# Date 2008-01-16 Time 01:41:06 PST -0800 (1200476466.22 s)
#phil __OFF__

Command line arguments: "../528.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27794
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 528

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.6953, 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: 3.35, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95122
Completeness in resolution range: 0.950277
Completeness with d_max=infinity: 0.947381

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8359
                             d_min =   1.9512

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95122
Completeness in resolution range: 0.950277
Completeness with d_max=infinity: 0.947381

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8363 -  4.1755 [2168/2197]  1954   214   9.9%
  bin  2:  4.1755 -  3.3265 [2069/2088]  1860   209  10.1%
  bin  3:  3.3265 -  2.9096 [2057/2077]  1851   206  10.0%
  bin  4:  2.9096 -  2.6452 [2045/2070]  1846   199   9.7%
  bin  5:  2.6452 -  2.4565 [2027/2047]  1819   208  10.3%
  bin  6:  2.4565 -  2.3123 [2011/2057]  1810   201  10.0%
  bin  7:  2.3123 -  2.1968 [1981/2013]  1781   200  10.1%
  bin  8:  2.1968 -  2.1015 [2009/2045]  1811   198   9.9%
  bin  9:  2.1015 -  2.0208 [1986/2016]  1784   202  10.2%
  bin 10:  2.0208 -  1.9512 [1236/2004]  1114   122   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_528/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:
        1.61 -     2.27: 29
        2.27 -     2.93: 1587
        2.93 -     3.58: 4580
        3.58 -     4.24: 9330
        4.24 -     4.90: 13308
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.612 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.683 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.690 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.744 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.789 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28829 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_528/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_528/model_refine_001.geo

CPU time processing inputs: 8.86


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.69535 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 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4701   r_free= 0.4686   ksol= 0.00   Bsol= 0.00   scale= 0.810    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.271368                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6573 0.99   1405  155 0.3908 0.3878      6.5803      6.6045|
|  2:  4.6573 -  3.7157 0.99   1360  148 0.3895 0.3804      6.7656      6.7512|
|  3:  3.7157 -  3.2517 0.99   1326  153 0.4269 0.4062      6.6576      6.7459|
|  4:  3.2517 -  2.9569 0.99   1323  148 0.4443 0.4709      6.5048      6.4822|
|  5:  2.9569 -  2.7464 0.99   1309  144 0.4893 0.4840      6.3691      6.3613|
|  6:  2.7464 -  2.5854 0.98   1301  144 0.4898 0.5388      6.2575      6.2242|
|  7:  2.5854 -  2.4565 0.99   1306  144 0.5112 0.4627      6.2487      6.1942|
|  8:  2.4565 -  2.3500 0.98   1286  144 0.5180 0.5395      6.1589      6.1882|
|  9:  2.3500 -  2.2599 0.98   1295  147 0.5105 0.4806      6.1181      6.0617|
| 10:  2.2599 -  2.1822 0.98   1278  135 0.5319 0.5249      6.1073      6.1304|
| 11:  2.1822 -  2.1141 0.99   1280  146 0.5349 0.5201      6.0395      6.0308|
| 12:  2.1141 -  2.0538 0.98   1274  139 0.5042 0.5277      5.9646      5.9955|
| 13:  2.0538 -  1.9999 0.97   1271  137 0.5278 0.5024      5.8789      5.8355|
| 14:  1.9999 -  1.9512 0.48    616   75 0.5523 0.5667      5.8364       5.746|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6573  1405   155  0.68  36.37   0.81     0.71      76898.43|
|  2:  4.6573 -  3.7157  1360   148  0.69  35.78   0.89     0.78     108738.19|
|  3:  3.7157 -  3.2517  1326   153  0.60  44.18   0.85     0.73     116241.66|
|  4:  3.2517 -  2.9569  1323   148  0.52  50.38   0.82     0.63     101739.52|
|  5:  2.9569 -  2.7464  1309   144  0.43  57.47   0.76     0.53      83487.45|
|  6:  2.7464 -  2.5854  1301   144  0.41  59.24   0.74     0.48      70433.74|
|  7:  2.5854 -  2.4565  1306   144  0.40  59.68   0.75     0.46      62765.39|
|  8:  2.4565 -  2.3500  1286   144  0.39  60.73   0.73     0.46      56710.05|
|  9:  2.3500 -  2.2599  1295   147  0.40  59.98   0.76     0.47      50568.48|
| 10:  2.2599 -  2.1822  1278   135  0.39  60.96   0.76     0.47      46620.23|
| 11:  2.1822 -  2.1141  1280   146  0.37  62.35   0.77     0.46      43938.42|
| 12:  2.1141 -  2.0538  1274   139  0.34  64.61   0.78     0.43      43158.94|
| 13:  2.0538 -  1.9999  1271   137  0.30  67.90   0.76     0.39      37828.72|
| 14:  1.9999 -  1.9512   616    75  0.30  67.47   0.71     0.35      30819.25|
|alpha:            min =        0.35 max =            0.78 mean =         0.54|
|beta:             min =    30819.25 max =       116241.66 mean =     68283.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.98 mean =        55.52|
|phase err.(test): min =        0.00 max =           89.94 mean =        55.96|
|-----------------------------------------------------------------------------|

