance to " O   HOH Z  11 " =    1.212
peak=    3.664 closest distance to " O   HOH Z 374 " =    2.384
peak=    3.660 closest distance to " O   HOH Z  85 " =    1.307
peak=    3.654 closest distance to " CG  PRO A 243 " =    1.257
peak=    3.653 closest distance to " O   HOH Z   4 " =    1.566
peak=    3.653 closest distance to " O   HOH Z 403 " =    1.693
peak=    3.650 closest distance to " O   HOH Z  48 " =    2.208
peak=    3.649 closest distance to " O   HOH Z 352 " =    1.297
peak=    3.649 closest distance to " O   HOH Z 137 " =    1.614
peak=    3.644 closest distance to " CA  VAL A 126 " =    1.098
peak=    3.639 closest distance to " CA  THR A 221 " =    0.876
peak=    3.637 closest distance to " O   HOH Z 273 " =    2.731
peak=    3.637 closest distance to " CG AARG A 275 " =    1.099
peak=    3.633 closest distance to " O   HOH Z 128 " =    2.063
peak=    3.633 closest distance to " CB  ALA A   9 " =    1.560
peak=    3.628 closest distance to " NE2 GLN A  58 " =    4.116
peak=    3.620 closest distance to " CD BLYS A 290 " =    1.121
peak=    3.619 closest distance to " CD2 LEU A 255 " =    1.209
peak=    3.615 closest distance to " O   HOH Z 419 " =    1.672
peak=    3.614 closest distance to " O   HOH Z 422 " =    2.546
peak=    3.614 closest distance to " O   HOH Z  54 " =    1.542
peak=    3.612 closest distance to " O   HOH Z 217 " =    1.451
peak=    3.607 closest distance to " O   HOH Z  63 " =    2.378
peak=    3.603 closest distance to " CD  LYS A 166 " =    1.396
peak=    3.600 closest distance to " CA  GLY A 211 " =    1.228
peak=    3.599 closest distance to " CA  LEU A 282 " =    1.012
peak=    3.596 closest distance to " NZ  LYS A 117 " =    3.214
peak=    3.590 closest distance to " O   HOH Z 261 " =    1.881
peak=    3.589 closest distance to " O   HOH Z 155 " =    1.561
peak=    3.588 closest distance to " O   HOH Z  92 " =    0.870
peak=    3.587 closest distance to " ND2 ASN A 187 " =    1.682
peak=    3.577 closest distance to " O   HOH Z  49 " =    2.418
peak=    3.575 closest distance to " O   HOH Z 366 " =    2.874
peak=    3.569 closest distance to " CD  ARG A 269 " =    0.928
peak=    3.565 closest distance to " C   ALA A 299 " =    0.954
peak=    3.564 closest distance to " O   HOH Z 394 " =    1.614
peak=    3.564 closest distance to " O   HOH Z 265 " =    2.438
peak=    3.561 closest distance to " CA  LYS A 117 " =    1.249
peak=    3.560 closest distance to " O   HOH Z 284 " =    1.388
peak=    3.559 closest distance to " CG  GLN A  88 " =    1.053
peak=    3.557 closest distance to " O   THR A  31 " =    1.543
peak=    3.556 closest distance to " O   ALA A 158 " =    1.237
peak=    3.554 closest distance to " CG1 ILE A  33 " =    1.328
peak=    3.538 closest distance to " O   HOH Z 236 " =    1.833
peak=    3.530 closest distance to " O   HOH Z 357 " =    2.116
peak=    3.529 closest distance to " O   HOH Z 116 " =    1.714
peak=    3.518 closest distance to " O   SER A  26 " =    1.607
peak=    3.513 closest distance to " OG BSER A 164 " =    2.210
peak=    3.498 closest distance to " O   HOH Z 213 " =    1.860
peak=    3.497 closest distance to " O   HOH Z 250 " =    1.233
peak=    3.495 closest distance to " CZ AARG A 102 " =    1.848
peak=    3.495 closest distance to " CA  GLN A 194 " =    1.264
peak=    3.492 closest distance to " O   HOH Z 108 " =    1.903
peak=    3.490 closest distance to " O   HOH Z 373 " =    1.582
peak=    3.487 closest distance to " O   HOH Z 102 " =    1.193
peak=    3.487 closest distance to " O   HOH Z  30 " =    1.213
peak=    3.486 closest distance to " O   HOH Z  21 " =    1.922
peak=    3.484 closest distance to " NH2BARG A 145 " =    2.328
peak=    3.482 closest distance to " CB  SER A 141 " =    1.066
peak=    3.481 closest distance to " O   HOH Z  40 " =    1.432
peak=    3.478 closest distance to " O   HOH Z 316 " =    0.898
peak=    3.477 closest distance to " CZ2 TRP A 179 " =    1.718
peak=    3.471 closest distance to " O   HOH Z 420 " =    2.120
peak=    3.469 closest distance to " CG  GLN A  58 " =    2.665
peak=    3.463 closest distance to " CE1 TYR A 186 " =    1.215
peak=    3.462 closest distance to " CA  ALA A 248 " =    1.159
peak=    3.461 closest distance to " O   HOH Z 331 " =    1.335
peak=    3.458 closest distance to " OD1 ASN A 217 " =    1.756
peak=    3.454 closest distance to " OE1 GLN A  11 " =    1.693
peak=    3.453 closest distance to " CB  SER A  26 " =    1.607
peak=    3.452 closest distance to " CB  ARG A  79 " =    1.394
peak=    3.451 closest distance to " CA  ASN A 176 " =    1.061
peak=    3.446 closest distance to " CA  ASN A  74 " =    1.191
peak=    3.444 closest distance to " O   HOH Z 197 " =    2.600
peak=    3.444 closest distance to " O   HOH Z 407 " =    2.575
