# Date 2008-01-16 Time 03:30:36 PST -0800 (1200483036.18 s)
#phil __OFF__

Command line arguments: "../1264.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25250
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1264

-------------------------------------------------------------------------------
  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: (72.0062, 46.6953, 88.5498, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3688 1.99366
Completeness in resolution range: 0.935304
Completeness with d_max=infinity: 0.932632

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3688
                             d_min =   1.9937

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: (72.0062, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3688 1.99366
Completeness in resolution range: 0.935304
Completeness with d_max=infinity: 0.932632

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3693 -  4.2674 [2202/2229]  1981   221  10.0%
  bin  2:  4.2674 -  3.3992 [2118/2138]  1906   212  10.0%
  bin  3:  3.3992 -  2.9731 [2084/2103]  1878   206   9.9%
  bin  4:  2.9731 -  2.7029 [2069/2099]  1859   210  10.1%
  bin  5:  2.7029 -  2.5100 [2057/2076]  1859   198   9.6%
  bin  6:  2.5100 -  2.3626 [2055/2080]  1842   213  10.4%
  bin  7:  2.3626 -  2.2446 [2032/2060]  1826   206  10.1%
  bin  8:  2.2446 -  2.1472 [2015/2051]  1813   202  10.0%
  bin  9:  2.1472 -  2.0647 [2033/2075]  1836   197   9.7%
  bin 10:  2.0647 -  1.9937 [ 924/2033]   830    94  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1264/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:
        1.81 -     2.42: 11
        2.42 -     3.04: 2166
        3.04 -     3.66: 4590
        3.66 -     4.28: 8855
        4.28 -     4.90: 12144
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.171 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.171 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.323 3.040 -x,y-1/2,-z+1/2
  ... (remaining 27761 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_1264/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1264/model_refine_001.geo

CPU time processing inputs: 9.03


============================ 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 = 72.00625 46.69535 88.54975 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: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5002   r_free= 0.4932   ksol= 0.00   Bsol= 0.00   scale= 0.763    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.299738                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.7604 0.99   1426  158 0.4178 0.3930      6.6403      6.5839|
|  2:  4.7604 -  3.7972 0.99   1381  155 0.4273 0.4615      6.8405      6.9282|
|  3:  3.7972 -  3.3228 0.99   1342  144 0.4735 0.4242      6.7049      6.6557|
|  4:  3.3228 -  3.0215 0.99   1345  156 0.5027 0.4653      6.5487      6.4982|
|  5:  3.0215 -  2.8063 0.99   1333  149 0.5284 0.5105      6.3823      6.3903|
|  6:  2.8063 -  2.6417 0.99   1332  147 0.5158 0.5681       6.277      6.2249|
|  7:  2.6417 -  2.5100 0.99   1324  138 0.5514 0.5150      6.2513      6.1948|
|  8:  2.5100 -  2.4012 0.98   1302  153 0.5493 0.5292      6.1832      6.1939|
|  9:  2.4012 -  2.3091 0.98   1302  144 0.5312 0.6191      6.1262      6.2028|
| 10:  2.3091 -  2.2296 1.00   1323  151 0.5398 0.5154      6.1008      6.0775|
| 11:  2.2296 -  2.1601 0.98   1307  139 0.5315 0.4860      6.0383      6.0474|
| 12:  2.1601 -  2.0985 0.98   1293  144 0.5372 0.5205      5.9462      5.9787|
| 13:  2.0985 -  2.0434 0.96   1259  139 0.5388 0.4829      5.8846      5.7964|
| 14:  2.0434 -  1.9937 0.28    361   42 0.5229 0.5594      5.8444      5.8596|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3693 -  4.7604  1426   158  0.68  36.24   0.77     0.71      79729.35|
|  2:  4.7604 -  3.7972  1381   155  0.67  37.42   0.85     0.74     120281.93|
|  3:  3.7972 -  3.3228  1342   144  0.56  47.18   0.80     0.68     126967.02|
|  4:  3.3228 -  3.0215  1345   156  0.46  54.92   0.76     0.56     112298.28|
|  5:  3.0215 -  2.8063  1333   149  0.37  62.28   0.71     0.45      89447.63|
|  6:  2.8063 -  2.6417  1332   147  0.31  66.94   0.70     0.35      79766.42|
|  7:  2.6417 -  2.5100  1324   138  0.26  70.55   0.70     0.30      73710.00|
|  8:  2.5100 -  2.4012  1302   153  0.23  73.04   0.69     0.27      67664.02|
|  9:  2.4012 -  2.3091  1302   144  0.24  71.77   0.70     0.29      62168.62|
| 10:  2.3091 -  2.2296  1323   151  0.25  71.30   0.72     0.29      55031.07|
| 11:  2.2296 -  2.1601  1307   139  0.26  70.97   0.76     0.32      51407.05|
| 12:  2.1601 -  2.0985  1293   144  0.27  70.13   0.71     0.34      46251.04|
| 13:  2.0985 -  2.0434  1259   139  0.27  70.03   0.69     0.35      39758.40|
| 14:  2.0434 -  1.9937   361    42  0.31  66.79   0.71     0.33      31380.64|
|alpha:            min =        0.27 max =            0.74 mean =         0.44|
|beta:             min =    31380.64 max =       126967.02 mean =     76831.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.53|
|phase err.(test): min =        0.00 max =           89.93 mean =        61.44|
|-----------------------------------------------------------------------------|

============================== 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 = 19.768646             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.798   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.881451              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.848   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      676 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1478 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2578 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3847 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4998 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6415 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7575 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.583 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.641 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    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: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5042   r_free= 0.4990   ksol= 0.00   Bsol= 0.00   scale= 0.736    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.300545                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4928   r_free= 0.4859   ksol= 0.32   Bsol= 50.00   scale= 0.948   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.68,5.87,10.54,0.00,0.00,0.00); trace/3= 8.36                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.296280                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.441094             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.501   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.613654              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.475   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4928      final r-factor (work) = 0.4245          |
| start r-factor (free) = 0.4859      final r-factor (free) = 0.4436          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 109.4750 = 17.44 * 0.50 * 6.2946 + 1.00 * 54.5828                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.5205 = 17.44 * 0.50 * 6.2341 + 1.00 * 0.1559                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4245      final r-factor (work) = 0.3783          |
| start r-factor (free) = 0.4436      final r-factor (free) = 0.4310          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0741 = 1.61 * 1.00 * 6.2341 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9737 = 1.61 * 1.00 * 6.1675 + 1.00 * 0.0216                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.27   16.56    None  None   None       |
|    all(noH): 2823   0      0.00    87.27   16.56    None  None   None       |
|    Sol.    : 438    0      0.00    84.66   29.56    None  None   None       |
|    Mac.    : 2385   0      0.00    87.27   14.18    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 -   8.727: 1063   |   5:    43.635 -  52.362:   93        |
|      1:     8.727 -  17.454:  729   |   6:    52.362 -  61.089:   39        |
|      2:    17.454 -  26.181:  411   |   7:    61.089 -  69.816:   31        |
|      3:    26.181 -  34.908:  282   |   8:    69.816 -  78.543:   14        |