============================== 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 = 11.891633             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.122   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.128859              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.724   (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 |  1.126 -  1.503:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.503 -  1.881:       17 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.881 -  2.258:      152 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.258 -  2.635:      639 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.635 -  3.013:     1464 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.013 -  3.390:     2605 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.390 -  3.768:     4031 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.768 -  4.145:     5182 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.145 -  4.523:     6753 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.523 -  4.900:     7968 |
|-----------------------------------------------------------------------------|
|-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 |       53.015 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.126 |       2.118 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.495)------------------------------------------|
|    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 = 11.495)------------------------------------------|
|    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 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4772   r_free= 0.4756   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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: 6.274436                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4615   r_free= 0.4582   ksol= 0.39   Bsol= 20.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.47,7.61,9.74,0.00,0.00,0.00); trace/3= 7.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.267344                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.121082             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.600   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.028268              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.851   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4615      final r-factor (work) = 0.3851          |
| start r-factor (free) = 0.4582      final r-factor (free) = 0.4028          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 84.7495 = 10.12 * 0.50 * 6.2709 + 1.00 * 53.0154                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.4262 = 10.12 * 0.50 * 6.1844 + 1.00 * 0.1300                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3851      final r-factor (work) = 0.3355          |
| start r-factor (free) = 0.4028      final r-factor (free) = 0.3852          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3735 = 1.03 * 1.00 * 6.1844 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2775 = 1.03 * 1.00 * 6.0900 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.495)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.39   12.83    None  None   None       |
|    all(noH): 2823   0      0.00    81.39   12.83    None  None   None       |
|    Sol.    : 438    0      0.00    81.00   26.47    None  None   None       |
|    Mac.    : 2385   0      0.00    81.39   10.32    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 -   8.139: 1242   |   5:    40.694 -  48.832:   56        |
|      1:     8.139 -  16.277:  797   |   6:    48.832 -  56.971:   21        |
|      2:    16.277 -  24.416:  351   |   7:    56.971 -  65.110:    9        |
|      3:    24.416 -  32.555:  232   |   8:    65.110 -  73.248:    5        |
|      4:    32.555 -  40.694:  105   |   9:    73.248 -  81.387:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3355 r_free = 0.3852             target_work(ml) = 6.075         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3348 r_free = 0.3854             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3348   r_free= 0.3854   ksol= 0.39   Bsol= 20.00   scale= 1.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.47,7.61,9.74,0.00,0.00,0.00); trace/3= 7.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.074459                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3314   r_free= 0.3820   ksol= 0.34   Bsol= 30.88   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.28,3.84,6.63,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.073743                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.150342              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.722   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.484679              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.844  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3314      final r-factor (work) = 0.2485          |
| start r-factor (free) = 0.3820      final r-factor (free) = 0.3035          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.8913 = 7.15 * 0.50 * 6.0868 + 1.00 * 0.1300                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3651 = 7.15 * 0.50 * 5.9536 + 1.00 * 0.0799                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2485      final r-factor (work) = 0.2274          |
| start r-factor (free) = 0.3035      final r-factor (free) = 0.2837          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9140 = 0.48 * 1.00 * 5.9536 + 1.00 * 0.0284                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8187 = 0.48 * 1.00 * 5.7925 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.495)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.79   12.85    None  None   None       |
|    all(noH): 2823   0      0.00    81.79   12.85    None  None   None       |
|    Sol.    : 438    0      0.00    76.25   31.00    None  None   None       |
|    Mac.    : 2385   0      0.00    81.79   9.52     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 -   8.179: 1376   |   5:    40.895 -  49.074:   69        |
|      1:     8.179 -  16.358:  701   |   6:    49.074 -  57.253:   25        |
|      2:    16.358 -  24.537:  292   |   7:    57.253 -  65.432:    8        |
|      3:    24.537 -  32.716:  188   |   8:    65.432 -  73.611:    5        |
|      4:    32.716 -  40.895:  155   |   9:    73.611 -  81.790:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2274 r_free = 0.2837             target_work(ml) = 5.762         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2271 r_free = 0.2841             target_work(ml) = 5.762         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2271   r_free= 0.2841   ksol= 0.34   Bsol= 30.88   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.28,3.84,6.63,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.761700                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2261   r_free= 0.2830   ksol= 0.33   Bsol= 30.88   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.20,2.60,4.15,0.00,0.00,0.00); trace/3= 2.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.759449                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.683226              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.222  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.898970              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.442  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2261      final r-factor (work) = 0.1634          |
| start r-factor (free) = 0.2830      final r-factor (free) = 0.2151          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6506 = 4.68 * 0.50 * 5.7956 + 1.00 * 0.0796                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2693 = 4.68 * 0.50 * 5.6337 + 1.00 * 0.0774                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1634      final r-factor (work) = 0.1434          |
| start r-factor (free) = 0.2151      final r-factor (free) = 0.1933          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0755 = 0.90 * 1.00 * 5.6337 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8785 = 0.90 * 1.00 * 5.4133 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.495)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.02   13.33    None  None   None       |
|    all(noH): 2823   0      0.00    86.02   13.33    None  None   None       |
|    Sol.    : 438    0      2.52    80.52   37.39    None  None   None       |
|    Mac.    : 2385   0      0.00    86.02   8.91     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:     0.000 -   8.603: 1596   |   5:    43.012 -  51.615:   96        |
|      1:     8.603 -  17.205:  610   |   6:    51.615 -  60.217:   67        |
|      2:    17.205 -  25.807:  183   |   7:    60.217 -  68.820:   23        |
|      3:    25.807 -  34.410:  112   |   8:    68.820 -  77.422:   11        |
|      4:    34.410 -  43.012:  120   |   9:    77.422 -  86.025:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1434 r_free = 0.1933             target_work(ml) = 5.353         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1432 r_free = 0.1930             target_work(ml) = 5.351         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1432   r_free= 0.1930   ksol= 0.33   Bsol= 30.88   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.20,2.60,4.15,0.00,0.00,0.00); trace/3= 2.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.351297                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1428   r_free= 0.1911   ksol= 0.31   Bsol= 33.31   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.06,2.85,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.346153                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.726981              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.956   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.247046              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.678  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1428      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1911      final r-factor (free) = 0.1707          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4626 = 2.73 * 0.50 * 5.4164 + 1.00 * 0.0774                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2753 = 2.73 * 0.50 * 5.2902 + 1.00 * 0.0622                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1236      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1707      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3190 = 0.25 * 1.00 * 5.2902 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2995 = 0.25 * 1.00 * 5.2206 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.495)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.54   12.90    None  None   None       |