peak=    3.433 closest distance to " O   HOH Z 283 " =    1.950
peak=    3.432 closest distance to " O   HOH Z  68 " =    1.740
peak=    3.429 closest distance to " CB  ALA A 291 " =    1.311
peak=    3.425 closest distance to " O   HOH Z 214 " =    1.035
peak=    3.425 closest distance to " O   HOH Z 406 " =    1.643
peak=    3.422 closest distance to " NZ  LYS A  76 " =    1.272
peak=    3.421 closest distance to " O   HOH Z 344 " =    1.467
peak=    3.420 closest distance to " CB BVAL A  41 " =    1.187
peak=    3.420 closest distance to " CB  ILE A 234 " =    0.833
peak=    3.413 closest distance to " O   HOH Z 355 " =    1.804
peak=    3.408 closest distance to " O   HOH Z 271 " =    1.815
peak=    3.408 closest distance to " CG  MET A 185 " =    1.303
peak=    3.400 closest distance to " O   HOH Z  44 " =    1.832
peak=    3.397 closest distance to " O   HOH Z 329 " =    3.359
peak=    3.392 closest distance to " O   HOH Z 171 " =    2.523
peak=    3.392 closest distance to " CA  ASP A 140 " =    1.164
peak=    3.383 closest distance to " O   HOH Z 215 " =    1.432
peak=    3.381 closest distance to " CA  LEU A 101 " =    1.616
peak=    3.380 closest distance to " C   LYS A 290 " =    1.314
peak=    3.378 closest distance to " O   HOH Z 280 " =    1.991
peak=    3.373 closest distance to " O   HOH Z 132 " =    3.459
peak=    3.367 closest distance to " OG1 THR A 294 " =    2.288
peak=    3.366 closest distance to " CB  LEU A 255 " =    0.787
peak=    3.362 closest distance to " O   HOH Z 402 " =    1.402
peak=    3.359 closest distance to " CB  GLN A  89 " =    1.099
peak=    3.359 closest distance to " CA  ALA A  51 " =    1.028
peak=    3.356 closest distance to " O   HOH Z 313 " =    1.800
peak=    3.354 closest distance to " CB  PRO A 198 " =    1.026
peak=    3.353 closest distance to " O   HOH Z 163 " =    1.972
peak=    3.352 closest distance to " O   HOH Z  10 " =    1.838
peak=    3.349 closest distance to " O   HOH Z 123 " =    1.051
peak=    3.349 closest distance to " CD2 TRP A 179 " =    1.385
peak=    3.347 closest distance to " O   HOH Z 425 " =    2.118
peak=    3.347 closest distance to " OD1 ASP A 286 " =    1.596
peak=    3.344 closest distance to " CD2 HIS A  81 " =    1.183
peak=    3.343 closest distance to " CB  TRP A 266 " =    0.999
peak=    3.341 closest distance to " O   HOH Z 367 " =    3.430
peak=    3.341 closest distance to " CG  ARG A  66 " =    0.862
peak=    3.340 closest distance to " O   HOH Z 278 " =    1.287
peak=    3.337 closest distance to " CG2 VAL A 257 " =    0.809
peak=    3.336 closest distance to " CG  GLN A  77 " =    2.277
peak=    3.334 closest distance to " O   HOH Z 359 " =    2.103
peak=    3.324 closest distance to " CG1 VAL A 153 " =    0.993
peak=    3.323 closest distance to " N   ASN A  39 " =    1.159
peak=    3.317 closest distance to " O   HOH Z 281 " =    4.355
peak=    3.312 closest distance to " O   HOH Z  19 " =    1.773
peak=    3.307 closest distance to " NH1BARG A 190 " =    2.013
peak=    3.305 closest distance to " NH2 ARG A 156 " =    1.086
peak=    3.303 closest distance to " CG  MET A 188 " =    1.584
peak=    3.302 closest distance to " O   HOH Z 191 " =    1.475
peak=    3.296 closest distance to " CG2 VAL A 174 " =    1.285
peak=    3.295 closest distance to " O   HOH Z 327 " =    1.584
peak=    3.293 closest distance to " CB  SER A 273 " =    0.834
peak=    3.291 closest distance to " O   HOH Z 336 " =    1.894
peak=    3.291 closest distance to " O   HOH Z 163 " =    1.355
peak=    3.291 closest distance to " O   HOH Z 248 " =    1.825
peak=    3.291 closest distance to " C   SER A  32 " =    1.124
peak=    3.288 closest distance to " CZ2 TRP A 274 " =    1.717
peak=    3.281 closest distance to " O   ASN A 217 " =    1.318
peak=    3.280 closest distance to " C   ALA A   1 " =    1.695
peak=    3.277 closest distance to " CG  LEU A 167 " =    1.135
peak=    3.276 closest distance to " CD1 LEU A 300 " =    1.095
peak=    3.273 closest distance to " CA  ASN A 215 " =    1.216
peak=    3.273 closest distance to " O   ALA A 165 " =    1.269
peak=    3.273 closest distance to " CA  ALA A 158 " =    1.068
peak=    3.273 closest distance to " O   HOH Z 426 " =    3.016
peak=    3.268 closest distance to " O   HOH Z 245 " =    1.354
peak=    3.263 closest distance to " O   HOH Z 322 " =    2.048
peak=    3.260 closest distance to " NH2BARG A 102 " =    0.920
peak=    3.257 closest distance to " O   HOH Z 334 " =    1.521
peak=    3.254 closest distance to " O   HOH Z  59 " =    2.072
peak=    3.253 closest distance to " O   HOH Z 114 " =    1.195
peak=    3.253 closest distance to " OD2 ASP A 298 " =    4.018
peak=    3.251 closest distance to " O   HOH Z 193 " =    1.450