|      4:    34.908 -  43.635:  154   |   9:    78.543 -  87.270:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3783 r_free = 0.4310             target_work(ml) = 6.152         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3780 r_free = 0.4315             target_work(ml) = 6.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3780   r_free= 0.4315   ksol= 0.32   Bsol= 50.00   scale= 1.093   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.68,5.87,10.54,0.00,0.00,0.00); trace/3= 8.36                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.151601                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3762   r_free= 0.4298   ksol= 0.34   Bsol= 69.66   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.12,3.16,7.01,0.00,0.00,0.00); trace/3= 5.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.153147                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.141481             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.774   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.587084              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.733  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3762      final r-factor (work) = 0.2988          |
| start r-factor (free) = 0.4298      final r-factor (free) = 0.3624          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.4813 = 11.14 * 0.50 * 6.1617 + 1.00 * 0.1559                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.9008 = 11.14 * 0.50 * 6.0657 + 1.00 * 0.1101                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2988      final r-factor (work) = 0.2767          |
| start r-factor (free) = 0.3624      final r-factor (free) = 0.3359          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5829 = 0.59 * 1.00 * 6.0657 + 1.00 * 0.0218                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5038 = 0.59 * 1.00 * 5.9458 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.81   15.56    None  None   None       |
|    all(noH): 2823   0      0.00    84.81   15.56    None  None   None       |
|    Sol.    : 438    0      0.00    84.81   33.96    None  None   None       |
|    Mac.    : 2385   0      0.00    84.25   12.18    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 -   8.481: 1156   |   5:    42.404 -  50.885:   79        |
|      1:     8.481 -  16.962:  731   |   6:    50.885 -  59.366:   39        |
|      2:    16.962 -  25.443:  376   |   7:    59.366 -  67.847:   31        |
|      3:    25.443 -  33.924:  239   |   8:    67.847 -  76.328:    9        |
|      4:    33.924 -  42.404:  153   |   9:    76.328 -  84.809:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2767 r_free = 0.3359             target_work(ml) = 5.915         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2765 r_free = 0.3353             target_work(ml) = 5.914         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2765   r_free= 0.3353   ksol= 0.34   Bsol= 69.66   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.12,3.16,7.01,0.00,0.00,0.00); trace/3= 5.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.914423                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2752   r_free= 0.3352   ksol= 0.34   Bsol= 67.61   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.60,1.79,4.57,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.916043                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.138203              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.299   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.551696              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.934  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2752      final r-factor (work) = 0.2146          |
| start r-factor (free) = 0.3352      final r-factor (free) = 0.2765          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3874 = 5.14 * 0.50 * 5.9465 + 1.00 * 0.1101                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0318 = 5.14 * 0.50 * 5.8218 + 1.00 * 0.0750                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2146      final r-factor (work) = 0.1913          |
| start r-factor (free) = 0.2765      final r-factor (free) = 0.2596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.6905 = 3.55 * 1.00 * 5.8218 + 1.00 * 0.0132                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.1380 = 3.55 * 1.00 * 5.6639 + 1.00 * 0.0217                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.93  16.79    None  None   None       |
|    all(noH): 2823   0      0.00    112.93  16.79    None  None   None       |
|    Sol.    : 438    0      0.00    109.49  45.09    None  None   None       |
|    Mac.    : 2385   0      0.00    112.93  11.59    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 -  11.293: 1569   |   5:    56.467 -  67.761:   82        |
|      1:    11.293 -  22.587:  639   |   6:    67.761 -  79.054:   51        |
|      2:    22.587 -  33.880:  211   |   7:    79.054 -  90.347:   26        |
|      3:    33.880 -  45.174:  123   |   8:    90.347 - 101.641:   12        |
|      4:    45.174 -  56.467:  105   |   9:   101.641 - 112.934:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1913 r_free = 0.2596             target_work(ml) = 5.636         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1909 r_free = 0.2598             target_work(ml) = 5.635         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1909   r_free= 0.2598   ksol= 0.34   Bsol= 67.61   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.60,1.79,4.57,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.635170                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1912   r_free= 0.2592   ksol= 0.35   Bsol= 86.62   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,1.04,3.41,0.00,0.00,0.00); trace/3= 2.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.634436                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.532388              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.301  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.260954              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.136  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1912      final r-factor (work) = 0.1586          |
| start r-factor (free) = 0.2592      final r-factor (free) = 0.2205          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9158 = 4.53 * 0.50 * 5.6663 + 1.00 * 0.0750                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6843 = 4.53 * 0.50 * 5.5628 + 1.00 * 0.0780                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1586      final r-factor (work) = 0.1519          |
| start r-factor (free) = 0.2205      final r-factor (free) = 0.2059          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4731 = 0.26 * 1.00 * 5.5628 + 1.00 * 0.0215                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4359 = 0.26 * 1.00 * 5.4580 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.62   14.96    None  None   None       |
|    all(noH): 2823   0      0.00    91.62   14.96    None  None   None       |
|    Sol.    : 438    0      2.68    91.62   40.10    None  None   None       |
|    Mac.    : 2385   0      0.00    90.07   10.34    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 -   9.162: 1423   |   5:    45.809 -  54.971:   87        |
|      1:     9.162 -  18.324:  778   |   6:    54.971 -  64.133:   53        |
|      2:    18.324 -  27.486:  190   |   7:    64.133 -  73.295:   35        |
|      3:    27.486 -  36.647:  126   |   8:    73.295 -  82.457:   16        |
|      4:    36.647 -  45.809:  106   |   9:    82.457 -  91.619:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1519 r_free = 0.2059             target_work(ml) = 5.416         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1517 r_free = 0.2056             target_work(ml) = 5.415         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1517   r_free= 0.2056   ksol= 0.35   Bsol= 86.62   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,1.04,3.41,0.00,0.00,0.00); trace/3= 2.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.415344                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1517   r_free= 0.2057   ksol= 0.34   Bsol= 76.66   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.01,0.52,2.57,0.00,0.00,0.00); trace/3= 1.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.416224                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.003911              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.900  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.170554              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.959  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1517      final r-factor (work) = 0.1322          |