|    all(noH): 2823   0      0.00    87.54   12.90    None  None   None       |
|    Sol.    : 438    0      2.64    84.05   35.84    None  None   None       |
|    Mac.    : 2385   0      0.00    87.54   8.69     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 -   8.754: 1661   |   5:    43.772 -  52.526:   95        |
|      1:     8.754 -  17.509:  604   |   6:    52.526 -  61.280:   45        |
|      2:    17.509 -  26.263:  152   |   7:    61.280 -  70.034:   19        |
|      3:    26.263 -  35.017:  126   |   8:    70.034 -  78.789:    9        |
|      4:    35.017 -  43.772:  108   |   9:    78.789 -  87.543:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1208 r_free = 0.1657             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1206 r_free = 0.1654             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1654   ksol= 0.31   Bsol= 33.31   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.06,2.85,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.200761                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1653   ksol= 0.32   Bsol= 33.31   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,1.97,2.48,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.200486                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.521808              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.391  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.646915              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.391  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1205      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1653      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0338 = 1.52 * 0.50 * 5.2201 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0015 = 1.52 * 0.50 * 5.1893 + 1.00 * 0.0529                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3668 = 0.65 * 1.00 * 5.1893 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3545 = 0.65 * 1.00 * 5.1682 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.495)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.17   13.02    None  None   None       |
|    all(noH): 2823   0      0.00    93.17   13.02    None  None   None       |
|    Sol.    : 438    0      2.50    87.27   36.54    None  None   None       |
|    Mac.    : 2385   0      0.00    93.17   8.71     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.317: 1722   |   5:    46.587 -  55.904:   84        |
|      1:     9.317 -  18.635:  566   |   6:    55.904 -  65.222:   42        |
|      2:    18.635 -  27.952:  146   |   7:    65.222 -  74.539:   18        |
|      3:    27.952 -  37.270:  131   |   8:    74.539 -  83.857:    4        |
|      4:    37.270 -  46.587:  106   |   9:    83.857 -  93.174:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1620             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1619             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1619   ksol= 0.32   Bsol= 33.31   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,1.97,2.48,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170152                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6573 0.99   1405  155 0.1018 0.1257       5.398      5.5293|
|  2:  4.6573 -  3.7157 0.99   1360  148 0.0888 0.1171      5.4526      5.6552|
|  3:  3.7157 -  3.2517 0.99   1326  153 0.1101 0.1514      5.4883      5.8183|
|  4:  3.2517 -  2.9569 0.99   1323  148 0.1276 0.1678      5.4781      5.6448|
|  5:  2.9569 -  2.7464 0.99   1309  144 0.1323 0.1621      5.3267      5.4621|
|  6:  2.7464 -  2.5854 0.98   1301  144 0.1262 0.1981      5.2244      5.5018|
|  7:  2.5854 -  2.4565 0.99   1306  144 0.1296 0.1724      5.1967      5.4432|
|  8:  2.4565 -  2.3500 0.98   1286  144 0.1190 0.1715      5.0963      5.2943|
|  9:  2.3500 -  2.2599 0.98   1295  147 0.1189 0.1923      5.0457      5.3027|
| 10:  2.2599 -  2.1822 0.98   1278  135 0.1183 0.1744       4.995      5.2294|
| 11:  2.1822 -  2.1141 0.99   1280  146 0.1169 0.1846      4.9549      5.3233|
| 12:  2.1141 -  2.0538 0.98   1274  139 0.1122 0.1713      4.8835      5.1232|
| 13:  2.0538 -  1.9999 0.97   1271  137 0.1202 0.1940      4.8193      5.0997|
| 14:  1.9999 -  1.9512 0.48    616   75 0.1105 0.1664      4.7203      4.9037|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6573  1405   155  0.94   8.85   0.99     0.97       7038.62|
|  2:  4.6573 -  3.7157  1360   148  0.95   7.78   1.03     1.01       8722.61|
|  3:  3.7157 -  3.2517  1326   153  0.93  11.64   1.04     1.03      10513.78|
|  4:  3.2517 -  2.9569  1323   148  0.92  13.79   1.02     1.01      10461.89|
|  5:  2.9569 -  2.7464  1309   144  0.90  15.99   1.00     0.96       8107.28|
|  6:  2.7464 -  2.5854  1301   144  0.90  16.23   0.99     0.97       7282.10|
|  7:  2.5854 -  2.4565  1306   144  0.90  15.93   0.99     0.96       6513.73|
|  8:  2.4565 -  2.3500  1286   144  0.90  16.25   1.00     0.96       5796.91|
|  9:  2.3500 -  2.2599  1295   147  0.90  15.75   1.02     0.99       5162.53|
| 10:  2.2599 -  2.1822  1278   135  0.90  16.02   1.01     0.98       4678.82|
| 11:  2.1822 -  2.1141  1280   146  0.90  16.38   1.01     0.97       4463.00|
| 12:  2.1141 -  2.0538  1274   139  0.91  15.29   1.01     0.99       4024.04|
| 13:  2.0538 -  1.9999  1271   137  0.89  16.96   1.02     1.02       3545.47|
| 14:  1.9999 -  1.9512   616    75  0.90  16.26   1.01     0.97       2924.34|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2924.34 max =        10513.78 mean =      6545.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.37|
|phase err.(test): min =        0.00 max =           88.21 mean =        13.88|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1625   ksol= 0.32   Bsol= 37.94   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,-0.07,0.44,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.172098                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1625   ksol= 0.32   Bsol= 37.94   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,-0.07,0.44,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.172098                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6573 0.99   1405  155 0.1002 0.1314      5.4062      5.5474|
|  2:  4.6573 -  3.7157 0.99   1360  148 0.0903 0.1191      5.4726      5.6752|
|  3:  3.7157 -  3.2517 0.99   1326  153 0.1109 0.1513      5.4974      5.8176|
|  4:  3.2517 -  2.9569 0.99   1323  148 0.1279 0.1664      5.4789      5.6365|
|  5:  2.9569 -  2.7464 0.99   1309  144 0.1331 0.1612      5.3271       5.459|
|  6:  2.7464 -  2.5854 0.98   1301  144 0.1265 0.1979      5.2224      5.4996|
|  7:  2.5854 -  2.4565 0.99   1306  144 0.1295 0.1724      5.1952      5.4423|
|  8:  2.4565 -  2.3500 0.98   1286  144 0.1190 0.1714      5.0947      5.2947|
|  9:  2.3500 -  2.2599 0.98   1295  147 0.1185 0.1919      5.0438      5.3012|
| 10:  2.2599 -  2.1822 0.98   1278  135 0.1178 0.1745      4.9918      5.2287|
| 11:  2.1822 -  2.1141 0.99   1280  146 0.1164 0.1843      4.9535      5.3214|
| 12:  2.1141 -  2.0538 0.98   1274  139 0.1122 0.1721       4.884      5.1258|
| 13:  2.0538 -  1.9999 0.97   1271  137 0.1199 0.1931      4.8181      5.0958|
| 14:  1.9999 -  1.9512 0.48    616   75 0.1107 0.1655      4.7168      4.9011|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6573  1405   155  0.94   9.22   0.99     0.96       7501.37|
|  2:  4.6573 -  3.7157  1360   148  0.95   8.00   1.03     1.01       9128.90|
|  3:  3.7157 -  3.2517  1326   153  0.93  11.77   1.04     1.03      10711.87|
|  4:  3.2517 -  2.9569  1323   148  0.92  13.75   1.02     1.01      10395.36|
|  5:  2.9569 -  2.7464  1309   144  0.90  15.94   1.00     0.96       8024.40|
|  6:  2.7464 -  2.5854  1301   144  0.90  16.23   0.99     0.97       7247.76|
|  7:  2.5854 -  2.4565  1306   144  0.90  15.86   0.99     0.96       6474.60|
|  8:  2.4565 -  2.3500  1286   144  0.90  16.25   1.00     0.96       5789.98|
|  9:  2.3500 -  2.2599  1295   147  0.91  15.71   1.02     0.99       5149.61|
| 10:  2.2599 -  2.1822  1278   135  0.90  16.00   1.01     0.98       4664.67|
| 11:  2.1822 -  2.1141  1280   146  0.90  16.38   1.01     0.97       4461.55|
| 12:  2.1141 -  2.0538  1274   139  0.91  15.30   1.01     1.00       4030.83|
| 13:  2.0538 -  1.9999  1271   137  0.89  16.94   1.02     1.02       3538.00|
| 14:  1.9999 -  1.9512   616    75  0.90  16.18   1.01     0.98       2894.07|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2894.07 max =        10711.87 mean =      6608.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.41|
|phase err.(test): min =        0.00 max =           89.23 mean =        13.93|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.495)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.04    95.22   15.07    None  None   None       |
|    all(noH): 2823   0      2.04    95.22   15.07    None  None   None       |
|    Sol.    : 438    0      4.54    89.32   38.58    None  None   None       |
|    Mac.    : 2385   0      2.04    95.22   10.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.041 -  11.359: 1722   |   5:    48.628 -  57.946:   84        |
|      1:    11.359 -  20.676:  566   |   6:    57.946 -  67.263:   42        |
|      2:    20.676 -  29.993:  146   |   7:    67.263 -  76.580:   18        |
|      3:    29.993 -  39.311:  131   |   8:    76.580 -  85.898:    4        |
|      4:    39.311 -  48.628:  106   |   9:    85.898 -  95.215:    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)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.394 - 5.586
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 322
   mapped sites are within: 0.729 - 5.586