peak=    3.251 closest distance to " O   PHE A  38 " =    1.832
peak=    3.247 closest distance to " O   HOH Z 411 " =    1.819
peak=    3.243 closest distance to " O   HOH Z 244 " =    1.585
peak=    3.237 closest distance to " NH2 ARG A  79 " =    1.265
peak=    3.237 closest distance to " O   HOH Z 143 " =    1.157
peak=    3.235 closest distance to " O   GLY A  91 " =    1.549
peak=    3.233 closest distance to " O   HOH Z 279 " =    2.197
peak=    3.232 closest distance to " O   HOH Z 407 " =    3.742
peak=    3.228 closest distance to " CB  ALA A 248 " =    0.998
peak=    3.226 closest distance to " O   GLY A  23 " =    2.367
peak=    3.225 closest distance to " O   HOH Z 267 " =    2.174
peak=    3.225 closest distance to " CB  ALA A 100 " =    1.236
peak=    3.224 closest distance to " OD1 ASP A 231 " =    1.859
peak=    3.217 closest distance to " O   HOH Z 303 " =    1.660
peak=    3.217 closest distance to " CA  ARG A  36 " =    1.089
peak=    3.217 closest distance to " O   GLN A 278 " =    1.245
peak=    3.213 closest distance to " NZ  LYS A  48 " =    1.377
peak=    3.211 closest distance to " CA  THR A 264 " =    0.779
peak=    3.207 closest distance to " O   HOH Z 261 " =    1.553
peak=    3.206 closest distance to " CB  ASN A 142 " =    1.122
peak=    3.204 closest distance to " O   HOH Z 155 " =    2.692
peak=    3.202 closest distance to " CA  MET A  40 " =    1.067
peak=    3.202 closest distance to " N   ARG A 156 " =    1.296
peak=    3.201 closest distance to " CG  MET A  93 " =    1.050
peak=    3.192 closest distance to " NZ  LYS A  76 " =    1.850
peak=    3.190 closest distance to " O   HOH Z 345 " =    1.764
peak=    3.189 closest distance to " O   HOH Z 425 " =    1.345
peak=    3.184 closest distance to " O   SER A 164 " =    1.369
peak=    3.179 closest distance to " O   HOH Z 215 " =    1.189
peak=    3.176 closest distance to " O   HOH Z 403 " =    1.462
peak=    3.167 closest distance to " O   HOH Z 207 " =    2.165
peak=    3.164 closest distance to " O   HOH Z 282 " =    1.458
peak=    3.164 closest distance to " N   ARG A 190 " =    1.100
peak=    3.163 closest distance to " O   HOH Z 126 " =    1.577
peak=    3.163 closest distance to " O   HOH Z 227 " =    1.558
peak=    3.161 closest distance to " CD2 LEU A  83 " =    1.575
peak=    3.159 closest distance to " O   HOH Z 141 " =    1.565
peak=    3.155 closest distance to " O   HOH Z 290 " =    1.129
peak=    3.154 closest distance to " O   HOH Z 175 " =    3.473
peak=    3.153 closest distance to " O   HOH Z 423 " =    3.192
peak=    3.148 closest distance to " OG  SER A  97 " =    2.498
peak=    3.142 closest distance to " O   HOH Z 184 " =    1.977
peak=    3.140 closest distance to " CB  ARG A 102 " =    0.771
peak=    3.139 closest distance to " O   HOH Z  43 " =    2.681
peak=    3.138 closest distance to " CB  TYR A  30 " =    1.552
peak=    3.136 closest distance to " NE AARG A 275 " =    1.271
peak=    3.134 closest distance to " O   HOH Z  37 " =    2.522
peak=    3.132 closest distance to " CG  MET A 185 " =    1.052
peak=    3.125 closest distance to " O   HOH Z 270 " =    1.765
peak=    3.124 closest distance to " CB  ASN A  39 " =    0.783
peak=    3.124 closest distance to " CB  MET A  47 " =    1.421
peak=    3.123 closest distance to " O   HOH Z 154 " =    1.376
peak=    3.120 closest distance to " O   HOH Z 197 " =    2.017
peak=    3.114 closest distance to " OG BSER A 258 " =    3.472
peak=    3.112 closest distance to " CE  MET A  93 " =    1.390
peak=    3.112 closest distance to " CD1 ILE A 199 " =    0.913
peak=    3.105 closest distance to " O   HOH Z 152 " =    1.612
peak=    3.104 closest distance to " O   HOH Z 380 " =    2.128
peak=    3.103 closest distance to " O   HOH Z 409 " =    3.605
peak=    3.102 closest distance to " CB  ALA A  84 " =    1.220
peak=    3.101 closest distance to " O   HOH Z 438 " =    2.210
peak=    3.100 closest distance to " O   HOH Z 261 " =    2.050
peak=    3.099 closest distance to " CG2 ILE A 120 " =    1.354
peak=    3.095 closest distance to " O   HOH Z 211 " =    2.198
peak=    3.092 closest distance to " CB  THR A  31 " =    1.666
peak=    3.090 closest distance to " CG1 ILE A  49 " =    1.506
peak=    3.084 closest distance to " O   HOH Z 328 " =    2.038
peak=    3.083 closest distance to " CA  ARG A 195 " =    1.132
peak=    3.069 closest distance to " CB  ALA A 256 " =    1.141
peak=    3.066 closest distance to " CD1 LEU A  96 " =    0.865
peak=    3.064 closest distance to " CA  THR A 246 " =    1.238
peak=    3.054 closest distance to " O   HOH Z 381 " =    1.452
peak=    3.047 closest distance to " O   HOH Z 110 " =    1.605
peak=    3.039 closest distance to " O   HOH Z  85 " =    1.109