| start r-factor (free) = 0.2057      final r-factor (free) = 0.1834          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0082 = 4.00 * 0.50 * 5.4598 + 1.00 * 0.0780                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8296 = 4.00 * 0.50 * 5.3643 + 1.00 * 0.0905                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1322      final r-factor (work) = 0.1304          |
| start r-factor (free) = 0.1834      final r-factor (free) = 0.1800          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9263 = 0.17 * 1.00 * 5.3643 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9132 = 0.17 * 1.00 * 5.2976 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.87   14.46    None  None   None       |
|    all(noH): 2823   0      0.00    86.87   14.46    None  None   None       |
|    Sol.    : 438    0      3.17    86.87   38.11    None  None   None       |
|    Mac.    : 2385   0      0.00    77.48   10.12    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 -   8.687: 1347   |   5:    43.434 -  52.120:   95        |
|      1:     8.687 -  17.373:  848   |   6:    52.120 -  60.807:   53        |
|      2:    17.373 -  26.060:  204   |   7:    60.807 -  69.494:   30        |
|      3:    26.060 -  34.747:  115   |   8:    69.494 -  78.180:   16        |
|      4:    34.747 -  43.434:  106   |   9:    78.180 -  86.867:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1304 r_free = 0.1800             target_work(ml) = 5.286         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1302 r_free = 0.1800             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1302   r_free= 0.1800   ksol= 0.34   Bsol= 76.66   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.01,0.52,2.57,0.00,0.00,0.00); trace/3= 1.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.284885                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.7604 0.99   1426  158 0.1056 0.1485      5.4641       5.665|
|  2:  4.7604 -  3.7972 0.99   1381  155 0.0921 0.1247      5.5249        5.73|
|  3:  3.7972 -  3.3228 0.99   1342  144 0.1208 0.1716      5.5837       5.894|
|  4:  3.3228 -  3.0215 0.99   1345  156 0.1417 0.1913      5.5752      5.7722|
|  5:  3.0215 -  2.8063 0.99   1333  149 0.1608 0.1977      5.4918      5.6851|
|  6:  2.8063 -  2.6417 0.99   1332  147 0.1501 0.2240      5.3602       5.594|
|  7:  2.6417 -  2.5100 0.99   1324  138 0.1496 0.1821      5.3089       5.453|
|  8:  2.5100 -  2.4012 0.98   1302  153 0.1424 0.1873      5.2227      5.4439|
|  9:  2.4012 -  2.3091 0.98   1302  144 0.1440 0.2263      5.1904      5.4776|
| 10:  2.3091 -  2.2296 1.00   1323  151 0.1349 0.1815      5.0887      5.2465|
| 11:  2.2296 -  2.1601 0.98   1307  139 0.1361 0.2005      5.0683      5.4058|
| 12:  2.1601 -  2.0985 0.98   1293  144 0.1331 0.1992      4.9738      5.2301|
| 13:  2.0985 -  2.0434 0.96   1259  139 0.1330 0.1865      4.9093      5.1117|
| 14:  2.0434 -  1.9937 0.28    361   42 0.1277 0.1703      4.8282      5.0037|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3693 -  4.7604  1426   158  0.93  10.30   0.97     0.94       8757.10|
|  2:  4.7604 -  3.7972  1381   155  0.95   9.17   1.00     0.98      11118.31|
|  3:  3.7972 -  3.3228  1342   144  0.92  13.47   1.01     1.02      13189.91|
|  4:  3.3228 -  3.0215  1345   156  0.90  16.43   1.00     0.98      13395.84|
|  5:  3.0215 -  2.8063  1333   149  0.87  19.01   0.99     0.97      11350.76|
|  6:  2.8063 -  2.6417  1332   147  0.87  19.35   0.97     0.94       9461.60|
|  7:  2.6417 -  2.5100  1324   138  0.88  18.51   0.99     0.95       8315.31|
|  8:  2.5100 -  2.4012  1302   153  0.88  18.66   0.99     0.96       7110.70|
|  9:  2.4012 -  2.3091  1302   144  0.88  18.96   1.00     0.94       6784.86|
| 10:  2.3091 -  2.2296  1323   151  0.88  18.13   1.01     0.97       5615.45|
| 11:  2.2296 -  2.1601  1307   139  0.88  18.39   1.00     0.94       5401.55|
| 12:  2.1601 -  2.0985  1293   144  0.89  18.05   1.00     0.99       4808.23|
| 13:  2.0985 -  2.0434  1259   139  0.87  19.68   0.99     0.97       4399.56|
| 14:  2.0434 -  1.9937   361    42  0.90  16.88   0.97     0.94       3490.97|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     3490.97 max =        13395.84 mean =      8389.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.70|
|phase err.(test): min =        0.00 max =           89.24 mean =        16.06|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1800   ksol= 0.32   Bsol= 66.65   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.32,-0.80,1.13,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.284763                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1800   ksol= 0.32   Bsol= 66.65   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.32,-0.80,1.13,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.284763                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.7604 0.99   1426  158 0.1051 0.1479       5.458      5.6613|
|  2:  4.7604 -  3.7972 0.99   1381  155 0.0916 0.1244      5.5209      5.7262|
|  3:  3.7972 -  3.3228 0.99   1342  144 0.1206 0.1713      5.5821       5.893|
|  4:  3.3228 -  3.0215 0.99   1345  156 0.1420 0.1918       5.577      5.7745|
|  5:  3.0215 -  2.8063 0.99   1333  149 0.1611 0.1977      5.4938      5.6872|
|  6:  2.8063 -  2.6417 0.99   1332  147 0.1505 0.2249      5.3625      5.5973|
|  7:  2.6417 -  2.5100 0.99   1324  138 0.1498 0.1823      5.3106      5.4545|
|  8:  2.5100 -  2.4012 0.98   1302  153 0.1425 0.1875      5.2239      5.4453|
|  9:  2.4012 -  2.3091 0.98   1302  144 0.1441 0.2264       5.191      5.4781|
| 10:  2.3091 -  2.2296 1.00   1323  151 0.1351 0.1816      5.0894      5.2462|
| 11:  2.2296 -  2.1601 0.98   1307  139 0.1361 0.2002       5.068      5.4045|
| 12:  2.1601 -  2.0985 0.98   1293  144 0.1331 0.1994      4.9739      5.2306|
| 13:  2.0985 -  2.0434 0.96   1259  139 0.1331 0.1866      4.9099      5.1124|
| 14:  2.0434 -  1.9937 0.28    361   42 0.1277 0.1704      4.8289      5.0046|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3693 -  4.7604  1426   158  0.93  10.27   0.97     0.94       8695.79|
|  2:  4.7604 -  3.7972  1381   155  0.95   9.14   1.00     0.98      11060.64|
|  3:  3.7972 -  3.3228  1342   144  0.92  13.43   1.01     1.01      13145.86|
|  4:  3.3228 -  3.0215  1345   156  0.90  16.43   0.99     0.97      13415.26|
|  5:  3.0215 -  2.8063  1333   149  0.87  19.04   0.98     0.96      11404.08|
|  6:  2.8063 -  2.6417  1332   147  0.87  19.41   0.97     0.93       9508.17|
|  7:  2.6417 -  2.5100  1324   138  0.88  18.56   0.98     0.94       8353.22|
|  8:  2.5100 -  2.4012  1302   153  0.88  18.70   0.98     0.95       7134.03|
|  9:  2.4012 -  2.3091  1302   144  0.88  18.99   0.99     0.93       6805.32|
| 10:  2.3091 -  2.2296  1323   151  0.88  18.13   1.00     0.96       5617.03|
| 11:  2.2296 -  2.1601  1307   139  0.88  18.38   0.99     0.93       5396.79|
| 12:  2.1601 -  2.0985  1293   144  0.89  18.03   0.99     0.98       4804.80|
| 13:  2.0985 -  2.0434  1259   139  0.87  19.68   0.98     0.96       4403.50|
| 14:  2.0434 -  1.9937   361    42  0.90  16.90   0.96     0.93       3496.57|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     3496.57 max =        13415.26 mean =      8391.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.70|
|phase err.(test): min =        0.00 max =           89.24 mean =        16.08|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.16    88.03   15.62    None  None   None       |
|    all(noH): 2823   0      1.16    88.03   15.62    None  None   None       |
|    Sol.    : 438    0      4.33    88.03   39.27    None  None   None       |
|    Mac.    : 2385   0      1.16    78.64   11.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.160 -   9.847: 1347   |   5:    44.593 -  53.280:   95        |
|      1:     9.847 -  18.533:  848   |   6:    53.280 -  61.967:   53        |
|      2:    18.533 -  27.220:  204   |   7:    61.967 -  70.654:   30        |
|      3:    27.220 -  35.907:  115   |   8:    70.654 -  79.340:   16        |