peak=   10.625 closest distance to " CB  VAL A 230 " =    1.425
peak=    9.373 closest distance to " CG2 VAL A 296 " =    1.390
peak=    5.983 closest distance to " CG  LEU A   5 " =    1.235
peak=    5.899 closest distance to " O   HOH Z 278 " =    1.608
peak=    5.750 closest distance to " NE2 GLN A  11 " =    1.173
peak=    5.511 closest distance to " CD2 LEU A   5 " =    1.250
peak=    5.422 closest distance to " CD1AILE A 234 " =    1.009
peak=    5.353 closest distance to " O   HOH Z 124 " =    1.558
peak=    5.270 closest distance to " NH2 ARG A  56 " =    2.079
peak=    5.262 closest distance to " CB  ARG A 275 " =    0.930
peak=    5.220 closest distance to " O   HOH Z 142 " =    1.804
peak=    5.193 closest distance to " O   HOH Z 132 " =    1.548
peak=    5.140 closest distance to " O   HOH Z 202 " =    1.403
peak=    5.075 closest distance to " O   HOH Z 236 " =    1.503
peak=    5.001 closest distance to " O   HOH Z 199 " =    1.039
peak=    4.953 closest distance to " CG  PRO A 213 " =    1.263
peak=    4.951 closest distance to " CB  GLN A 223 " =    1.445
peak=    4.890 closest distance to " O   HOH Z 193 " =    1.698
peak=    4.865 closest distance to " CG  PRO A  54 " =    1.248
peak=    4.836 closest distance to " O   HOH Z 209 " =    2.333
peak=    4.791 closest distance to " CG  PRO A 198 " =    1.259
peak=    4.770 closest distance to " CD2 LEU A 228 " =    1.190
peak=    4.735 closest distance to " O   HOH Z 263 " =    1.435
peak=    4.713 closest distance to " O   HOH Z 427 " =    2.829
peak=    4.697 closest distance to " O   HOH Z 272 " =    1.865
peak=    4.696 closest distance to " O   HOH Z 279 " =    1.145
peak=    4.685 closest distance to " CB  ASN A 187 " =    1.892
peak=    4.668 closest distance to " O   HOH Z  97 " =    2.139
peak=    4.605 closest distance to " CB  SER A  63 " =    1.275
peak=    4.573 closest distance to " O   HOH Z   3 " =    2.004
peak=    4.566 closest distance to " CB  VAL A 230 " =    1.130
peak=    4.566 closest distance to " CB  PRO A  54 " =    0.971
peak=    4.564 closest distance to " O   HOH Z 260 " =    1.349
peak=    4.548 closest distance to " CB  SER A   3 " =    1.347
peak=    4.484 closest distance to " CA  GLY A 241 " =    3.756
peak=    4.449 closest distance to " CG  LEU A 228 " =    1.176
peak=    4.442 closest distance to " CB  GLN A 183 " =    1.334
peak=    4.439 closest distance to " O   HOH Z 143 " =    1.068
peak=    4.434 closest distance to " O   HOH Z 326 " =    1.474
peak=    4.404 closest distance to " O   HOH Z  59 " =    1.752
peak=    4.329 closest distance to " CB  ASN A 148 " =    1.353
peak=    4.309 closest distance to " O   HOH Z 247 " =    1.235
peak=    4.299 closest distance to " O   HOH Z 232 " =    2.161
peak=    4.274 closest distance to " O   HOH Z 346 " =    1.544
peak=    4.217 closest distance to " O   HOH Z  78 " =    1.764
peak=    4.214 closest distance to " CB  TYR A 169 " =    0.874
peak=    4.213 closest distance to " O   HOH Z 134 " =    1.441
peak=    4.210 closest distance to " CA  VAL A  41 " =    0.859
peak=    4.183 closest distance to " O   HOH Z 108 " =    1.412
peak=    4.137 closest distance to " CB  TRP A 179 " =    1.251
peak=    4.098 closest distance to " O   SER A  87 " =    2.353
peak=    4.092 closest distance to " O   HOH Z 284 " =    1.600
peak=    4.073 closest distance to " O   HOH Z 316 " =    2.845
peak=    4.069 closest distance to " O   HOH Z 203 " =    1.620
peak=    4.067 closest distance to " OD1 ASN A  69 " =    2.591
peak=    4.062 closest distance to " O   HOH Z 298 " =    1.846
peak=    4.050 closest distance to " O   HOH Z  93 " =    2.423
peak=    4.033 closest distance to " O   HOH Z 213 " =    1.840
peak=    4.030 closest distance to " O   HOH Z  48 " =    1.496
peak=    4.029 closest distance to " O   HOH Z 371 " =    3.294
peak=    4.025 closest distance to " O   HOH Z 344 " =    1.314
peak=    4.013 closest distance to " O   HOH Z 192 " =    1.364
peak=    4.007 closest distance to " O   HOH Z 368 " =    2.124
peak=    4.007 closest distance to " CG1BVAL A  72 " =    1.381
peak=    4.005 closest distance to " O   HOH Z 276 " =    1.377
peak=    4.003 closest distance to " CB  VAL A 265 " =    1.224
peak=    4.000 closest distance to " O   HOH Z 234 " =    3.777
peak=    3.997 closest distance to " CB  VAL A 296 " =    0.982
peak=    3.996 closest distance to " O   HOH Z 345 " =    3.054
peak=    3.993 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.979 closest distance to " NZ  LYS A 117 " =    3.173
peak=    3.975 closest distance to " CG  PRO A 243 " =    1.228
peak=    3.971 closest distance to " CG2 VAL A 257 " =    0.838
peak=    3.954 closest distance to " O   HOH Z  50 " =    1.568
peak=    3.954 closest distance to " O   HOH Z 423 " =    1.856
peak=    3.948 closest distance to " CB  GLU A 152 " =    1.189
peak=    3.947 closest distance to " CB  GLU A 128 " =    1.117
peak=    3.933 closest distance to " O   HOH Z 133 " =    1.512
peak=    3.929 closest distance to " CB  ARG A 102 " =    0.807
peak=    3.928 closest distance to " CA  ALA A  21 " =    1.099
peak=    3.921 closest distance to " O   PRO A 198 " =    1.551
peak=    3.920 closest distance to " CA  TYR A  30 " =    1.041
peak=    3.905 closest distance to " O   HOH Z 425 " =    1.366
peak=    3.903 closest distance to " O   HOH Z 303 " =    2.080
peak=    3.881 closest distance to " O   HOH Z  97 " =    1.397
peak=    3.877 closest distance to " O   HOH Z  54 " =    1.582
peak=    3.874 closest distance to " OE1 GLU A   2 " =    2.072
peak=    3.866 closest distance to " CG  LEU A 167 " =    1.105
peak=    3.865 closest distance to " O   HOH Z 227 " =    1.703
peak=    3.857 closest distance to " O   HOH Z 334 " =    2.932
peak=    3.857 closest distance to " O   HOH Z  15 " =    2.251
peak=    3.849 closest distance to " O   HOH Z 123 " =    1.117
peak=    3.829 closest distance to " O   HOH Z 189 " =    2.553
peak=    3.816 closest distance to " O   HOH Z 344 " =    2.739
peak=    3.815 closest distance to " O   HOH Z 322 " =    2.155
peak=    3.808 closest distance to " O   HOH Z  61 " =    1.578
peak=    3.804 closest distance to " CZ AARG A 102 " =    1.769
peak=    3.795 closest distance to " O   HOH Z  85 " =    1.310
peak=    3.772 closest distance to " CB  LEU A 255 " =    0.807
peak=    3.768 closest distance to " CB BVAL A  41 " =    1.215
peak=    3.764 closest distance to " CB  LEU A 228 " =    1.419
peak=    3.745 closest distance to " O   HOH Z 392 " =    2.844
peak=    3.737 closest distance to " O   HOH Z 214 " =    2.007
peak=    3.732 closest distance to " O   HOH Z 193 " =    1.589
peak=    3.730 closest distance to " OD2 ASP A 286 " =    2.637
peak=    3.729 closest distance to " CB  ARG A 139 " =    0.917
peak=    3.718 closest distance to " C   LYS A 290 " =    1.274