peak=    3.035 closest distance to " CA  ALA A 233 " =    1.559
peak=    2.926 closest distance to " O   HOH Z 271 " =    2.031

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.652 - 5.169
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 201
   mapped sites are within: 0.719 - 5.169

peak=   -5.340 closest distance to " CG2 VAL A 230 " =    0.812
peak=   -4.434 closest distance to " O   HOH Z 266 " =    4.293
peak=   -4.343 closest distance to " CB  ALA A 161 " =    2.588
peak=   -4.285 closest distance to " OG ASER A 134 " =    1.261
peak=   -4.240 closest distance to " CD  ARG A  14 " =    3.275
peak=   -4.237 closest distance to " O   HOH Z 274 " =    2.673
peak=   -4.221 closest distance to " CA  SER A 164 " =    2.065
peak=   -4.209 closest distance to " CG2BVAL A  41 " =    2.711
peak=   -4.185 closest distance to " CD  ARG A 156 " =    2.042
peak=   -4.185 closest distance to " O   HOH Z  92 " =    1.231
peak=   -4.152 closest distance to " O   HOH Z  13 " =    1.296
peak=   -4.071 closest distance to " O   HOH Z 231 " =    1.639
peak=   -4.044 closest distance to " CB  TYR A  15 " =    2.144
peak=   -4.040 closest distance to " CD  ARG A 139 " =    1.711
peak=   -3.952 closest distance to " O   HOH Z 166 " =    1.794
peak=   -3.928 closest distance to " C   ALA A 158 " =    1.206
peak=   -3.926 closest distance to " O   HOH Z  11 " =    1.653
peak=   -3.914 closest distance to " CG2 THR A   4 " =    1.915
peak=   -3.908 closest distance to " O   HOH Z 290 " =    0.980
peak=   -3.883 closest distance to " CD  GLN A  88 " =    2.261
peak=   -3.871 closest distance to " NH2 ARG A  66 " =    1.547
peak=   -3.869 closest distance to " CG  LYS A 193 " =    2.420
peak=   -3.855 closest distance to " CE2 TYR A  30 " =    2.834
peak=   -3.847 closest distance to " O   ASN A 187 " =    1.427
peak=   -3.846 closest distance to " C   HIS A 108 " =    1.151
peak=   -3.824 closest distance to " CD1 LEU A 101 " =    2.476
peak=   -3.824 closest distance to " CB  SER A 134 " =    1.758
peak=   -3.821 closest distance to " NH2 ARG A  79 " =    1.900
peak=   -3.787 closest distance to " O   ALA A 161 " =    1.565
peak=   -3.781 closest distance to " O   HOH Z 292 " =    4.287
peak=   -3.763 closest distance to " CB  ALA A 248 " =    1.929
peak=   -3.748 closest distance to " O   HOH Z 198 " =    2.349
peak=   -3.744 closest distance to " O   PRO A 198 " =    1.309
peak=   -3.739 closest distance to " CG  LEU A 228 " =    1.015
peak=   -3.738 closest distance to " N   SER A 276 " =    1.298
peak=   -3.736 closest distance to " ND2 ASN A  45 " =    1.073
peak=   -3.724 closest distance to " CD  GLN A  88 " =    1.042
peak=   -3.711 closest distance to " N   GLN A  58 " =    1.741
peak=   -3.710 closest distance to " O   HOH Z  43 " =    1.665
peak=   -3.689 closest distance to " CD1 LEU A 228 " =    2.325
peak=   -3.682 closest distance to " CZ  TYR A 169 " =    1.841
peak=   -3.681 closest distance to " O   HOH Z  19 " =    2.169
peak=   -3.661 closest distance to " O   HOH Z 377 " =    1.858
peak=   -3.660 closest distance to " CG  GLN A 223 " =    2.376
peak=   -3.660 closest distance to " O   HOH Z 165 " =    2.105
peak=   -3.653 closest distance to " CD2 LEU A 300 " =    2.865
peak=   -3.653 closest distance to " NH1 ARG A  56 " =    2.503
peak=   -3.647 closest distance to " CG  ASP A 231 " =    0.818
peak=   -3.638 closest distance to " C   ASN A 187 " =    1.845
peak=   -3.633 closest distance to " O   HOH Z  97 " =    1.720
peak=   -3.631 closest distance to " CG  ASP A  50 " =    2.215
peak=   -3.627 closest distance to " O   HOH Z 166 " =    1.566
peak=   -3.621 closest distance to " CD  LYS A 289 " =    2.441
peak=   -3.607 closest distance to " O   HOH Z 388 " =    1.966
peak=   -3.604 closest distance to " NH2AARG A 275 " =    5.169
peak=   -3.602 closest distance to " CG  ASN A  45 " =    1.707
peak=   -3.578 closest distance to " OE2 GLU A   2 " =    1.891
peak=   -3.571 closest distance to " O   HOH Z 407 " =    3.062
peak=   -3.567 closest distance to " O   HOH Z  98 " =    1.645
peak=   -3.566 closest distance to " CE  MET A 105 " =    2.113
peak=   -3.553 closest distance to " O   GLY A 196 " =    1.028
peak=   -3.544 closest distance to " CA  GLY A  35 " =    2.087
peak=   -3.544 closest distance to " N   ALA A 226 " =    2.078
peak=   -3.542 closest distance to " O   HOH Z 423 " =    2.205
peak=   -3.542 closest distance to " O   HOH Z 103 " =    1.791
peak=   -3.538 closest distance to " N   THR A 157 " =    1.498
peak=   -3.538 closest distance to " N   GLN A 122 " =    1.580
peak=   -3.532 closest distance to " CD2 LEU A 237 " =    2.619
peak=   -3.523 closest distance to " CB  PRO A 243 " =    2.662
peak=   -3.521 closest distance to " O   HOH Z 426 " =    2.270