|      4:    35.907 -  44.593:  106   |   9:    79.340 -  88.027:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 334         
Filter by distance & map next to the model:
   mapped sites are within: 0.369 - 4.921
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 334
   mapped sites are within: 0.718 - 4.921

peak=   10.185 closest distance to " CB  VAL A 230 " =    1.480
peak=    7.687 closest distance to " O   HOH Z 103 " =    0.995
peak=    7.670 closest distance to " O   HOH Z  70 " =    1.681
peak=    7.268 closest distance to " CG2 VAL A 296 " =    1.316
peak=    6.298 closest distance to " CG  ARG A 138 " =    1.261
peak=    6.243 closest distance to " CD2 LEU A   5 " =    1.263
peak=    5.640 closest distance to " O   HOH Z 222 " =    1.422
peak=    5.446 closest distance to " O   HOH Z 102 " =    1.449
peak=    5.004 closest distance to " NE2 GLN A  11 " =    1.164
peak=    4.965 closest distance to " CB  GLN A 223 " =    1.563
peak=    4.904 closest distance to " O   HOH Z 144 " =    2.126
peak=    4.896 closest distance to " NH1 ARG A 138 " =    1.102
peak=    4.888 closest distance to " O   HOH Z 232 " =    2.073
peak=    4.797 closest distance to " NH1 ARG A  56 " =    1.163
peak=    4.791 closest distance to " CB  ASP A 124 " =    0.793
peak=    4.760 closest distance to " CG  LEU A   5 " =    1.257
peak=    4.739 closest distance to " O   HOH Z 369 " =    1.905
peak=    4.730 closest distance to " O   HOH Z  42 " =    2.076
peak=    4.723 closest distance to " CG  PRO A  54 " =    1.410
peak=    4.677 closest distance to " NH1AARG A 145 " =    1.255
peak=    4.663 closest distance to " O   HOH Z   7 " =    1.510
peak=    4.650 closest distance to " CB  SER A  63 " =    1.348
peak=    4.499 closest distance to " O   HOH Z   9 " =    1.949
peak=    4.494 closest distance to " CB  ASN A 148 " =    1.419
peak=    4.454 closest distance to " CZ  PHE A 218 " =    1.100
peak=    4.450 closest distance to " CG  PRO A 280 " =    1.059
peak=    4.449 closest distance to " CG  LEU A 228 " =    1.218
peak=    4.370 closest distance to " CD2 LEU A 228 " =    1.382
peak=    4.339 closest distance to " CG  ASN A  60 " =    1.152
peak=    4.326 closest distance to " O   HOH Z 406 " =    1.644
peak=    4.300 closest distance to " O   HOH Z 298 " =    2.343
peak=    4.292 closest distance to " CA  VAL A 230 " =    1.186
peak=    4.269 closest distance to " O   HOH Z 425 " =    1.615
peak=    4.249 closest distance to " O   HOH Z 265 " =    1.884
peak=    4.245 closest distance to " CA  ALA A  51 " =    0.976
peak=    4.218 closest distance to " CG  LEU A 167 " =    1.278
peak=    4.208 closest distance to " OE1 GLN A  55 " =    1.327
peak=    4.201 closest distance to " O   HOH Z 287 " =    2.198
peak=    4.201 closest distance to " NH2 ARG A  56 " =    1.392
peak=    4.182 closest distance to " CB  ASN A  60 " =    0.962
peak=    4.156 closest distance to " O   PRO A 198 " =    1.544
peak=    4.135 closest distance to " CB  VAL A 265 " =    1.362
peak=    4.131 closest distance to " CB  GLN A 183 " =    1.241
peak=    4.109 closest distance to " O   SER A  87 " =    2.315
peak=    4.101 closest distance to " CZ3 TRP A 266 " =    1.110
peak=    4.084 closest distance to " O   HOH Z 411 " =    3.044
peak=    4.050 closest distance to " O   HOH Z 250 " =    1.233
peak=    4.047 closest distance to " O   HOH Z 193 " =    1.986
peak=    4.041 closest distance to " O   HOH Z 111 " =    1.688
peak=    4.040 closest distance to " CB  GLU A 152 " =    1.238
peak=    4.032 closest distance to " O   HOH Z  57 " =    1.673
peak=    4.019 closest distance to " O   HOH Z 290 " =    1.700
peak=    3.982 closest distance to " O   HOH Z 184 " =    1.755
peak=    3.974 closest distance to " CB  PRO A  54 " =    0.987
peak=    3.955 closest distance to " CA  ASN A 127 " =    1.087
peak=    3.949 closest distance to " CE3 TRP A  85 " =    1.060
peak=    3.928 closest distance to " CD  ARG A 159 " =    0.728
peak=    3.921 closest distance to " OE1 GLN A 278 " =    1.319
peak=    3.914 closest distance to " CB  ASN A  39 " =    0.901
peak=    3.914 closest distance to " O   HOH Z 185 " =    1.968
peak=    3.888 closest distance to " CB  TRP A 266 " =    0.966
peak=    3.880 closest distance to " ND2 ASN A 187 " =    1.560
peak=    3.861 closest distance to " O   HOH Z 188 " =    2.901
peak=    3.857 closest distance to " CA  ASP A 162 " =    0.783
peak=    3.849 closest distance to " O   HOH Z 145 " =    1.746
peak=    3.836 closest distance to " O   HOH Z 427 " =    3.025
peak=    3.823 closest distance to " N   PHE A 130 " =    1.274
peak=    3.813 closest distance to " O   HOH Z 410 " =    1.472
peak=    3.806 closest distance to " CD  ARG A 195 " =    3.563
peak=    3.805 closest distance to " CG  PRO A 243 " =    1.053
peak=    3.800 closest distance to " CB  SER A 216 " =    0.966
peak=    3.792 closest distance to " CA  ALA A 184 " =    1.123
peak=    3.788 closest distance to " O   HOH Z 221 " =    1.520
peak=    3.786 closest distance to " CB  ASN A 142 " =    0.914
peak=    3.775 closest distance to " CG  PRO A 198 " =    1.347
peak=    3.772 closest distance to " CA  LEU A 282 " =    1.086
peak=    3.762 closest distance to " CA  ARG A 195 " =    1.390
peak=    3.750 closest distance to " O   ASP A 132 " =    4.036
peak=    3.736 closest distance to " CE  LYS A  76 " =    0.963
peak=    3.710 closest distance to " O   HOH Z 117 " =    1.211
peak=    3.704 closest distance to " O   HOH Z 303 " =    2.359
peak=    3.689 closest distance to " OE2 GLU A   2 " =    2.177
peak=    3.687 closest distance to " CG  ARG A 269 " =    1.848
peak=    3.682 closest distance to " O   HOH Z 148 " =    3.776
peak=    3.672 closest distance to " O   HOH Z 423 " =    1.693
peak=    3.662 closest distance to " CB  ALA A 242 " =    0.845
peak=    3.661 closest distance to " CD  ARG A 138 " =    1.372
peak=    3.655 closest distance to " CB  LEU A 237 " =    0.851
peak=    3.652 closest distance to " CB  ARG A 275 " =    1.060
peak=    3.644 closest distance to " O   HOH Z 313 " =    1.888
peak=    3.638 closest distance to " CA  ARG A 139 " =    1.140
peak=    3.637 closest distance to " CA  TYR A 116 " =    1.454
peak=    3.635 closest distance to " CA  ARG A 102 " =    1.125
peak=    3.628 closest distance to " CB  SER A   3 " =    1.748
peak=    3.627 closest distance to " CD  ARG A 269 " =    0.876
peak=    3.626 closest distance to " O   TYR A 116 " =    1.169
peak=    3.624 closest distance to " CB  ARG A 138 " =    1.465
peak=    3.623 closest distance to " CG2 THR A 221 " =    1.010
peak=    3.616 closest distance to " O   THR A 182 " =    1.408
peak=    3.613 closest distance to " CD1 LEU A 300 " =    1.174
peak=    3.612 closest distance to " CG  PRO A 213 " =    1.375
peak=    3.608 closest distance to " CB  GLU A  46 " =    0.959
peak=    3.604 closest distance to " CB  TYR A 169 " =    0.730
peak=    3.594 closest distance to " CG1 ILE A 151 " =    1.374
peak=    3.594 closest distance to " O   PRO A 198 " =    1.389
peak=    3.594 closest distance to " OD1 ASN A 217 " =    1.451
peak=    3.592 closest distance to " CA  ALA A 160 " =    1.211
peak=    3.592 closest distance to " CD  ARG A  66 " =    2.285
peak=    3.591 closest distance to " CG1 VAL A 296 " =    1.246
peak=    3.586 closest distance to " NH2AARG A 145 " =    1.096
peak=    3.584 closest distance to " CB  ARG A 190 " =    1.482
peak=    3.581 closest distance to " CB  ALA A   1 " =    4.921
peak=    3.577 closest distance to " CB  VAL A 202 " =    1.459
peak=    3.573 closest distance to " CG1 ILE A  49 " =    1.597
peak=    3.564 closest distance to " CA  PRO A  54 " =    0.813
peak=    3.563 closest distance to " NH1 ARG A  14 " =    0.931
peak=    3.562 closest distance to " CD  LYS A 166 " =    1.269
peak=    3.560 closest distance to " CG1 VAL A 153 " =    0.939
peak=    3.559 closest distance to " O   HOH Z  59 " =    1.852
peak=    3.557 closest distance to " CD1 ILE A  33 " =    1.998
peak=    3.550 closest distance to " NE2 HIS A 207 " =    1.097
peak=    3.549 closest distance to " CD1AILE A 234 " =    0.971
peak=    3.549 closest distance to " O   HOH Z 272 " =    1.804
peak=    3.544 closest distance to " CB  ALA A 248 " =    1.063
peak=    3.541 closest distance to " CB  TYR A  30 " =    1.198
peak=    3.540 closest distance to " CB  SER A 212 " =    1.296
peak=    3.538 closest distance to " CB  MET A  40 " =    0.803
peak=    3.538 closest distance to " O   HOH Z  88 " =    3.824