peak=    3.707 closest distance to " O   HOH Z 128 " =    1.883
peak=    3.701 closest distance to " C   ALA A 299 " =    0.947
peak=    3.689 closest distance to " CD  ARG A 269 " =    1.045
peak=    3.688 closest distance to " O   HOH Z 214 " =    1.162
peak=    3.688 closest distance to " O   TRP A 274 " =    1.902
peak=    3.687 closest distance to " CB  PRO A 198 " =    0.984
peak=    3.682 closest distance to " O   HOH Z  43 " =    2.215
peak=    3.677 closest distance to " O   HOH Z 118 " =    1.532
peak=    3.676 closest distance to " ND2 ASN A 187 " =    1.622
peak=    3.675 closest distance to " CB  ASN A 148 " =    1.873
peak=    3.674 closest distance to " CB  ARG A  79 " =    1.255
peak=    3.673 closest distance to " NH1 ARG A  14 " =    1.034
peak=    3.670 closest distance to " O   HOH Z 369 " =    1.922
peak=    3.665 closest distance to " CD BLYS A 290 " =    1.176
peak=    3.664 closest distance to " O   HOH Z 403 " =    1.612
peak=    3.664 closest distance to " CA  PHE A 283 " =    1.322
peak=    3.661 closest distance to " CA  THR A 221 " =    0.909
peak=    3.651 closest distance to " O   HOH Z 334 " =    1.481
peak=    3.649 closest distance to " O   HOH Z  88 " =    3.183
peak=    3.648 closest distance to " CG2 THR A 221 " =    1.082
peak=    3.643 closest distance to " CA  LEU A 282 " =    1.178
peak=    3.639 closest distance to " CG  ARG A  66 " =    2.774
peak=    3.638 closest distance to " O   HOH Z 273 " =    2.771
peak=    3.637 closest distance to " O   HOH Z 366 " =    2.976
peak=    3.635 closest distance to " CB  GLU A 277 " =    3.510
peak=    3.628 closest distance to " O   HOH Z 280 " =    1.601
peak=    3.627 closest distance to " O   HOH Z 249 " =    1.168
peak=    3.624 closest distance to " O   HOH Z 108 " =    1.753
peak=    3.614 closest distance to " O   HOH Z 287 " =    1.710
peak=    3.612 closest distance to " O   SER A  26 " =    1.538
peak=    3.607 closest distance to " O   HOH Z  59 " =    2.208
peak=    3.602 closest distance to " CB  SER A 216 " =    0.797
peak=    3.601 closest distance to " CG1 ILE A  33 " =    1.378
peak=    3.597 closest distance to " O   HOH Z  66 " =    2.148
peak=    3.597 closest distance to " O   HOH Z 172 " =    3.734
peak=    3.590 closest distance to " O   HOH Z 374 " =    2.408
peak=    3.589 closest distance to " O   HOH Z  40 " =    1.357
peak=    3.582 closest distance to " O   HOH Z 303 " =    1.682
peak=    3.581 closest distance to " CA  THR A 264 " =    0.729
peak=    3.571 closest distance to " O   HOH Z 357 " =    1.829
peak=    3.571 closest distance to " O   HOH Z  44 " =    1.914
peak=    3.564 closest distance to " CG  ASN A  60 " =    1.222
peak=    3.559 closest distance to " CA  VAL A 126 " =    1.024
peak=    3.559 closest distance to " NZ  LYS A  76 " =    1.349
peak=    3.555 closest distance to " O   HOH Z 281 " =    4.459
peak=    3.555 closest distance to " OG  SER A  97 " =    2.597
peak=    3.527 closest distance to " CG  ARG A 138 " =    1.032
peak=    3.526 closest distance to " CB  VAL A 202 " =    1.727
peak=    3.525 closest distance to " O   HOH Z 261 " =    1.547
peak=    3.520 closest distance to " CE1 TYR A 186 " =    1.247
peak=    3.518 closest distance to " NE2 GLN A  58 " =    5.586
peak=    3.509 closest distance to " CA  ASN A 215 " =    1.177
peak=    3.506 closest distance to " NE2 GLN A  58 " =    4.052
peak=    3.503 closest distance to " O   HOH Z 403 " =    1.308
peak=    3.488 closest distance to " CG  MET A 188 " =    1.371
peak=    3.488 closest distance to " O   MET A 105 " =    1.757
peak=    3.481 closest distance to " O   HOH Z 426 " =    1.459
peak=    3.477 closest distance to " O   HOH Z 112 " =    1.550
peak=    3.475 closest distance to " CA  LEU A 101 " =    1.507
peak=    3.470 closest distance to " O   HOH Z 313 " =    1.840
peak=    3.470 closest distance to " O   HOH Z 261 " =    2.015
peak=    3.468 closest distance to " O   HOH Z  68 " =    1.640
peak=    3.452 closest distance to " CG AARG A 275 " =    1.104
peak=    3.446 closest distance to " O   HOH Z 148 " =    3.185
peak=    3.442 closest distance to " O   HOH Z 389 " =    1.690
peak=    3.431 closest distance to " CD2 HIS A  81 " =    1.173
peak=    3.430 closest distance to " O   HOH Z  11 " =    1.434
peak=    3.427 closest distance to " CB  TRP A 266 " =    1.034
peak=    3.424 closest distance to " CD  LYS A 119 " =    1.420
peak=    3.421 closest distance to " O   HOH Z 116 " =    1.666
peak=    3.417 closest distance to " CG1 VAL A 153 " =    0.944
peak=    3.407 closest distance to " O   HOH Z 128 " =    2.096
peak=    3.405 closest distance to " O   HOH Z 193 " =    1.993
peak=    3.403 closest distance to " N   ARG A 156 " =    1.282
peak=    3.403 closest distance to " O   HOH Z 383 " =    1.837
peak=    3.402 closest distance to " CA  ALA A 295 " =    1.116
peak=    3.400 closest distance to " O   HOH Z 289 " =    1.493
peak=    3.398 closest distance to " O   HOH Z 250 " =    1.297
peak=    3.395 closest distance to " N   ASN A  39 " =    1.101
peak=    3.391 closest distance to " CA  ALA A  51 " =    0.995
peak=    3.387 closest distance to " CB  TYR A  30 " =    1.620
peak=    3.384 closest distance to " O   HOH Z  10 " =    1.768
peak=    3.374 closest distance to " NH2BARG A 190 " =    1.769
peak=    3.374 closest distance to " CA  ASP A 191 " =    0.869
peak=    3.372 closest distance to " OG1 THR A 294 " =    2.351
peak=    3.368 closest distance to " CB  SER A 141 " =    1.115
peak=    3.365 closest distance to " CA  ALA A 154 " =    1.097
peak=    3.364 closest distance to " O   HOH Z 406 " =    1.712
peak=    3.362 closest distance to " N   TRP A 177 " =    1.686
peak=    3.362 closest distance to " NH2 ARG A 156 " =    1.058
peak=    3.359 closest distance to " O   HOH Z 422 " =    2.541
peak=    3.356 closest distance to " O   HOH Z 191 " =    1.454
peak=    3.353 closest distance to " CA  ILE A 234 " =    0.798
peak=    3.352 closest distance to " CA  GLN A 194 " =    1.180
peak=    3.351 closest distance to " CG  GLN A  88 " =    1.054
peak=    3.348 closest distance to " CG2 ILE A 120 " =    1.281
peak=    3.347 closest distance to " O   GLN A  58 " =    1.451
peak=    3.346 closest distance to " O   HOH Z 209 " =    2.334
peak=    3.346 closest distance to " CD1 ILE A  33 " =    1.612
peak=    3.343 closest distance to " CA  ARG A  36 " =    1.008
peak=    3.341 closest distance to " O   HOH Z 153 " =    3.651
peak=    3.334 closest distance to " O   THR A  31 " =    1.572
peak=    3.334 closest distance to " O   HOH Z 136 " =    1.085
peak=    3.325 closest distance to " O   HOH Z 180 " =    2.181
peak=    3.322 closest distance to " O   HOH Z  61 " =    1.547
peak=    3.321 closest distance to " CB  ALA A 295 " =    1.409