peak=   -3.521 closest distance to " OG BSER A 134 " =    1.238
peak=   -3.520 closest distance to " OD1 ASP A 200 " =    1.261
peak=   -3.518 closest distance to " CD1 PHE A  59 " =    1.807
peak=   -3.518 closest distance to " O   HOH Z 431 " =    1.707
peak=   -3.513 closest distance to " CD1 LEU A 255 " =    2.739
peak=   -3.501 closest distance to " CB  CYS A 254 " =    2.476
peak=   -3.495 closest distance to " O   HOH Z  17 " =    1.312
peak=   -3.486 closest distance to " O   HOH Z 266 " =    4.545
peak=   -3.475 closest distance to " O   LEU A 228 " =    2.353
peak=   -3.472 closest distance to " O   HOH Z 339 " =    1.793
peak=   -3.467 closest distance to " N   GLY A 133 " =    1.816
peak=   -3.461 closest distance to " O   HOH Z  71 " =    1.016
peak=   -3.459 closest distance to " O   VAL A  67 " =    2.636
peak=   -3.456 closest distance to " O   HOH Z  52 " =    1.654
peak=   -3.450 closest distance to " N   HIS A 115 " =    1.837
peak=   -3.431 closest distance to " ND2 ASN A  60 " =    1.457
peak=   -3.429 closest distance to " O   HOH Z 151 " =    1.410
peak=   -3.428 closest distance to " O   HOH Z  10 " =    1.437
peak=   -3.420 closest distance to " CG  GLU A  53 " =    1.355
peak=   -3.413 closest distance to " ND2 ASN A 187 " =    1.753
peak=   -3.406 closest distance to " O   HOH Z 113 " =    2.270
peak=   -3.406 closest distance to " O   HOH Z  93 " =    1.477
peak=   -3.404 closest distance to " O   MET A  40 " =    2.801
peak=   -3.403 closest distance to " CG  MET A 105 " =    0.918
peak=   -3.391 closest distance to " O   ALA A  51 " =    1.460
peak=   -3.391 closest distance to " O   HOH Z  63 " =    0.753
peak=   -3.388 closest distance to " CA  ASP A 298 " =    1.030
peak=   -3.386 closest distance to " CZ2 TRP A 179 " =    1.322
peak=   -3.384 closest distance to " CG  PHE A 283 " =    2.765
peak=   -3.365 closest distance to " OG  SER A  62 " =    1.441
peak=   -3.357 closest distance to " CG  TRP A 266 " =    1.581
peak=   -3.357 closest distance to " O   HOH Z 377 " =    1.178
peak=   -3.353 closest distance to " OD1 ASN A 249 " =    1.196
peak=   -3.349 closest distance to " OG  SER A 206 " =    1.727
peak=   -3.348 closest distance to " CG2 VAL A 112 " =    2.549
peak=   -3.345 closest distance to " CD2 TYR A 293 " =    2.143
peak=   -3.342 closest distance to " CB  ALA A  51 " =    1.722
peak=   -3.342 closest distance to " OXT GLY A 302 " =    3.376
peak=   -3.341 closest distance to " CB  ALA A 227 " =    2.353
peak=   -3.337 closest distance to " C   ASN A 285 " =    2.411
peak=   -3.316 closest distance to " CB  ALA A  43 " =    2.305
peak=   -3.316 closest distance to " O   GLU A  44 " =    1.711
peak=   -3.295 closest distance to " O   HOH Z 241 " =    1.454
peak=   -3.286 closest distance to " OG1 THR A  82 " =    1.418
peak=   -3.286 closest distance to " O   ALA A   8 " =    1.877
peak=   -3.283 closest distance to " CB  PRO A 163 " =    2.709
peak=   -3.282 closest distance to " CG  ARG A 138 " =    1.173
peak=   -3.279 closest distance to " CB  SER A 245 " =    2.429
peak=   -3.276 closest distance to " O   GLY A  80 " =    2.536
peak=   -3.268 closest distance to " C   VAL A 265 " =    0.858
peak=   -3.265 closest distance to " O   ASP A 191 " =    1.356
peak=   -3.265 closest distance to " O   HOH Z 292 " =    2.840
peak=   -3.263 closest distance to " O   HOH Z  12 " =    3.380
peak=   -3.261 closest distance to " O   ASP A 270 " =    1.815
peak=   -3.260 closest distance to " CG2 VAL A 296 " =    1.890
peak=   -3.259 closest distance to " OD2 ASP A 286 " =    2.497
peak=   -3.258 closest distance to " O   ALA A 158 " =    1.012
peak=   -3.257 closest distance to " CD2 LEU A 167 " =    1.795
peak=   -3.256 closest distance to " C   LEU A 143 " =    1.210
peak=   -3.255 closest distance to " CD1 TRP A 179 " =    1.096
peak=   -3.250 closest distance to " O   VAL A 197 " =    1.227
peak=   -3.250 closest distance to " CA  ASN A 127 " =    1.051
peak=   -3.247 closest distance to " CE3 TRP A 150 " =    2.096
peak=   -3.241 closest distance to " O   GLY A 211 " =    1.355
peak=   -3.240 closest distance to " ND2 ASN A  39 " =    1.336
peak=   -3.236 closest distance to " O   HOH Z 385 " =    1.947
peak=   -3.234 closest distance to " OG  SER A  97 " =    2.215
peak=   -3.234 closest distance to " N   ALA A 248 " =    1.649
peak=   -3.234 closest distance to " N   GLN A  77 " =    1.563
peak=   -3.233 closest distance to " O   HOH Z 205 " =    1.416
peak=   -3.231 closest distance to " CD  GLU A 152 " =    2.519
peak=   -3.225 closest distance to " O   HOH Z 295 " =    1.322
peak=   -3.221 closest distance to " O   HOH Z 210 " =    0.907
peak=   -3.220 closest distance to " CE BMET A  47 " =    1.713