peak=    3.534 closest distance to " O   HOH Z 112 " =    1.057
peak=    3.533 closest distance to " N   SER A 271 " =    1.004
peak=    3.527 closest distance to " CA  ILE A 234 " =    1.075
peak=    3.525 closest distance to " CD2 TRP A 179 " =    1.303
peak=    3.524 closest distance to " CG BARG A 275 " =    1.304
peak=    3.518 closest distance to " CA  GLY A 196 " =    0.735
peak=    3.517 closest distance to " O   HOH Z 298 " =    4.211
peak=    3.513 closest distance to " CB  GLU A 277 " =    3.678
peak=    3.510 closest distance to " O   HOH Z 258 " =    2.173
peak=    3.505 closest distance to " O   HOH Z 250 " =    1.030
peak=    3.505 closest distance to " O   HOH Z   4 " =    1.884
peak=    3.504 closest distance to " CD  GLN A 240 " =    1.610
peak=    3.503 closest distance to " CB  LEU A 228 " =    1.221
peak=    3.500 closest distance to " O   HOH Z  88 " =    3.236
peak=    3.499 closest distance to " CE1 TYR A 186 " =    1.235
peak=    3.496 closest distance to " O   ASP A 200 " =    1.714
peak=    3.496 closest distance to " ND2 ASN A 249 " =    1.990
peak=    3.495 closest distance to " CA  GLN A  94 " =    0.797
peak=    3.485 closest distance to " CD1 LEU A   5 " =    1.319
peak=    3.484 closest distance to " O   HOH Z 126 " =    1.649
peak=    3.484 closest distance to " ND2 ASN A 127 " =    1.115
peak=    3.471 closest distance to " O   HOH Z  53 " =    2.600
peak=    3.467 closest distance to " CG  GLU A  37 " =    0.998
peak=    3.467 closest distance to " N   CYS A 260 " =    0.808
peak=    3.465 closest distance to " CB  SER A 210 " =    0.950
peak=    3.461 closest distance to " O   HOH Z  30 " =    1.759
peak=    3.456 closest distance to " O   HOH Z 251 " =    1.566
peak=    3.453 closest distance to " CB  ALA A   9 " =    1.664
peak=    3.451 closest distance to " CD2 LEU A 255 " =    1.730
peak=    3.446 closest distance to " O   HOH Z 156 " =    2.816
peak=    3.446 closest distance to " CZ  PHE A  38 " =    1.156
peak=    3.445 closest distance to " NH2 ARG A 219 " =    1.581
peak=    3.444 closest distance to " CA  TYR A  30 " =    1.069
peak=    3.444 closest distance to " N   TYR A  15 " =    0.926
peak=    3.441 closest distance to " O   HOH Z  80 " =    1.875
peak=    3.439 closest distance to " OD1 ASP A  65 " =    1.811
peak=    3.437 closest distance to " OG1 THR A 264 " =    0.878
peak=    3.437 closest distance to " O   HOH Z 180 " =    2.196
peak=    3.433 closest distance to " CB  ALA A 100 " =    1.372
peak=    3.433 closest distance to " O   HOH Z  61 " =    1.654
peak=    3.433 closest distance to " O   HOH Z 273 " =    2.583
peak=    3.430 closest distance to " CB  LEU A  83 " =    0.770
peak=    3.422 closest distance to " O   HOH Z 145 " =    1.992
peak=    3.422 closest distance to " CA  ASP A 124 " =    0.759
peak=    3.420 closest distance to " O   HOH Z 214 " =    2.543
peak=    3.413 closest distance to " CB  ILE A 120 " =    1.284
peak=    3.407 closest distance to " CB  GLU A 175 " =    0.898
peak=    3.404 closest distance to " O   HOH Z 332 " =    1.561
peak=    3.400 closest distance to " CB  TYR A 169 " =    0.776
peak=    3.399 closest distance to " O   HOH Z 408 " =    3.093
peak=    3.395 closest distance to " CB  ALA A 291 " =    1.038
peak=    3.390 closest distance to " CA  SER A  87 " =    0.809
peak=    3.389 closest distance to " CB  ALA A 104 " =    0.756
peak=    3.387 closest distance to " CG2 VAL A 257 " =    0.886
peak=    3.386 closest distance to " CH2 TRP A  70 " =    1.185
peak=    3.383 closest distance to " O   HOH Z  69 " =    0.947
peak=    3.378 closest distance to " CE3 TRP A 274 " =    1.277
peak=    3.377 closest distance to " O   HOH Z   3 " =    2.076
peak=    3.376 closest distance to " OD1 ASP A 231 " =    1.946
peak=    3.375 closest distance to " CG2 ILE A 234 " =    1.025
peak=    3.373 closest distance to " CB  ALA A  10 " =    0.964
peak=    3.368 closest distance to " O   HOH Z 346 " =    1.668
peak=    3.367 closest distance to " CZ3 TRP A 266 " =    0.968
peak=    3.365 closest distance to " CG  GLN A  88 " =    1.047
peak=    3.364 closest distance to " O   HOH Z 213 " =    1.979
peak=    3.363 closest distance to " N   ASP A 162 " =    1.253
peak=    3.359 closest distance to " CB  GLN A  88 " =    1.374
peak=    3.357 closest distance to " O   MET A 105 " =    1.804
peak=    3.356 closest distance to " CB  PRO A 243 " =    1.325
peak=    3.356 closest distance to " O   HOH Z   2 " =    1.873
peak=    3.355 closest distance to " O   HOH Z  10 " =    1.854
peak=    3.349 closest distance to " O   HOH Z 126 " =    1.917
peak=    3.336 closest distance to " CB  ASP A 171 " =    0.873
peak=    3.332 closest distance to " CB  ARG A  79 " =    1.618
peak=    3.331 closest distance to " O   ALA A 165 " =    1.453
peak=    3.330 closest distance to " CA  ASN A 284 " =    0.881
peak=    3.330 closest distance to " O   THR A 251 " =    1.176
peak=    3.324 closest distance to " ND2BASN A 224 " =    0.994
peak=    3.322 closest distance to " CA  TYR A 186 " =    1.607
peak=    3.322 closest distance to " O   HOH Z 238 " =    3.177
peak=    3.317 closest distance to " O   HOH Z  63 " =    1.866
peak=    3.317 closest distance to " CA  ALA A 295 " =    1.146
peak=    3.315 closest distance to " N   ASN A  39 " =    1.157
peak=    3.314 closest distance to " CB  SER A  62 " =    0.858
peak=    3.313 closest distance to " ND2 ASN A  60 " =    3.091
peak=    3.308 closest distance to " CB  SER A  22 " =    1.073
peak=    3.308 closest distance to " CG  MET A 113 " =    1.677
peak=    3.306 closest distance to " O   HOH Z 411 " =    1.548
peak=    3.305 closest distance to " ND1 HIS A  81 " =    1.884
peak=    3.302 closest distance to " CA  ASP A 191 " =    0.974
peak=    3.302 closest distance to " OG  SER A 135 " =    1.231
peak=    3.298 closest distance to " O   HOH Z 215 " =    2.796
peak=    3.296 closest distance to " O   HOH Z 132 " =    2.667
peak=    3.294 closest distance to " CG  GLN A  89 " =    1.568
peak=    3.292 closest distance to " CB  PHE A 283 " =    0.834
peak=    3.289 closest distance to " OG1 THR A 279 " =    1.486
peak=    3.288 closest distance to " CA  ASP A 149 " =    1.207
peak=    3.286 closest distance to " CG  PHE A 204 " =    0.991
peak=    3.285 closest distance to " OG  SER A  28 " =    1.679
peak=    3.281 closest distance to " CA  ALA A 129 " =    1.325
peak=    3.278 closest distance to " CD ALYS A 290 " =    1.047
peak=    3.277 closest distance to " OG  SER A 276 " =    1.366
peak=    3.276 closest distance to " CB  TRP A 179 " =    1.261
peak=    3.275 closest distance to " NE1 TRP A 274 " =    0.971
peak=    3.270 closest distance to " O   ASN A 209 " =    1.513
peak=    3.265 closest distance to " O   HOH Z  76 " =    1.386
peak=    3.263 closest distance to " CA  VAL A 112 " =    1.110
peak=    3.262 closest distance to " CD  ARG A  14 " =    1.409
peak=    3.260 closest distance to " O   HOH Z 256 " =    1.962
peak=    3.260 closest distance to " CA  GLY A 267 " =    0.949
peak=    3.258 closest distance to " O   HOH Z 325 " =    4.229
peak=    3.257 closest distance to " O   HOH Z 171 " =    4.102
peak=    3.256 closest distance to " O   HOH Z 154 " =    1.794
peak=    3.247 closest distance to " O   HOH Z 124 " =    1.933
peak=    3.245 closest distance to " O   HOH Z  78 " =    2.371
peak=    3.244 closest distance to " O   HOH Z  49 " =    1.154
peak=    3.241 closest distance to " O   HOH Z 188 " =    2.087
peak=    3.240 closest distance to " O   ILE A  49 " =    1.178
peak=    3.239 closest distance to " O   HOH Z 282 " =    1.598
peak=    3.238 closest distance to " CA  ILE A 263 " =    0.997
peak=    3.235 closest distance to " O   HOH Z 398 " =    1.366
peak=    3.234 closest distance to " O   HOH Z 211 " =    1.585
peak=    3.231 closest distance to " CB  ASN A  45 " =    1.098
peak=    3.230 closest distance to " O   HOH Z  56 " =    1.736
peak=    3.230 closest distance to " CA  THR A 264 " =    0.806
peak=    3.228 closest distance to " CB  ASP A 107 " =    1.135
peak=    3.228 closest distance to " CB  ASN A 285 " =    0.909
peak=    3.227 closest distance to " O   HOH Z 409 " =    3.244
peak=    3.226 closest distance to " CG  MET A 185 " =    1.349
peak=    3.222 closest distance to " O   HOH Z  70 " =    1.340
peak=    3.222 closest distance to " O   HOH Z 167 " =    1.591
peak=    3.217 closest distance to " CD2 LEU A 237 " =    1.034