peak=    3.318 closest distance to " NH2BARG A 145 " =    2.045
peak=    3.317 closest distance to " O   HOH Z 222 " =    2.283
peak=    3.315 closest distance to " CB  SER A 273 " =    0.867
peak=    3.310 closest distance to " CA  ASP A 140 " =    1.134
peak=    3.303 closest distance to " CG2 ILE A  20 " =    1.589
peak=    3.303 closest distance to " O   HOH Z 158 " =    2.862
peak=    3.302 closest distance to " CG  PRO A 280 " =    1.007
peak=    3.301 closest distance to " O   HOH Z 152 " =    2.923
peak=    3.300 closest distance to " CA  ALA A 248 " =    1.241
peak=    3.296 closest distance to " CD  LYS A 166 " =    1.455
peak=    3.289 closest distance to " NH2 ARG A 219 " =    1.840
peak=    3.286 closest distance to " CD2 LEU A 255 " =    1.253
peak=    3.284 closest distance to " O   ALA A 158 " =    1.326
peak=    3.284 closest distance to " O   HOH Z 245 " =    1.360
peak=    3.283 closest distance to " CD1 LEU A 300 " =    1.262
peak=    3.282 closest distance to " O   GLN A 278 " =    1.333
peak=    3.282 closest distance to " CB  ALA A 291 " =    1.395
peak=    3.277 closest distance to " CB  VAL A 268 " =    0.779
peak=    3.275 closest distance to " O   HOH Z 327 " =    1.596
peak=    3.269 closest distance to " CB  ILE A 234 " =    0.897
peak=    3.268 closest distance to " ND1 HIS A  81 " =    1.452
peak=    3.267 closest distance to " SD BMET A  47 " =    1.145
peak=    3.266 closest distance to " O   HOH Z  59 " =    2.072
peak=    3.265 closest distance to " O   HOH Z 438 " =    2.187
peak=    3.264 closest distance to " O   HOH Z 271 " =    1.836
peak=    3.264 closest distance to " O   HOH Z 352 " =    1.292
peak=    3.263 closest distance to " CZ2 TRP A 274 " =    1.714
peak=    3.263 closest distance to " N   SER A 135 " =    1.220
peak=    3.262 closest distance to " N   TYR A  15 " =    0.927
peak=    3.261 closest distance to " CD2 TRP A 179 " =    1.411
peak=    3.256 closest distance to " OG BSER A 164 " =    2.213
peak=    3.254 closest distance to " OG  SER A  22 " =    2.758
peak=    3.250 closest distance to " CG  ARG A  66 " =    0.921
peak=    3.250 closest distance to " O   HOH Z 411 " =    1.747
peak=    3.247 closest distance to " N   SER A 288 " =    1.667
peak=    3.244 closest distance to " O   HOH Z  21 " =    1.820
peak=    3.240 closest distance to " O   HOH Z 355 " =    1.815
peak=    3.237 closest distance to " O   HOH Z 265 " =    2.163
peak=    3.229 closest distance to " O   HOH Z  40 " =    2.329
peak=    3.229 closest distance to " O   HOH Z 255 " =    1.725
peak=    3.226 closest distance to " CB  SER A  62 " =    1.203
peak=    3.225 closest distance to " O   HOH Z 374 " =    1.146
peak=    3.225 closest distance to " OD1 ASP A 231 " =    1.798
peak=    3.223 closest distance to " O   HOH Z 402 " =    1.335
peak=    3.222 closest distance to " O   HOH Z  89 " =    1.635
peak=    3.221 closest distance to " O   HOH Z 217 " =    1.208
peak=    3.220 closest distance to " NZ  LYS A  76 " =    1.802
peak=    3.219 closest distance to " O   HOH Z  40 " =    1.455
peak=    3.216 closest distance to " O   HOH Z 133 " =    2.334
peak=    3.216 closest distance to " O   HOH Z 267 " =    2.117
peak=    3.212 closest distance to " CG  MET A 185 " =    1.247
peak=    3.211 closest distance to " O   HOH Z 367 " =    3.624
peak=    3.211 closest distance to " CB  ARG A 190 " =    1.825
peak=    3.211 closest distance to " O   HOH Z 430 " =    1.954
peak=    3.209 closest distance to " CE AMET A  47 " =    1.400
peak=    3.201 closest distance to " O   HOH Z 426 " =    2.981
peak=    3.198 closest distance to " NH1BARG A 145 " =    1.405
peak=    3.197 closest distance to " OG  SER A  62 " =    3.019
peak=    3.192 closest distance to " O   HOH Z  30 " =    2.101
peak=    3.191 closest distance to " O   SER A 164 " =    1.351
peak=    3.190 closest distance to " O   HOH Z 155 " =    1.602
peak=    3.186 closest distance to " O   HOH Z 409 " =    3.568
peak=    3.185 closest distance to " CB  GLN A 278 " =    0.803
peak=    3.180 closest distance to " CE  MET A  40 " =    1.085
peak=    3.180 closest distance to " O   HOH Z 248 " =    1.770
peak=    3.178 closest distance to " O   HOH Z  53 " =    2.418
peak=    3.178 closest distance to " O   HOH Z 171 " =    2.350
peak=    3.177 closest distance to " CA  ASN A 176 " =    1.071
peak=    3.177 closest distance to " O   HOH Z 283 " =    1.719
peak=    3.175 closest distance to " N   GLN A 278 " =    1.014
peak=    3.174 closest distance to " CA  LYS A 117 " =    1.227
peak=    3.171 closest distance to " CB  ALA A   9 " =    1.586
peak=    3.168 closest distance to " OE1 GLN A  11 " =    1.631
peak=    3.166 closest distance to " O   HOH Z   4 " =    1.695
peak=    3.165 closest distance to " O   HOH Z 185 " =    1.591
peak=    3.165 closest distance to " O   HOH Z 433 " =    1.830
peak=    3.164 closest distance to " O   HOH Z  14 " =    2.158
peak=    3.157 closest distance to " OH  TYR A 116 " =    1.036
peak=    3.150 closest distance to " O   HOH Z 394 " =    1.679
peak=    3.148 closest distance to " N   PHE A 130 " =    1.373
peak=    3.141 closest distance to " CB  ALA A   1 " =    1.188
peak=    3.138 closest distance to " O   GLY A  57 " =    2.445
peak=    3.132 closest distance to " NE1 TRP A 274 " =    0.975
peak=    3.127 closest distance to " O   HOH Z 329 " =    3.162
peak=    3.126 closest distance to " O   HOH Z  43 " =    2.664
peak=    3.124 closest distance to " CB  THR A  31 " =    1.654
peak=    3.112 closest distance to " O   HOH Z 334 " =    1.248
peak=    3.109 closest distance to " O   HOH Z  49 " =    2.211
peak=    3.104 closest distance to " CG  LEU A 281 " =    0.997
peak=    3.103 closest distance to " O   HOH Z  88 " =    2.381
peak=    3.103 closest distance to " O   HOH Z 125 " =    2.403
peak=    3.101 closest distance to " O   HOH Z 215 " =    1.588
peak=    3.097 closest distance to " O   HOH Z 189 " =    2.681
peak=    3.097 closest distance to " CB  SER A  26 " =    1.544
peak=    3.095 closest distance to " O   HOH Z 152 " =    1.662
peak=    3.090 closest distance to " CG AARG A 275 " =    1.116
peak=    3.089 closest distance to " CA  ALA A 233 " =    1.406
peak=    3.086 closest distance to " O   HOH Z  89 " =    2.114
peak=    3.086 closest distance to " OG1 THR A 221 " =    1.358
peak=    3.085 closest distance to " O   HOH Z 285 " =    1.644
peak=    3.077 closest distance to " CA  ASN A  74 " =    1.269
peak=    3.076 closest distance to " O   HOH Z  78 " =    2.262
peak=    3.073 closest distance to " O   HOH Z 148 " =    2.166
peak=    3.072 closest distance to " O   HOH Z 368 " =    3.671
peak=    3.069 closest distance to " CB  ALA A 137 " =    1.198
peak=    3.034 closest distance to " CA  ALA A 158 " =    1.107
peak=    3.020 closest distance to " O   HOH Z 389 " =    1.217