peak=   -3.219 closest distance to " CB  ALA A 291 " =    2.482
peak=   -3.216 closest distance to " O   HOH Z 234 " =    4.169
peak=   -3.216 closest distance to " O   ASP A 231 " =    2.486
peak=   -3.210 closest distance to " O   SER A 271 " =    2.014
peak=   -3.208 closest distance to " O   HOH Z  60 " =    2.204
peak=   -3.206 closest distance to " O   HOH Z 125 " =    2.855
peak=   -3.204 closest distance to " CG2AVAL A  41 " =    2.972
peak=   -3.202 closest distance to " N   ALA A  43 " =    2.595
peak=   -3.199 closest distance to " N   ALA A 248 " =    2.519
peak=   -3.188 closest distance to " OD2 ASP A 171 " =    1.779
peak=   -3.187 closest distance to " OG1 THR A 178 " =    1.154
peak=   -3.185 closest distance to " CG  GLN A  58 " =    1.365
peak=   -3.183 closest distance to " CB  ASN A  39 " =    2.190
peak=   -3.180 closest distance to " O   HOH Z 419 " =    0.944
peak=   -3.176 closest distance to " O   HOH Z 265 " =    1.849
peak=   -3.176 closest distance to " O   ALA A 256 " =    1.469
peak=   -3.173 closest distance to " CB  ALA A 291 " =    2.194
peak=   -3.172 closest distance to " O   HOH Z 211 " =    1.771
peak=   -3.172 closest distance to " OD1 ASP A 191 " =    1.607
peak=   -3.171 closest distance to " O   ALA A 184 " =    1.580
peak=   -3.165 closest distance to " OE1 GLN A  77 " =    1.719
peak=   -3.162 closest distance to " O   HOH Z 311 " =    3.558
peak=   -3.161 closest distance to " NH2 ARG A  79 " =    1.765
peak=   -3.159 closest distance to " OG  SER A  26 " =    1.151
peak=   -3.154 closest distance to " CA  ARG A  66 " =    1.794
peak=   -3.153 closest distance to " CD1 TYR A 247 " =    2.360
peak=   -3.150 closest distance to " O   HOH Z 396 " =    1.496
peak=   -3.145 closest distance to " O   HOH Z 429 " =    1.909
peak=   -3.138 closest distance to " N   ARG A 138 " =    1.110
peak=   -3.138 closest distance to " O   PRO A 198 " =    1.357
peak=   -3.138 closest distance to " OE1 GLN A  73 " =    2.350
peak=   -3.138 closest distance to " O   HOH Z 427 " =    1.481
peak=   -3.135 closest distance to " O   SER A 146 " =    0.875
peak=   -3.132 closest distance to " O   HOH Z  40 " =    3.281
peak=   -3.129 closest distance to " NH2 ARG A  66 " =    4.566
peak=   -3.127 closest distance to " O   HOH Z  47 " =    1.360
peak=   -3.125 closest distance to " N   ALA A 248 " =    2.011
peak=   -3.122 closest distance to " O   ALA A 160 " =    1.305
peak=   -3.122 closest distance to " CG  PHE A  59 " =    2.175
peak=   -3.120 closest distance to " O   HOH Z 346 " =    1.787
peak=   -3.119 closest distance to " O   HOH Z 389 " =    4.555
peak=   -3.117 closest distance to " CG1 VAL A 112 " =    2.662
peak=   -3.116 closest distance to " O   ARG A 275 " =    2.183
peak=   -3.115 closest distance to " NE  ARG A 138 " =    1.782
peak=   -3.113 closest distance to " O   HOH Z 389 " =    1.537
peak=   -3.105 closest distance to " CD1 TYR A  30 " =    2.342
peak=   -3.105 closest distance to " O   HOH Z 310 " =    1.538
peak=   -3.097 closest distance to " NH2 ARG A 156 " =    1.233
peak=   -3.097 closest distance to " CG2 THR A  82 " =    2.140
peak=   -3.094 closest distance to " CD2 TRP A 274 " =    1.025
peak=   -3.081 closest distance to " O   HOH Z 430 " =    1.898
peak=   -3.068 closest distance to " CG  MET A 105 " =    2.236
peak=   -3.050 closest distance to " NE2 GLN A  73 " =    1.661
peak=   -3.050 closest distance to " O   HOH Z 210 " =    0.719
peak=   -3.011 closest distance to " O   HOH Z  97 " =    0.854

================= 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    :  0.4651 0.4726   6.268655e+00   6.267237e+00
   1_bss:  0.4567 0.4626   6.267289e+00   6.256433e+00
   1_xyz:  0.3798 0.4067   6.152055e+00   6.193346e+00
   1_adp:  0.3315 0.3836   6.068916e+00   6.162407e+00
   1_occ:  0.3310 0.3839   6.068664e+00   6.162504e+00
   2_bss:  0.3277 0.3818   6.068682e+00   6.161135e+00
   2_xyz:  0.2560 0.3144   5.863387e+00   6.013152e+00
   2_adp:  0.2371 0.2951   5.802882e+00   5.966104e+00
   2_occ:  0.2369 0.2953   5.802287e+00   5.966885e+00
   3_bss:  0.2356 0.2929   5.800560e+00   5.963211e+00
   3_xyz:  0.1800 0.2366   5.565812e+00   5.771718e+00
   3_adp:  0.1647 0.2227   5.493227e+00   5.714128e+00
   3_occ:  0.1645 0.2226   5.492664e+00   5.713553e+00
   4_bss:  0.1643 0.2221   5.490082e+00   5.710586e+00
   4_xyz:  0.1341 0.1834   5.302071e+00   5.530776e+00
   4_adp:  0.1267 0.1752   5.253293e+00   5.484612e+00
   4_occ:  0.1266 0.1751   5.252583e+00   5.484347e+00
   5_bss:  0.1270 0.1757   5.254988e+00   5.486014e+00
   5_xyz:  0.1168 0.1664   5.194248e+00   5.436502e+00
   5_adp:  0.1151 0.1640   5.181537e+00   5.422630e+00
   5_occ:  0.1150 0.1639   5.180974e+00   5.422408e+00