peak=    3.215 closest distance to " N   ARG A 156 " =    1.364
peak=    3.214 closest distance to " O   HOH Z 235 " =    1.678
peak=    3.208 closest distance to " CD1 LEU A  96 " =    0.876
peak=    3.204 closest distance to " CD  PRO A  54 " =    0.943
peak=    3.203 closest distance to " CG BARG A 275 " =    1.543
peak=    3.196 closest distance to " CA  ILE A 106 " =    0.836
peak=    3.196 closest distance to " O   HOH Z 238 " =    3.741
peak=    3.193 closest distance to " O   HOH Z  35 " =    4.839
peak=    3.192 closest distance to " O   HOH Z 368 " =    2.059
peak=    3.190 closest distance to " CB  ARG A 102 " =    0.813
peak=    3.189 closest distance to " CA  GLU A 152 " =    0.970
peak=    3.187 closest distance to " O   HOH Z 109 " =    2.799
peak=    3.186 closest distance to " O   HOH Z 153 " =    3.912
peak=    3.186 closest distance to " N   SER A  12 " =    1.639
peak=    3.178 closest distance to " O   HOH Z 298 " =    2.358
peak=    3.177 closest distance to " O   HOH Z   1 " =    1.893
peak=    3.177 closest distance to " O   HOH Z 302 " =    1.740
peak=    3.175 closest distance to " O   HOH Z 316 " =    3.200
peak=    3.175 closest distance to " O   HOH Z 281 " =    2.547
peak=    3.173 closest distance to " O   HOH Z 116 " =    2.029
peak=    3.172 closest distance to " O   HOH Z 148 " =    2.086
peak=    3.171 closest distance to " O   HOH Z   1 " =    1.744
peak=    3.170 closest distance to " CB  GLU A 236 " =    1.180
peak=    3.166 closest distance to " CA  GLY A 241 " =    0.853
peak=    3.160 closest distance to " O   HOH Z 409 " =    2.571
peak=    3.155 closest distance to " N   ALA A 256 " =    1.109
peak=    3.154 closest distance to " CB  HIS A 108 " =    0.783
peak=    3.153 closest distance to " O   HOH Z  89 " =    1.728
peak=    3.151 closest distance to " O   ASP A 124 " =    1.194
peak=    3.151 closest distance to " O   HOH Z 327 " =    2.116
peak=    3.151 closest distance to " CB  ALA A  21 " =    1.114
peak=    3.149 closest distance to " O   HOH Z 162 " =    2.773
peak=    3.139 closest distance to " CD1 ILE A 199 " =    1.046
peak=    3.139 closest distance to " O   HOH Z 334 " =    1.589
peak=    3.137 closest distance to " O   THR A 220 " =    1.344
peak=    3.135 closest distance to " O   HOH Z 173 " =    1.751
peak=    3.134 closest distance to " N   GLY A 133 " =    3.826
peak=    3.134 closest distance to " O   HOH Z 282 " =    4.159
peak=    3.125 closest distance to " CG2 ILE A 120 " =    1.366
peak=    3.123 closest distance to " O   HOH Z 273 " =    1.767
peak=    3.123 closest distance to " O   HOH Z 417 " =    3.286
peak=    3.123 closest distance to " N   GLU A 152 " =    1.546
peak=    3.122 closest distance to " O   HOH Z  27 " =    1.150
peak=    3.119 closest distance to " CG  GLN A 144 " =    0.880
peak=    3.119 closest distance to " CE2 TYR A 186 " =    0.995
peak=    3.117 closest distance to " CB  ALA A  43 " =    0.917
peak=    3.117 closest distance to " CE1 HIS A 115 " =    1.056
peak=    3.116 closest distance to " CA  LYS A 117 " =    1.160
peak=    3.113 closest distance to " O   HOH Z 403 " =    1.541
peak=    3.112 closest distance to " CG1 ILE A  20 " =    1.281
peak=    3.109 closest distance to " O   HOH Z 345 " =    3.967
peak=    3.103 closest distance to " CG  ARG A 159 " =    0.958
peak=    3.101 closest distance to " O   PHE A  61 " =    1.481
peak=    3.100 closest distance to " O   HOH Z   1 " =    1.674
peak=    3.099 closest distance to " O   HOH Z 110 " =    1.579
peak=    3.095 closest distance to " O   HOH Z 380 " =    1.744
peak=    3.092 closest distance to " C   GLU A 277 " =    1.474
peak=    3.089 closest distance to " CE2 TYR A 169 " =    0.992
peak=    3.073 closest distance to " O   HOH Z 344 " =    2.861
peak=    3.073 closest distance to " CB  ASP A 140 " =    0.718
peak=    3.070 closest distance to " CG  MET A 185 " =    0.936
peak=    3.059 closest distance to " CA  HIS A  86 " =    0.727
peak=    3.057 closest distance to " CG1AVAL A 121 " =    0.841
peak=    3.053 closest distance to " O   HOH Z 134 " =    2.602
peak=    3.050 closest distance to " CD  ARG A 195 " =    0.990
peak=    3.050 closest distance to " O   HOH Z 189 " =    3.793
peak=    3.047 closest distance to " CA  MET A 105 " =    0.846
peak=    3.042 closest distance to " OH  TYR A 214 " =    1.258

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 234         
Filter by distance & map next to the model:
   mapped sites are within: 0.073 - 5.552
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 226 from: 234
   mapped sites are within: 0.715 - 5.552

peak=   -5.572 closest distance to " CG2 VAL A 230 " =    0.715
peak=   -4.701 closest distance to " O   PRO A 198 " =    1.358
peak=   -4.615 closest distance to " CG  ARG A 219 " =    2.527
peak=   -4.581 closest distance to " O   HOH Z 110 " =    1.121
peak=   -4.496 closest distance to " CG1 VAL A 250 " =    2.704
peak=   -4.360 closest distance to " O   HOH Z  52 " =    0.982
peak=   -4.332 closest distance to " CG2 VAL A 296 " =    0.849
peak=   -4.232 closest distance to " OD1 ASN A  60 " =    0.816
peak=   -4.209 closest distance to " OE1 GLN A  55 " =    0.998
peak=   -4.163 closest distance to " O   HOH Z 275 " =    1.891
peak=   -4.154 closest distance to " CD1 LEU A   5 " =    2.559
peak=   -4.100 closest distance to " CD  ARG A  14 " =    3.181
peak=   -4.081 closest distance to " CZ2 TRP A  92 " =    2.915
peak=   -4.068 closest distance to " O   HOH Z 103 " =    1.020
peak=   -4.045 closest distance to " O   PRO A 163 " =    2.093
peak=   -4.026 closest distance to " O   HOH Z 115 " =    1.339
peak=   -4.023 closest distance to " CD  ARG A 138 " =    1.159
peak=   -4.017 closest distance to " O   GLY A 203 " =    2.592
peak=   -4.014 closest distance to " O   HOH Z 216 " =    1.148
peak=   -4.008 closest distance to " O   HOH Z 162 " =    2.668
peak=   -4.004 closest distance to " O   HOH Z 183 " =    1.390
peak=   -3.972 closest distance to " CD1 LEU A 101 " =    2.581
peak=   -3.952 closest distance to " O   HOH Z 231 " =    1.969
peak=   -3.926 closest distance to " O   HOH Z 118 " =    0.946
peak=   -3.921 closest distance to " OG  SER A  97 " =    2.341
peak=   -3.913 closest distance to " C   ALA A 158 " =    1.411
peak=   -3.912 closest distance to " O   HOH Z 111 " =    1.693
peak=   -3.907 closest distance to " CD  LYS A 289 " =    2.365
peak=   -3.895 closest distance to " OE1 GLN A  88 " =    1.160
peak=   -3.889 closest distance to " O   HOH Z 166 " =    1.596
peak=   -3.874 closest distance to " O   HOH Z 394 " =    1.545
peak=   -3.844 closest distance to " CG  GLN A  88 " =    0.885
peak=   -3.839 closest distance to " CG1 VAL A 112 " =    2.703
peak=   -3.831 closest distance to " O   HOH Z 102 " =    1.219
peak=   -3.794 closest distance to " CB  ALA A 161 " =    2.731
peak=   -3.791 closest distance to " O   HOH Z 100 " =    0.820
peak=   -3.773 closest distance to " O   HOH Z  44 " =    0.823
peak=   -3.763 closest distance to " CA  GLY A  98 " =    2.078
peak=   -3.757 closest distance to " CD  GLN A  58 " =    1.128
peak=   -3.757 closest distance to " CD2 LEU A 237 " =    2.441
peak=   -3.751 closest distance to " CE2 TRP A  70 " =    2.481
peak=   -3.750 closest distance to " O   HOH Z 145 " =    1.070
peak=   -3.747 closest distance to " O   HOH Z  37 " =    2.186
peak=   -3.720 closest distance to " CA  GLY A 241 " =    3.088
peak=   -3.718 closest distance to " CB  ASP A  27 " =    2.518
peak=   -3.714 closest distance to " O   HOH Z  60 " =    1.060
peak=   -3.704 closest distance to " O   HOH Z 359 " =    3.163
peak=   -3.694 closest distance to " OG  SER A 141 " =    1.810
peak=   -3.674 closest distance to " OG  SER A  87 " =    1.515
peak=   -3.668 closest distance to " O   HOH Z 368 " =    1.363
peak=   -3.638 closest distance to " CD1 TYR A 247 " =    2.695
peak=   -3.632 closest distance to " CD1 PHE A  59 " =    2.077
peak=   -3.630 closest distance to " O   HOH Z 207 " =    1.125
peak=   -3.628 closest distance to " C   LEU A 222 " =    1.176
peak=   -3.620 closest distance to " N   ASP A 132 " =    2.054
peak=   -3.617 closest distance to " N   ALA A 226 " =    2.095
peak=   -3.602 closest distance to " O   HOH Z 407 " =    3.131
peak=   -3.596 closest distance to " O   HOH Z  69 " =    1.502
peak=   -3.588 closest distance to " CB  ALA A  43 " =    2.668
peak=   -3.585 closest distance to " CD  ARG A 156 " =    2.190