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 175         
Filter by distance & map next to the model:
   mapped sites are within: 0.669 - 5.185
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 173 from: 175
   mapped sites are within: 0.808 - 5.185

peak=   -4.800 closest distance to " CG2 VAL A 230 " =    0.808
peak=   -4.327 closest distance to " O   PRO A 163 " =    2.012
peak=   -4.308 closest distance to " OXT GLY A 302 " =    2.770
peak=   -4.275 closest distance to " CD  ARG A 156 " =    2.045
peak=   -4.251 closest distance to " SG  CYS A 254 " =    3.128
peak=   -4.218 closest distance to " O   HOH Z  43 " =    1.862
peak=   -4.159 closest distance to " O   HOH Z  11 " =    1.898
peak=   -4.144 closest distance to " O   ILE A 109 " =    2.557
peak=   -4.099 closest distance to " O   HOH Z  92 " =    1.443
peak=   -4.089 closest distance to " O   HOH Z 231 " =    1.505
peak=   -4.031 closest distance to " O   ALA A 161 " =    1.581
peak=   -4.028 closest distance to " OG ASER A 134 " =    1.191
peak=   -4.014 closest distance to " CD1 LEU A 255 " =    2.755
peak=   -4.010 closest distance to " N   GLN A  58 " =    1.845
peak=   -4.009 closest distance to " CG  LYS A 193 " =    2.264
peak=   -4.003 closest distance to " CD1 LEU A 101 " =    2.450
peak=   -4.001 closest distance to " N   SER A 276 " =    1.153
peak=   -3.951 closest distance to " O   HOH Z 290 " =    0.973
peak=   -3.920 closest distance to " CA  TYR A  68 " =    2.676
peak=   -3.911 closest distance to " CB  ALA A 248 " =    1.954
peak=   -3.911 closest distance to " O   VAL A  67 " =    2.716
peak=   -3.891 closest distance to " O   HOH Z 266 " =    4.329
peak=   -3.883 closest distance to " CE2 TYR A  30 " =    2.890
peak=   -3.879 closest distance to " O   PRO A 198 " =    1.270
peak=   -3.864 closest distance to " ND2 ASN A  45 " =    0.966
peak=   -3.859 closest distance to " O   HOH Z  98 " =    1.645
peak=   -3.834 closest distance to " O   HOH Z 388 " =    1.921
peak=   -3.834 closest distance to " CB  TYR A  15 " =    2.167
peak=   -3.827 closest distance to " O   HOH Z 166 " =    2.017
peak=   -3.812 closest distance to " O   HOH Z 198 " =    2.196
peak=   -3.805 closest distance to " N   ALA A 248 " =    1.680
peak=   -3.783 closest distance to " NH2 ARG A  79 " =    1.920
peak=   -3.720 closest distance to " O   HOH Z 165 " =    2.102
peak=   -3.698 closest distance to " OG BSER A 134 " =    1.212
peak=   -3.687 closest distance to " CB  ALA A  51 " =    1.813
peak=   -3.683 closest distance to " O   HOH Z 111 " =    4.565
peak=   -3.674 closest distance to " CD  ARG A 139 " =    1.710
peak=   -3.668 closest distance to " O   ASN A 187 " =    1.397
peak=   -3.664 closest distance to " CG  LEU A 228 " =    1.042
peak=   -3.663 closest distance to " O   HOH Z 423 " =    2.203
peak=   -3.655 closest distance to " OD1 ASN A 249 " =    1.225
peak=   -3.652 closest distance to " O   HOH Z  63 " =    0.888
peak=   -3.633 closest distance to " N   HIS A 115 " =    2.032
peak=   -3.631 closest distance to " CB  PRO A 243 " =    2.602
peak=   -3.625 closest distance to " CG2 VAL A 296 " =    1.758
peak=   -3.625 closest distance to " CG  GLN A 223 " =    1.987
peak=   -3.622 closest distance to " O   HOH Z 193 " =    1.788
peak=   -3.606 closest distance to " O   HOH Z  56 " =    2.066
peak=   -3.604 closest distance to " CG  ASP A 231 " =    0.809
peak=   -3.604 closest distance to " CG  ASP A  50 " =    2.277
peak=   -3.593 closest distance to " CZ  TYR A 169 " =    1.739
peak=   -3.591 closest distance to " CB  ASN A  39 " =    2.049
peak=   -3.586 closest distance to " C   HIS A 108 " =    1.160
peak=   -3.577 closest distance to " O   HOH Z 166 " =    1.415
peak=   -3.576 closest distance to " CG  PHE A 283 " =    2.678
peak=   -3.563 closest distance to " O   ALA A  51 " =    1.386
peak=   -3.554 closest distance to " OG BSER A 134 " =    1.660
peak=   -3.554 closest distance to " O   MET A  40 " =    2.582
peak=   -3.540 closest distance to " CE2 PHE A 218 " =    2.605
peak=   -3.538 closest distance to " O   HOH Z 308 " =    1.703
peak=   -3.537 closest distance to " O   HOH Z  11 " =    1.866
peak=   -3.533 closest distance to " O   HOH Z  13 " =    1.379
peak=   -3.520 closest distance to " OXT GLY A 302 " =    3.584
peak=   -3.507 closest distance to " O   HOH Z 365 " =    1.335
peak=   -3.506 closest distance to " O   ASP A 231 " =    2.558
peak=   -3.506 closest distance to " O   HOH Z 134 " =    2.548
peak=   -3.494 closest distance to " O   SER A 135 " =    1.547
peak=   -3.489 closest distance to " OG  SER A 206 " =    1.588
peak=   -3.488 closest distance to " NH2AARG A 275 " =    5.157
peak=   -3.484 closest distance to " O   HOH Z 211 " =    1.177
peak=   -3.480 closest distance to " C   ASN A 285 " =    2.279
peak=   -3.466 closest distance to " CD  LYS A 289 " =    2.548
peak=   -3.466 closest distance to " O   ALA A   8 " =    1.838
peak=   -3.465 closest distance to " CD1 LEU A 228 " =    2.135
peak=   -3.462 closest distance to " C   ASN A 187 " =    1.868
peak=   -3.461 closest distance to " O   HOH Z 103 " =    1.747
peak=   -3.458 closest distance to " CA  ASN A 127 " =    1.070
peak=   -3.458 closest distance to " ND2 ASN A  45 " =    1.047
peak=   -3.457 closest distance to " O   HOH Z 407 " =    2.999
peak=   -3.448 closest distance to " O   HOH Z  71 " =    1.265
peak=   -3.447 closest distance to " O   HOH Z 350 " =    2.161
peak=   -3.441 closest distance to " CD  GLN A  88 " =    0.877
peak=   -3.438 closest distance to " CA  ASP A 298 " =    1.042
peak=   -3.414 closest distance to " CG  MET A 105 " =    0.891
peak=   -3.414 closest distance to " OD1 ASP A 200 " =    1.195
peak=   -3.408 closest distance to " CZ  PHE A  59 " =    1.475
peak=   -3.408 closest distance to " C   ALA A 158 " =    1.211
peak=   -3.399 closest distance to " OG  SER A   3 " =    1.586
peak=   -3.397 closest distance to " CB  ALA A 291 " =    2.281
peak=   -3.392 closest distance to " CD2 LEU A 300 " =    2.813
peak=   -3.389 closest distance to " ND2 ASN A  60 " =    1.309
peak=   -3.388 closest distance to " N   PHE A  59 " =    2.311
peak=   -3.387 closest distance to " CG  GLU A 277 " =    1.144
peak=   -3.385 closest distance to " O   HOH Z 377 " =    1.928
peak=   -3.377 closest distance to " C   LEU A 143 " =    1.178
peak=   -3.364 closest distance to " CD1 TYR A 247 " =    2.871
peak=   -3.362 closest distance to " CD  GLU A 152 " =    2.523
peak=   -3.356 closest distance to " O   GLY A  57 " =    1.381
peak=   -3.355 closest distance to " O   HOH Z 281 " =    3.043
peak=   -3.349 closest distance to " CB  ASP A 132 " =    2.219
peak=   -3.347 closest distance to " O   ALA A 100 " =    2.489
peak=   -3.345 closest distance to " O   PRO A 198 " =    1.310
peak=   -3.343 closest distance to " CE  MET A 105 " =    1.884
peak=   -3.324 closest distance to " O   HOH Z 250 " =    1.408
peak=   -3.321 closest distance to " ND2 ASN A  39 " =    1.370
peak=   -3.319 closest distance to " O   HOH Z 313 " =    1.688
peak=   -3.314 closest distance to " O   LEU A 228 " =    2.320
peak=   -3.310 closest distance to " O   HOH Z 339 " =    1.742
peak=   -3.307 closest distance to " O   SER A 146 " =    0.884
peak=   -3.305 closest distance to " O   HOH Z 210 " =    1.006
peak=   -3.303 closest distance to " CA  GLY A 133 " =    1.878
peak=   -3.300 closest distance to " O   HOH Z 100 " =    1.087
peak=   -3.298 closest distance to " O   HOH Z 184 " =    1.101
peak=   -3.293 closest distance to " O   HOH Z  97 " =    0.915
peak=   -3.292 closest distance to " OE1 GLN A  73 " =    2.352
peak=   -3.291 closest distance to " O   HOH Z  93 " =    1.479
peak=   -3.283 closest distance to " CD2 LEU A   5 " =    1.156
peak=   -3.278 closest distance to " OE1 GLN A  88 " =    1.030
peak=   -3.278 closest distance to " O   HOH Z 205 " =    1.469
peak=   -3.277 closest distance to " O   HOH Z 191 " =    5.185
peak=   -3.274 closest distance to " N   ALA A 226 " =    2.027
peak=   -3.268 closest distance to " O   TRP A  70 " =    1.526
peak=   -3.265 closest distance to " N   GLN A  58 " =    1.299
peak=   -3.261 closest distance to " O   PRO A 243 " =    2.541
peak=   -3.259 closest distance to " O   GLY A 211 " =    1.249
peak=   -3.259 closest distance to " O   HOH Z 148 " =    1.820
peak=   -3.257 closest distance to " O   HOH Z 143 " =    1.189
peak=   -3.255 closest distance to " O   HOH Z 150 " =    1.492
peak=   -3.253 closest distance to " CA  GLY A  35 " =    2.065
peak=   -3.249 closest distance to " O   HOH Z 385 " =    1.842
peak=   -3.244 closest distance to " O   HOH Z 297 " =    2.842
peak=   -3.243 closest distance to " N   THR A  52 " =    1.787
peak=   -3.241 closest distance to " O   VAL A 197 " =    1.056
peak=   -3.232 closest distance to " O   HOH Z 266 " =    4.562
peak=   -3.230 closest distance to " OH  TYR A 214 " =    1.281
peak=   -3.230 closest distance to " O   HOH Z 185 " =    2.190
peak=   -3.228 closest distance to " NE1 TRP A 274 " =    1.180
peak=   -3.226 closest distance to " CG  PRO A 243 " =    1.352
peak=   -3.226 closest distance to " CG  TRP A 266 " =    1.572
peak=   -3.222 closest distance to " O   HOH Z 423 " =    1.125
peak=   -3.205 closest distance to " OD1 ASP A 191 " =    1.533
peak=   -3.200 closest distance to " O   HOH Z 256 " =    1.182
peak=   -3.200 closest distance to " CE BMET A  47 " =    1.359
peak=   -3.197 closest distance to " O   HOH Z 344 " =    2.420
peak=   -3.186 closest distance to " O   HOH Z 427 " =    1.522
peak=   -3.186 closest distance to " O   HOH Z 175 " =    4.332
peak=   -3.179 closest distance to " O   HOH Z 351 " =    1.407
peak=   -3.169 closest distance to " CG  PRO A 163 " =    2.724
peak=   -3.167 closest distance to " O   HOH Z  15 " =    1.650
peak=   -3.166 closest distance to " O   VAL A 153 " =    2.341
peak=   -3.156 closest distance to " O   HOH Z 234 " =    4.122
peak=   -3.152 closest distance to " O   HOH Z 417 " =    2.643
peak=   -3.152 closest distance to " OD1 ASP A 191 " =    1.394
peak=   -3.151 closest distance to " O   HOH Z 341 " =    1.176
peak=   -3.150 closest distance to " OG1 THR A  82 " =    1.372
peak=   -3.125 closest distance to " O   GLY A  80 " =    2.470
peak=   -3.123 closest distance to " O   HOH Z 310 " =    1.656
peak=   -3.121 closest distance to " O   HOH Z 222 " =    1.431
peak=   -3.114 closest distance to " CB  ASP A 132 " =    2.101
peak=   -3.113 closest distance to " N   ALA A  43 " =    2.520
peak=   -3.109 closest distance to " CE  LYS A  76 " =    2.883
peak=   -3.105 closest distance to " CG2 VAL A 189 " =    1.979
peak=   -3.099 closest distance to " O   SER A  22 " =    2.268
peak=   -3.099 closest distance to " ND2 ASN A 252 " =    1.609
peak=   -3.099 closest distance to " N   GLN A  77 " =    1.578
peak=   -3.094 closest distance to " O   TRP A  92 " =    1.760
peak=   -3.078 closest distance to " O   HOH Z 410 " =    2.069
peak=   -3.074 closest distance to " CD2 TYR A 293 " =    2.121
peak=   -3.067 closest distance to " CD2 LEU A 228 " =    2.246
peak=   -3.067 closest distance to " CG  GLU A   2 " =    2.023
peak=   -3.040 closest distance to " CD2 LEU A 237 " =    2.648
peak=   -3.018 closest distance to " O   HOH Z 353 " =    2.240
peak=   -3.014 closest distance to " O   HOH Z 352 " =    0.995