   5_bss:  0.1150 0.1639   5.180974e+00   5.422408e+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:  0.362  20.001   6.542   7.800   9.663   0.000   0.000   0.000
   1_xyz:  0.362  20.001   6.542   7.800   9.663   0.000   0.000   0.000
   1_adp:  0.362  20.001   6.542   7.800   9.663   0.000   0.000   0.000
   1_occ:  0.362  20.001   6.542   7.800   9.663   0.000   0.000   0.000
   2_bss:  0.344  50.000   3.061   4.221   6.551   0.000   0.000   0.000
   2_xyz:  0.344  50.000   3.061   4.221   6.551   0.000   0.000   0.000
   2_adp:  0.344  50.000   3.061   4.221   6.551   0.000   0.000   0.000
   2_occ:  0.344  50.000   3.061   4.221   6.551   0.000   0.000   0.000
   3_bss:  0.323  35.242   1.917   3.060   4.166   0.000   0.000   0.000
   3_xyz:  0.323  35.242   1.917   3.060   4.166   0.000   0.000   0.000
   3_adp:  0.323  35.242   1.917   3.060   4.166   0.000   0.000   0.000
   3_occ:  0.323  35.242   1.917   3.060   4.166   0.000   0.000   0.000
   4_bss:  0.319  38.626   1.473   2.204   2.627   0.000   0.000   0.000
   4_xyz:  0.319  38.626   1.473   2.204   2.627   0.000   0.000   0.000
   4_adp:  0.319  38.626   1.473   2.204   2.627   0.000   0.000   0.000
   4_occ:  0.319  38.626   1.473   2.204   2.627   0.000   0.000   0.000
   5_bss:  0.319  38.626   1.502   2.056   2.261   0.000   0.000   0.000
   5_xyz:  0.319  38.626   1.502   2.056   2.261   0.000   0.000   0.000
   5_adp:  0.319  38.626   1.502   2.056   2.261   0.000   0.000   0.000
   5_occ:  0.319  38.626   1.502   2.056   2.261   0.000   0.000   0.000
   5_bss:  0.319  40.566  -0.437   0.116   0.321   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.883 0.4336  0.5112    68511.112
   1_bss:  56.755 0.4324  0.6358    64961.281
   1_xyz:  47.768 0.5457  0.7922    49086.080
   1_adp:  44.191 0.5905  0.8905    43958.695
   1_occ:  44.236 0.5900  0.8897    44083.304
   2_bss:  43.928 0.5937  0.7970    43749.873
   2_xyz:  33.634 0.7160  0.9416    27313.720
   2_adp:  30.882 0.7476  0.9800    23940.591
   2_occ:  30.909 0.7473  0.9792    23961.887
   3_bss:  30.695 0.7494  0.9271    23651.982
   3_xyz:  23.515 0.8264  0.9880    14581.214
   3_adp:  21.646 0.8458  0.9967    12857.483
   3_occ:  21.639 0.8459  0.9964    12845.269
   4_bss:  21.482 0.8473  0.9634    12684.685
   4_xyz:  17.380 0.8855  0.9851     8644.074
   4_adp:  16.228 0.8962  0.9857     7858.710
   4_occ:  16.211 0.8964  0.9856     7853.136
   5_bss:  16.253 0.8961  0.9796     7928.084
   5_xyz:  15.220 0.9049  0.9839     7099.149
   5_adp:  14.876 0.9079  0.9831     6902.956
   5_occ:  14.867 0.9080  0.9830     6902.288
   5_bss:  14.867 0.9080  0.9830     6902.288
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3320e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3320e+01
   1_xyz:   1.626  0.012  0.105 18.162  0.007  4.108   1.3292e-01
   1_adp:   1.626  0.012  0.105 18.162  0.007  4.108   1.3292e-01
   1_occ:   1.626  0.012  0.105 18.162  0.007  4.108   1.3292e-01
   2_bss:   1.626  0.012  0.105 18.162  0.007  4.108   1.3292e-01
   2_xyz:   1.082  0.008  0.076 16.075  0.004  4.111   7.2497e-02
   2_adp:   1.082  0.008  0.076 16.075  0.004  4.111   7.2497e-02
   2_occ:   1.082  0.008  0.076 16.075  0.004  4.111   7.2497e-02
   3_bss:   1.082  0.008  0.076 16.075  0.004  4.111   7.2497e-02
   3_xyz:   0.999  0.007  0.072 15.251  0.004  4.122   6.2468e-02
   3_adp:   0.999  0.007  0.072 15.251  0.004  4.122   6.2468e-02
   3_occ:   0.999  0.007  0.072 15.251  0.004  4.122   6.2468e-02
   4_bss:   0.999  0.007  0.072 15.251  0.004  4.122   6.2468e-02
   4_xyz:   1.016  0.006  0.076 15.436  0.004  4.126   6.1112e-02
   4_adp:   1.016  0.006  0.076 15.436  0.004  4.126   6.1112e-02
   4_occ:   1.016  0.006  0.076 15.436  0.004  4.126   6.1112e-02
   5_bss:   1.016  0.006  0.076 15.436  0.004  4.126   6.1112e-02
   5_xyz:   1.047  0.007  0.079 15.407  0.004  4.115   6.3946e-02
   5_adp:   1.047  0.007  0.079 15.407  0.004  4.115   6.3946e-02
   5_occ:   1.047  0.007  0.079 15.407  0.004  4.115   6.3946e-02
   5_bss:   1.047  0.007  0.079 15.407  0.004  4.115   6.3946e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9107e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9107e+00
   1_xyz:  13.935  0.159  0.442 87.314  0.055  2.201   9.2859e-02
   1_adp:  13.935  0.159  0.442 87.314  0.055  2.201   9.2859e-02
   1_occ:  13.935  0.159  0.442 87.314  0.055  2.201   9.2859e-02
   2_bss:  13.935  0.159  0.442 87.314  0.055  2.201   9.2859e-02
   2_xyz:   7.222  0.073  0.250 81.578  0.025  2.276   5.5566e-02
   2_adp:   7.222  0.073  0.250 81.578  0.025  2.276   5.5566e-02
   2_occ:   7.222  0.073  0.250 81.578  0.025  2.276   5.5566e-02
   3_bss:   7.222  0.073  0.250 81.578  0.025  2.276   5.5566e-02