peak=   -3.582 closest distance to " OG BSER A 134 " =    1.500
peak=   -3.577 closest distance to " O   HOH Z 144 " =    1.591
peak=   -3.562 closest distance to " O   HOH Z 241 " =    1.044
peak=   -3.559 closest distance to " CG  ARG A 259 " =    2.451
peak=   -3.555 closest distance to " O   HOH Z 118 " =    1.718
peak=   -3.552 closest distance to " CG  GLN A 103 " =    2.379
peak=   -3.544 closest distance to " O   HOH Z  70 " =    1.884
peak=   -3.540 closest distance to " CH2 TRP A 179 " =    1.113
peak=   -3.536 closest distance to " CG  LEU A   5 " =    0.952
peak=   -3.535 closest distance to " NH2AARG A 275 " =    5.552
peak=   -3.534 closest distance to " CB  ALA A 129 " =    2.584
peak=   -3.521 closest distance to " O   HOH Z  37 " =    1.400
peak=   -3.520 closest distance to " CB  HIS A  86 " =    1.174
peak=   -3.518 closest distance to " O   HOH Z 377 " =    0.779
peak=   -3.515 closest distance to " OE1 GLN A  77 " =    1.006
peak=   -3.510 closest distance to " O   HOH Z 351 " =    1.479
peak=   -3.508 closest distance to " CB  PRO A 163 " =    2.466
peak=   -3.505 closest distance to " O   HOH Z 290 " =    1.084
peak=   -3.502 closest distance to " CG2AVAL A  41 " =    2.871
peak=   -3.488 closest distance to " O   HOH Z 108 " =    1.090
peak=   -3.479 closest distance to " CG  ARG A 138 " =    0.785
peak=   -3.477 closest distance to " CD  PRO A 243 " =    1.955
peak=   -3.474 closest distance to " CA  GLY A  91 " =    2.360
peak=   -3.471 closest distance to " O   HOH Z 138 " =    1.298
peak=   -3.470 closest distance to " CD2 LEU A 143 " =    2.567
peak=   -3.466 closest distance to " CD  GLU A 277 " =    0.847
peak=   -3.456 closest distance to " CG1 VAL A 296 " =    1.571
peak=   -3.453 closest distance to " CG2BVAL A  41 " =    2.338
peak=   -3.450 closest distance to " CE3 TRP A  70 " =    1.899
peak=   -3.448 closest distance to " O   HOH Z   9 " =    1.543
peak=   -3.445 closest distance to " O   HOH Z 426 " =    1.780
peak=   -3.441 closest distance to " N   THR A  52 " =    1.712
peak=   -3.440 closest distance to " OD1 ASP A 171 " =    1.698
peak=   -3.438 closest distance to " O   SER A 271 " =    2.279
peak=   -3.437 closest distance to " CB  PHE A 130 " =    1.329
peak=   -3.436 closest distance to " CB  ALA A 291 " =    2.251
peak=   -3.435 closest distance to " O   HOH Z 109 " =    0.846
peak=   -3.433 closest distance to " CD  GLN A  88 " =    1.008
peak=   -3.427 closest distance to " O   HOH Z  44 " =    2.485
peak=   -3.424 closest distance to " O   SER A  62 " =    1.787
peak=   -3.424 closest distance to " N   LYS A 166 " =    2.002
peak=   -3.422 closest distance to " O   GLY A  80 " =    2.708
peak=   -3.420 closest distance to " CD2 TYR A 293 " =    2.020
peak=   -3.415 closest distance to " N   ALA A  43 " =    2.736
peak=   -3.412 closest distance to " O   HOH Z 103 " =    1.075
peak=   -3.412 closest distance to " C   ASN A 285 " =    2.519
peak=   -3.412 closest distance to " CE2 TYR A  30 " =    2.723
peak=   -3.404 closest distance to " CG  TRP A 266 " =    1.763
peak=   -3.403 closest distance to " CG1 VAL A 112 " =    2.937
peak=   -3.397 closest distance to " CA  GLY A 133 " =    2.299
peak=   -3.395 closest distance to " NH2 ARG A  56 " =    1.021
peak=   -3.390 closest distance to " CB  TRP A  85 " =    2.609
peak=   -3.388 closest distance to " O   HOH Z 142 " =    1.464
peak=   -3.377 closest distance to " O   HOH Z 166 " =    2.490
peak=   -3.377 closest distance to " CG1 VAL A  78 " =    2.444
peak=   -3.374 closest distance to " O   HOH Z 398 " =    0.756
peak=   -3.373 closest distance to " OG  SER A  62 " =    4.358
peak=   -3.370 closest distance to " O   HOH Z 133 " =    2.105
peak=   -3.368 closest distance to " CG1 VAL A 125 " =    1.794
peak=   -3.367 closest distance to " SD  MET A 105 " =    0.993
peak=   -3.366 closest distance to " N   SER A 212 " =    1.965
peak=   -3.364 closest distance to " N   THR A 157 " =    1.669
peak=   -3.362 closest distance to " OE1 GLN A 278 " =    1.020
peak=   -3.360 closest distance to " CB  VAL A 230 " =    0.998
peak=   -3.358 closest distance to " O   HOH Z 133 " =    1.117
peak=   -3.349 closest distance to " CG2 VAL A 202 " =    2.848
peak=   -3.349 closest distance to " O   HOH Z 435 " =    3.048
peak=   -3.342 closest distance to " O   HOH Z  10 " =    1.573
peak=   -3.337 closest distance to " OE1 GLU A  44 " =    0.893
peak=   -3.334 closest distance to " CD2 TYR A 247 " =    2.491
peak=   -3.330 closest distance to " O   HOH Z 177 " =    1.989
peak=   -3.328 closest distance to " O   HOH Z 198 " =    0.971
peak=   -3.325 closest distance to " O   HOH Z 140 " =    1.567
peak=   -3.325 closest distance to " O   HOH Z 340 " =    1.497
peak=   -3.325 closest distance to " O   HOH Z 255 " =    2.456
peak=   -3.322 closest distance to " O   HOH Z 171 " =    0.928
peak=   -3.314 closest distance to " CA  GLY A 241 " =    2.489
peak=   -3.314 closest distance to " O   GLY A 211 " =    1.411
peak=   -3.313 closest distance to " O   HOH Z 118 " =    1.066
peak=   -3.308 closest distance to " O   HOH Z  11 " =    1.870
peak=   -3.301 closest distance to " CA  SER A  62 " =    2.760
peak=   -3.300 closest distance to " CE1 TYR A 169 " =    2.621
peak=   -3.288 closest distance to " CG  LEU A 228 " =    0.934
peak=   -3.284 closest distance to " CG2 THR A  52 " =    2.684
peak=   -3.282 closest distance to " CE BMET A  47 " =    1.492
peak=   -3.279 closest distance to " N   GLN A  55 " =    1.611
peak=   -3.277 closest distance to " O   HOH Z  63 " =    1.714
peak=   -3.276 closest distance to " NH2 ARG A  79 " =    2.171
peak=   -3.275 closest distance to " CG2 ILE A  20 " =    2.708
peak=   -3.274 closest distance to " CE3 TRP A 150 " =    2.396
peak=   -3.270 closest distance to " O   HOH Z 385 " =    2.096
peak=   -3.262 closest distance to " O   HOH Z 144 " =    1.429
peak=   -3.258 closest distance to " O   HOH Z 368 " =    1.568
peak=   -3.257 closest distance to " CB  VAL A 189 " =    2.358
peak=   -3.257 closest distance to " O   HOH Z 357 " =    1.937
peak=   -3.256 closest distance to " O   SER A 276 " =    1.622
peak=   -3.256 closest distance to " O   HOH Z 389 " =    2.298
peak=   -3.252 closest distance to " O   VAL A 125 " =    2.449
peak=   -3.250 closest distance to " ND2 ASN A  45 " =    2.445
peak=   -3.247 closest distance to " OG  SER A  28 " =    2.138
peak=   -3.247 closest distance to " OG1 THR A  82 " =    2.088
peak=   -3.246 closest distance to " CG  GLU A  53 " =    1.451
peak=   -3.246 closest distance to " C   ARG A 269 " =    1.469
peak=   -3.246 closest distance to " OD1 ASN A 176 " =    1.434
peak=   -3.245 closest distance to " NH2 ARG A 219 " =    1.705
peak=   -3.237 closest distance to " SD BMET A  47 " =    0.918
peak=   -3.235 closest distance to " O   VAL A 189 " =    2.612
peak=   -3.234 closest distance to " O   HOH Z 434 " =    1.710
peak=   -3.227 closest distance to " CG  LEU A 282 " =    2.614
peak=   -3.220 closest distance to " OD2 ASP A  50 " =    2.241
peak=   -3.217 closest distance to " CE1 PHE A  16 " =    2.829
peak=   -3.215 closest distance to " O   HOH Z  53 " =    1.711
peak=   -3.209 closest distance to " SG ACYS A 201 " =    2.446
peak=   -3.205 closest distance to " O   HOH Z  44 " =    2.189
peak=   -3.205 closest distance to " CG1BVAL A  72 " =    2.432
peak=   -3.203 closest distance to " CD2 LEU A   5 " =    0.970
peak=   -3.202 closest distance to " CA  GLY A 203 " =    2.666
peak=   -3.200 closest distance to " CB  TYR A  15 " =    2.132
peak=   -3.200 closest distance to " CB  ALA A   9 " =    2.649
peak=   -3.193 closest distance to " O   PHE A 218 " =    1.568
peak=   -3.191 closest distance to " CD  GLU A 152 " =    0.776
peak=   -3.190 closest distance to " O   HOH Z 390 " =    2.142
peak=   -3.188 closest distance to " SG BCYS A 201 " =    1.220
peak=   -3.186 closest distance to " CG  PRO A 163 " =    2.773
peak=   -3.183 closest distance to " O   HOH Z 252 " =    3.655
peak=   -3.182 closest distance to " O   HOH Z 251 " =    4.842
peak=   -3.178 closest distance to " CD  GLN A 223 " =    0.836
peak=   -3.177 closest distance to " CB  ALA A 161 " =    1.711
peak=   -3.174 closest distance to " CZ2 TRP A 274 " =    0.905
peak=   -3.173 closest distance to " O   HOH Z 244 " =    1.969
peak=   -3.171 closest distance to " O   HOH Z 357 " =    1.883
peak=   -3.168 closest distance to " CD1 ILE A 239 " =    2.250