================= 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    :  0.4701 0.4686   6.271368e+00   6.264770e+00
   1_bss:  0.4615 0.4582   6.267344e+00   6.253010e+00
   1_xyz:  0.3851 0.4028   6.158701e+00   6.188247e+00
   1_adp:  0.3355 0.3852   6.074604e+00   6.160934e+00
   1_occ:  0.3348 0.3854   6.074459e+00   6.161562e+00
   2_bss:  0.3314 0.3820   6.073743e+00   6.159126e+00
   2_xyz:  0.2485 0.3035   5.831619e+00   5.984166e+00
   2_adp:  0.2274 0.2837   5.761780e+00   5.930543e+00
   2_occ:  0.2271 0.2841   5.761700e+00   5.930892e+00
   3_bss:  0.2261 0.2830   5.759449e+00   5.927858e+00
   3_xyz:  0.1634 0.2151   5.471400e+00   5.682058e+00
   3_adp:  0.1434 0.1933   5.352500e+00   5.577826e+00
   3_occ:  0.1432 0.1930   5.351297e+00   5.576496e+00
   4_bss:  0.1428 0.1911   5.346153e+00   5.570001e+00
   4_xyz:  0.1236 0.1707   5.228274e+00   5.461080e+00
   4_adp:  0.1208 0.1657   5.202063e+00   5.428365e+00
   4_occ:  0.1206 0.1654   5.200761e+00   5.427007e+00
   5_bss:  0.1205 0.1653   5.200486e+00   5.426709e+00
   5_xyz:  0.1172 0.1611   5.174934e+00   5.401152e+00
   5_adp:  0.1155 0.1620   5.170581e+00   5.404216e+00
   5_occ:  0.1155 0.1619   5.170152e+00   5.403716e+00
   5_bss:  0.1157 0.1625   5.172098e+00   5.405052e+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:  0.386  19.999   6.472   7.608   9.743   0.000   0.000   0.000
   1_xyz:  0.386  19.999   6.472   7.608   9.743   0.000   0.000   0.000
   1_adp:  0.386  19.999   6.472   7.608   9.743   0.000   0.000   0.000
   1_occ:  0.386  19.999   6.472   7.608   9.743   0.000   0.000   0.000
   2_bss:  0.343  30.878   3.280   3.840   6.625   0.000   0.000   0.000
   2_xyz:  0.343  30.878   3.280   3.840   6.625   0.000   0.000   0.000
   2_adp:  0.343  30.878   3.280   3.840   6.625   0.000   0.000   0.000
   2_occ:  0.343  30.878   3.280   3.840   6.625   0.000   0.000   0.000
   3_bss:  0.326  30.878   2.196   2.597   4.153   0.000   0.000   0.000
   3_xyz:  0.326  30.878   2.196   2.597   4.153   0.000   0.000   0.000
   3_adp:  0.326  30.878   2.196   2.597   4.153   0.000   0.000   0.000
   3_occ:  0.326  30.878   2.196   2.597   4.153   0.000   0.000   0.000
   4_bss:  0.309  33.309   1.797   2.058   2.852   0.000   0.000   0.000
   4_xyz:  0.309  33.309   1.797   2.058   2.852   0.000   0.000   0.000
   4_adp:  0.309  33.309   1.797   2.058   2.852   0.000   0.000   0.000
   4_occ:  0.309  33.309   1.797   2.058   2.852   0.000   0.000   0.000
   5_bss:  0.317  33.309   1.669   1.972   2.482   0.000   0.000   0.000
   5_xyz:  0.317  33.309   1.669   1.972   2.482   0.000   0.000   0.000
   5_adp:  0.317  33.309   1.669   1.972   2.482   0.000   0.000   0.000
   5_occ:  0.317  33.309   1.669   1.972   2.482   0.000   0.000   0.000
   5_bss:  0.318  37.945  -0.372  -0.070   0.441   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.568 0.4514  0.5359    68288.378
   1_bss:  55.991 0.4433  0.6574    64767.095
   1_xyz:  46.066 0.5684  0.8318    47931.643
   1_adp:  43.436 0.6010  0.9120    44223.447
   1_occ:  43.542 0.5996  0.9099    44353.800
   2_bss:  43.254 0.6028  0.8119    43828.015
   2_xyz:  32.410 0.7299  0.9612    25389.629
   2_adp:  29.415 0.7640  0.9974    21913.449
   2_occ:  29.430 0.7639  0.9970    21940.928
   3_bss:  29.252 0.7656  0.9423    21711.283
   3_xyz:  21.075 0.8509  0.9996    11968.008
   3_adp:  18.367 0.8771  1.0089     9635.757
   3_occ:  18.335 0.8774  1.0087     9590.629
   4_bss:  18.144 0.8790  0.9819     9395.038
   4_xyz:  15.723 0.9002  0.9928     7405.660
   4_adp:  14.904 0.9076  0.9951     6942.273
   4_occ:  14.870 0.9078  0.9951     6921.723
   5_bss:  14.863 0.9079  0.9880     6919.351
   5_xyz:  14.293 0.9127  0.9896     6527.816
   5_adp:  14.334 0.9126  0.9868     6553.788
   5_occ:  14.322 0.9127  0.9867     6545.958
   5_bss:  14.359 0.9124  0.9864     6608.771
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3015e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3015e+01
   1_xyz:   1.595  0.012  0.103 18.210  0.006  4.107   1.2999e-01
   1_adp:   1.595  0.012  0.103 18.210  0.006  4.107   1.2999e-01
   1_occ:   1.595  0.012  0.103 18.210  0.006  4.107   1.2999e-01
   2_bss:   1.595  0.012  0.103 18.210  0.006  4.107   1.2999e-01
   2_xyz:   1.110  0.008  0.083 16.345  0.005  4.120   7.9901e-02
   2_adp:   1.110  0.008  0.083 16.345  0.005  4.120   7.9901e-02
   2_occ:   1.110  0.008  0.083 16.345  0.005  4.120   7.9901e-02
   3_bss:   1.110  0.008  0.083 16.345  0.005  4.120   7.9901e-02
   3_xyz:   1.106  0.008  0.079 15.895  0.004  4.115   7.7401e-02
   3_adp:   1.106  0.008  0.079 15.895  0.004  4.115   7.7401e-02
   3_occ:   1.106  0.008  0.079 15.895  0.004  4.115   7.7401e-02
   4_bss:   1.106  0.008  0.079 15.895  0.004  4.115   7.7401e-02
   4_xyz:   1.018  0.006  0.075 15.808  0.004  4.116   6.2196e-02
   4_adp:   1.018  0.006  0.075 15.808  0.004  4.116   6.2196e-02
   4_occ:   1.018  0.006  0.075 15.808  0.004  4.116   6.2196e-02
   5_bss:   1.018  0.006  0.075 15.808  0.004  4.116   6.2196e-02
   5_xyz:   0.914  0.005  0.069 15.400  0.003  4.110   5.2947e-02
   5_adp:   0.914  0.005  0.069 15.400  0.003  4.110   5.2947e-02
   5_occ:   0.914  0.005  0.069 15.400  0.003  4.110   5.2947e-02
   5_bss:   0.914  0.005  0.069 15.400  0.003  4.110   5.2947e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.126   6.8706e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.126   6.8706e+00
   1_xyz:  13.540  0.155  0.439 84.945  0.049  2.242   8.9485e-02
   1_adp:  13.540  0.155  0.439 84.945  0.049  2.242   8.9485e-02
   1_occ:  13.540  0.155  0.439 84.945  0.049  2.242   8.9485e-02
   2_bss:  13.540  0.155  0.439 84.945  0.049  2.242   8.9485e-02
   2_xyz:   7.408  0.101  0.319 85.901  0.041  2.279   8.4336e-02
   2_adp:   7.408  0.101  0.319 85.901  0.041  2.279   8.4336e-02
   2_occ:   7.408  0.101  0.319 85.901  0.041  2.279   8.4336e-02
   3_bss:   7.408  0.101  0.319 85.901  0.041  2.279   8.4336e-02
   3_xyz:   6.903  0.060  0.440 84.549  0.029  2.332   1.7149e-01
   3_adp:   6.903  0.060  0.440 84.549  0.029  2.332   1.7149e-01
   3_occ:   6.903  0.060  0.440 84.549  0.029  2.332   1.7149e-01
   4_bss:   6.903  0.060  0.440 84.549  0.029  2.332   1.7149e-01
   4_xyz:   7.374  0.037  0.435 82.863  0.035  2.322   4.2231e-02
   4_adp:   7.374  0.037  0.435 82.863  0.035  2.322   4.2231e-02
   4_occ:   7.374  0.037  0.435 82.863  0.035  2.322   4.2231e-02
   5_bss:   7.374  0.037  0.435 82.863  0.035  2.322   4.2231e-02
   5_xyz:   6.020  0.043  0.379 83.906  0.032  2.336   3.0411e-02
   5_adp:   6.020  0.043  0.379 83.906  0.032  2.336   3.0411e-02
   5_occ:   6.020  0.043  0.379 83.906  0.032  2.336   3.0411e-02
   5_bss:   6.020  0.043  0.379 83.906  0.032  2.336   3.0411e-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:  81.39   0.00  12.83  81.39   0.00  10.32  81.00   0.00  26.47
   1_occ:  81.39   0.00  12.83  81.39   0.00  10.32  81.00   0.00  26.47
   2_bss:  81.39   0.00  12.83  81.39   0.00  10.32  81.00   0.00  26.47
   2_xyz:  81.39   0.00  12.83  81.39   0.00  10.32  81.00   0.00  26.47
   2_adp:  81.79   0.00  12.85  81.79   0.00   9.52  76.25   0.00  31.00
   2_occ:  81.79   0.00  12.85  81.79   0.00   9.52  76.25   0.00  31.00
   3_bss:  81.79   0.00  12.85  81.79   0.00   9.52  76.25   0.00  31.00
   3_xyz:  81.79   0.00  12.85  81.79   0.00   9.52  76.25   0.00  31.00
   3_adp:  86.02   0.00  13.33  86.02   0.00   8.91  80.52   2.52  37.39
   3_occ:  86.02   0.00  13.33  86.02   0.00   8.91  80.52   2.52  37.39
   4_bss:  86.02   0.00  13.33  86.02   0.00   8.91  80.52   2.52  37.39
   4_xyz:  86.02   0.00  13.33  86.02   0.00   8.91  80.52   2.52  37.39
   4_adp:  87.54   0.00  12.90  87.54   0.00   8.69  84.05   2.64  35.84
   4_occ:  87.54   0.00  12.90  87.54   0.00   8.69  84.05   2.64  35.84
   5_bss:  87.54   0.00  12.90  87.54   0.00   8.69  84.05   2.64  35.84
   5_xyz:  87.54   0.00  12.90  87.54   0.00   8.69  84.05   2.64  35.84
   5_adp:  93.17   0.00  13.02  93.17   0.00   8.71  87.27   2.50  36.54
   5_occ:  93.17   0.00  13.02  93.17   0.00   8.71  87.27   2.50  36.54
   5_bss:  95.22   2.04  15.07  95.22   2.04  10.75  89.32   4.54  38.58
------------------------------------------------------------------------
 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:    1.217    0.014    0.403
   1_adp:    1.217    0.014    0.403
   1_occ:    1.217    0.014    0.403
   2_bss:    1.217    0.014    0.403
   2_xyz:    1.547    0.032    0.571
   2_adp:    1.547    0.032    0.571
   2_occ:    1.547    0.032    0.571
   3_bss:    1.547    0.032    0.571
   3_xyz:    1.510    0.020    0.658
   3_adp:    1.510    0.020    0.658
   3_occ:    1.510    0.020    0.658
   4_bss:    1.510    0.020    0.658
   4_xyz:    1.624    0.039    0.686
   4_adp:    1.624    0.039    0.686
   4_occ:    1.624    0.039    0.686
   5_bss:    1.624    0.039    0.686
   5_xyz:    1.687    0.037    0.697
   5_adp:    1.687    0.037    0.697
   5_occ:    1.687    0.037    0.697
   5_bss:    1.687    0.037    0.697
------------------------------------------------------------------------

CPU time actual refinement: 334.99


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_528/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_528/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_528/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_528/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_528/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.84 
  Macro-tasks:
    bulk solvent and scale       = 44.49  
    individual site refinement   = 135.32 
    weights calculation          = 33.28  
    collect and process          = 6.75   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 219.96 
  Micro-tasks:
    mask                            = 2.22   
    f_calc                          = 102.68 
    alpha_beta                      = 8.72   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 107.94 
    fmodel                         = 7.58   
    r_factors                      = 0.19   
    phase_errors                   = 11.44  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 242.20 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.709 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    640 calls, 102.16 s
gradients_fft:          586 calls,  96.61 s

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

# Date 2008-01-16 Time 01:46:54 PST -0800 (1200476814.73 s)
Start R-work = 0.4701, R-free = 0.4686 (no bulk solvent and anisotropic scale)
Final R-work = 0.1324, R-free = 0.1791 (no bulk solvent and anisotropic scale)

Start R-work = 0.4615, R-free = 0.4582
Final R-work = 0.1157, R-free = 0.1625