   3_xyz:   6.604  0.052  0.314 88.049  0.045  2.382   1.1838e-01
   3_adp:   6.604  0.052  0.314 88.049  0.045  2.382   1.1838e-01
   3_occ:   6.604  0.052  0.314 88.049  0.045  2.382   1.1838e-01
   4_bss:   6.604  0.052  0.314 88.049  0.045  2.382   1.1838e-01
   4_xyz:   6.826  0.039  0.408 80.387  0.033  2.359   4.3342e-02
   4_adp:   6.826  0.039  0.408 80.387  0.033  2.359   4.3342e-02
   4_occ:   6.826  0.039  0.408 80.387  0.033  2.359   4.3342e-02
   5_bss:   6.826  0.039  0.408 80.387  0.033  2.359   4.3342e-02
   5_xyz:   6.827  0.038  0.510 83.215  0.029  2.338   4.6787e-02
   5_adp:   6.827  0.038  0.510 83.215  0.029  2.338   4.6787e-02
   5_occ:   6.827  0.038  0.510 83.215  0.029  2.338   4.6787e-02
   5_bss:   6.827  0.038  0.510 83.215  0.029  2.338   4.6787e-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:  70.61   0.00  12.67  70.61   0.00  10.09  65.83   0.00  26.74
   1_occ:  70.61   0.00  12.67  70.61   0.00  10.09  65.83   0.00  26.74
   2_bss:  70.61   0.00  12.67  70.61   0.00  10.09  65.83   0.00  26.74
   2_xyz:  70.61   0.00  12.67  70.61   0.00  10.09  65.83   0.00  26.74
   2_adp:  93.10   0.00  13.25  93.10   0.00   9.79  70.66   0.00  32.12
   2_occ:  93.10   0.00  13.25  93.10   0.00   9.79  70.66   0.00  32.12
   3_bss:  93.10   0.00  13.25  93.10   0.00   9.79  70.66   0.00  32.12
   3_xyz:  93.10   0.00  13.25  93.10   0.00   9.79  70.66   0.00  32.12
   3_adp:  83.74   0.00  13.89  83.74   0.00   9.47  77.86   2.36  37.92
   3_occ:  83.74   0.00  13.89  83.74   0.00   9.47  77.86   2.36  37.92
   4_bss:  83.74   0.00  13.89  83.74   0.00   9.47  77.86   2.36  37.92
   4_xyz:  83.74   0.00  13.89  83.74   0.00   9.47  77.86   2.36  37.92
   4_adp:  97.52   0.00  13.84  97.52   0.00   9.20  82.80   2.88  39.05
   4_occ:  97.52   0.00  13.84  97.52   0.00   9.20  82.80   2.88  39.05
   5_bss:  97.52   0.00  13.84  97.52   0.00   9.20  82.80   2.88  39.05
   5_xyz:  97.52   0.00  13.84  97.52   0.00   9.20  82.80   2.88  39.05
   5_adp: 101.09   0.00  13.36 101.09   0.00   8.97  83.21   2.31  37.26
   5_occ: 101.09   0.00  13.36 101.09   0.00   8.97  83.21   2.31  37.26
   5_bss: 103.03   1.94  15.30 103.03   1.94  10.91  85.15   4.25  39.20
------------------------------------------------------------------------
 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:    1.210    0.011    0.406
   1_adp:    1.210    0.011    0.406
   1_occ:    1.210    0.011    0.406
   2_bss:    1.210    0.011    0.406
   2_xyz:    1.716    0.022    0.546
   2_adp:    1.716    0.022    0.546
   2_occ:    1.716    0.022    0.546
   3_bss:    1.716    0.022    0.546
   3_xyz:    1.584    0.049    0.612
   3_adp:    1.584    0.049    0.612
   3_occ:    1.584    0.049    0.612
   4_bss:    1.584    0.049    0.612
   4_xyz:    1.627    0.043    0.678
   4_adp:    1.627    0.043    0.678
   4_occ:    1.627    0.043    0.678
   5_bss:    1.627    0.043    0.678
   5_xyz:    1.709    0.039    0.692
   5_adp:    1.709    0.039    0.692
   5_occ:    1.709    0.039    0.692
   5_bss:    1.709    0.039    0.692
------------------------------------------------------------------------

CPU time actual refinement: 362.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_671/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_671/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_671/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_671/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_671/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 362.37 
  Macro-tasks:
    bulk solvent and scale       = 41.17  
    individual site refinement   = 154.33 
    weights calculation          = 32.88  
    collect and process          = 6.47   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 234.94 
  Micro-tasks:
    mask                            = 2.57   
    f_calc                          = 117.78 
    alpha_beta                      = 8.26   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 127.00 
    fmodel                         = 7.09   
    r_factors                      = 0.24   
    phase_errors                   = 10.54  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 274.93 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.071 micro seconds
Total CPU time: 6.27 minutes
from_scatterers_fft:    652 calls, 117.48 s
gradients_fft:          596 calls, 113.66 s

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

# Date 2008-01-16 Time 02:09:12 PST -0800 (1200478152.81 s)
Start R-work = 0.4651, R-free = 0.4726 (no bulk solvent and anisotropic scale)
Final R-work = 0.1320, R-free = 0.1810 (no bulk solvent and anisotropic scale)

Start R-work = 0.4567, R-free = 0.4626
Final R-work = 0.1150, R-free = 0.1639