peak=   -3.165 closest distance to " O   HOH Z 281 " =    2.763
peak=   -3.164 closest distance to " O   HOH Z 114 " =    1.730
peak=   -3.159 closest distance to " CZ3 TRP A 266 " =    1.029
peak=   -3.159 closest distance to " CD2 LEU A 143 " =    2.576
peak=   -3.156 closest distance to " O   HOH Z 437 " =    1.811
peak=   -3.156 closest distance to " SG BCYS A 201 " =    2.209
peak=   -3.152 closest distance to " CB  ALA A 227 " =    2.511
peak=   -3.151 closest distance to " O   HOH Z 166 " =    1.428
peak=   -3.151 closest distance to " O   HOH Z  49 " =    1.375
peak=   -3.147 closest distance to " C   ASN A 148 " =    1.597
peak=   -3.143 closest distance to " CG2 VAL A 112 " =    2.554
peak=   -3.142 closest distance to " CZ  TYR A 169 " =    1.929
peak=   -3.141 closest distance to " O   HOH Z 298 " =    2.440
peak=   -3.141 closest distance to " O   HOH Z 341 " =    0.850
peak=   -3.139 closest distance to " CZ  ARG A  56 " =    1.116
peak=   -3.127 closest distance to " O   GLY A  17 " =    1.208
peak=   -3.120 closest distance to " CG  ARG A 269 " =    2.308
peak=   -3.119 closest distance to " ND2 ASN A 173 " =    1.940
peak=   -3.117 closest distance to " C   LYS A  76 " =    1.506
peak=   -3.113 closest distance to " CA  ASP A 298 " =    1.121
peak=   -3.098 closest distance to " CA  SER A 135 " =    1.278
peak=   -3.090 closest distance to " O   HOH Z 250 " =    1.195
peak=   -3.088 closest distance to " CE2 PHE A 218 " =    2.547
peak=   -3.085 closest distance to " O   HOH Z  32 " =    1.924
peak=   -3.082 closest distance to " ND2 ASN A  60 " =    3.962
peak=   -3.070 closest distance to " C   VAL A 265 " =    0.823
peak=   -3.061 closest distance to " O   HOH Z 380 " =    1.089
peak=   -3.052 closest distance to " O   HOH Z 292 " =    1.588
peak=   -3.041 closest distance to " OE1 GLN A  88 " =    1.520
peak=   -3.041 closest distance to " O   HOH Z 112 " =    1.118
peak=   -3.041 closest distance to " CB  ALA A 248 " =    2.402
peak=   -3.040 closest distance to " N   PHE A  59 " =    1.729
peak=   -3.031 closest distance to " CE  LYS A 166 " =    1.048
peak=   -3.023 closest distance to " O   HOH Z 115 " =    1.342

================= 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    :  0.5002 0.4932   6.299738e+00   6.289066e+00
   1_bss:  0.4928 0.4859   6.296280e+00   6.284004e+00
   1_xyz:  0.4245 0.4436   6.215952e+00   6.239910e+00
   1_adp:  0.3783 0.4310   6.151676e+00   6.224255e+00
   1_occ:  0.3780 0.4315   6.151601e+00   6.225762e+00
   2_bss:  0.3762 0.4298   6.153147e+00   6.225541e+00
   2_xyz:  0.2988 0.3624   5.973779e+00   6.111223e+00
   2_adp:  0.2767 0.3359   5.914838e+00   6.061907e+00
   2_occ:  0.2765 0.3353   5.914423e+00   6.061144e+00
   3_bss:  0.2752 0.3352   5.916043e+00   6.061738e+00
   3_xyz:  0.2146 0.2765   5.713969e+00   5.898277e+00
   3_adp:  0.1913 0.2596   5.635571e+00   5.845758e+00
   3_occ:  0.1909 0.2598   5.635170e+00   5.846014e+00
   4_bss:  0.1912 0.2592   5.634436e+00   5.845061e+00
   4_xyz:  0.1586 0.2205   5.469984e+00   5.706522e+00
   4_adp:  0.1519 0.2059   5.416324e+00   5.633621e+00
   4_occ:  0.1517 0.2056   5.415344e+00   5.632428e+00
   5_bss:  0.1517 0.2057   5.416224e+00   5.632516e+00
   5_xyz:  0.1322 0.1834   5.301988e+00   5.530665e+00
   5_adp:  0.1304 0.1800   5.285558e+00   5.510008e+00
   5_occ:  0.1302 0.1800   5.284885e+00   5.509686e+00
   5_bss:  0.1301 0.1800   5.284763e+00   5.509843e+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:  0.319  50.000   8.676   5.872  10.542   0.000   0.000   0.000
   1_xyz:  0.319  50.000   8.676   5.872  10.542   0.000   0.000   0.000
   1_adp:  0.319  50.000   8.676   5.872  10.542   0.000   0.000   0.000
   1_occ:  0.319  50.000   8.676   5.872  10.542   0.000   0.000   0.000
   2_bss:  0.336  69.661   5.120   3.158   7.013   0.000   0.000   0.000
   2_xyz:  0.336  69.661   5.120   3.158   7.013   0.000   0.000   0.000
   2_adp:  0.336  69.661   5.120   3.158   7.013   0.000   0.000   0.000
   2_occ:  0.336  69.661   5.120   3.158   7.013   0.000   0.000   0.000
   3_bss:  0.336  67.612   2.600   1.793   4.569   0.000   0.000   0.000
   3_xyz:  0.336  67.612   2.600   1.793   4.569   0.000   0.000   0.000
   3_adp:  0.336  67.612   2.600   1.793   4.569   0.000   0.000   0.000
   3_occ:  0.336  67.612   2.600   1.793   4.569   0.000   0.000   0.000
   4_bss:  0.345  86.617   1.712   1.038   3.405   0.000   0.000   0.000
   4_xyz:  0.345  86.617   1.712   1.038   3.405   0.000   0.000   0.000
   4_adp:  0.345  86.617   1.712   1.038   3.405   0.000   0.000   0.000
   4_occ:  0.345  86.617   1.712   1.038   3.405   0.000   0.000   0.000
   5_bss:  0.336  76.659   1.008   0.516   2.572   0.000   0.000   0.000
   5_xyz:  0.336  76.659   1.008   0.516   2.572   0.000   0.000   0.000
   5_adp:  0.336  76.659   1.008   0.516   2.572   0.000   0.000   0.000
   5_occ:  0.336  76.659   1.008   0.516   2.572   0.000   0.000   0.000
   5_bss:  0.321  66.648  -0.323  -0.804   1.127   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.518 0.3737  0.4366    76832.189
   1_bss:  60.871 0.3817  0.5679    75646.431
   1_xyz:  53.242 0.4786  0.6940    60071.510
   1_adp:  50.455 0.5139  0.8130    56148.479
   1_occ:  50.667 0.5112  0.8072    56497.380
   2_bss:  50.584 0.5122  0.7256    56392.438
   2_xyz:  40.045 0.6407  0.8921    37244.528
   2_adp:  36.154 0.6876  0.9404    31966.011
   2_occ:  36.155 0.6876  0.9398    31898.226
   3_bss:  36.132 0.6879  0.8748    31968.216
   3_xyz:  28.179 0.7772  0.9609    20371.149
   3_adp:  26.223 0.7984  0.9659    17886.966
   3_occ:  26.229 0.7984  0.9651    17878.232
   4_bss:  26.163 0.7990  0.9347    17805.499
   4_xyz:  21.789 0.8432  0.9678    12697.823
   4_adp:  19.753 0.8641  0.9755    10995.660
   4_occ:  19.730 0.8643  0.9754    10958.788
   5_bss:  19.728 0.8643  0.9523    10964.081
   5_xyz:  17.178 0.8880  0.9655     8677.763
   5_adp:  16.644 0.8931  0.9653     8405.083
   5_occ:  16.633 0.8932  0.9652     8389.430
   5_bss:  16.640 0.8931  0.9582     8391.629
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4583e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4583e+01
   1_xyz:   1.780  0.015  0.112 18.426  0.007  4.108   1.5590e-01
   1_adp:   1.780  0.015  0.112 18.426  0.007  4.108   1.5590e-01
   1_occ:   1.780  0.015  0.112 18.426  0.007  4.108   1.5590e-01
   2_bss:   1.780  0.015  0.112 18.426  0.007  4.108   1.5590e-01
   2_xyz:   1.333  0.011  0.088 16.954  0.006  4.108   1.1014e-01
   2_adp:   1.333  0.011  0.088 16.954  0.006  4.108   1.1014e-01
   2_occ:   1.333  0.011  0.088 16.954  0.006  4.108   1.1014e-01
   3_bss:   1.333  0.011  0.088 16.954  0.006  4.108   1.1014e-01
   3_xyz:   1.138  0.008  0.083 15.908  0.005  4.133   7.5002e-02
   3_adp:   1.138  0.008  0.083 15.908  0.005  4.133   7.5002e-02
   3_occ:   1.138  0.008  0.083 15.908  0.005  4.133   7.5002e-02
   4_bss:   1.138  0.008  0.083 15.908  0.005  4.133   7.5002e-02
   4_xyz:   1.124  0.010  0.082 15.872  0.004  4.117   7.7965e-02
   4_adp:   1.124  0.010  0.082 15.872  0.004  4.117   7.7965e-02
   4_occ:   1.124  0.010  0.082 15.872  0.004  4.117   7.7965e-02
   5_bss:   1.124  0.010  0.082 15.872  0.004  4.117   7.7965e-02
   5_xyz:   1.234  0.012  0.092 15.506  0.004  4.118   9.0512e-02
   5_adp:   1.234  0.012  0.092 15.506  0.004  4.118   9.0512e-02
   5_occ:   1.234  0.012  0.092 15.506  0.004  4.118   9.0512e-02
   5_bss:   1.234  0.012  0.092 15.506  0.004  4.118   9.0512e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0775e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0775e+00
   1_xyz:  14.738  0.178  0.457 86.113  0.047  2.108   1.1219e-01
   1_adp:  14.738  0.178  0.457 86.113  0.047  2.108   1.1219e-01
   1_occ:  14.738  0.178  0.457 86.113  0.047  2.108   1.1219e-01
   2_bss:  14.738  0.178  0.457 86.113  0.047  2.108   1.1219e-01
   2_xyz:   8.166  0.099  0.289 81.902  0.051  2.084   1.5430e-01
   2_adp:   8.166  0.099  0.289 81.902  0.051  2.084   1.5430e-01
   2_occ:   8.166  0.099  0.289 81.902  0.051  2.084   1.5430e-01
   3_bss:   8.166  0.099  0.289 81.902  0.051  2.084   1.5430e-01
   3_xyz:   7.890  0.058  0.275 81.716  0.050  2.286   5.1215e-02
   3_adp:   7.890  0.058  0.275 81.716  0.050  2.286   5.1215e-02
   3_occ:   7.890  0.058  0.275 81.716  0.050  2.286   5.1215e-02
   4_bss:   7.890  0.058  0.275 81.716  0.050  2.286   5.1215e-02
   4_xyz:   8.371  0.063  0.312 89.852  0.041  2.269   5.6944e-02
   4_adp:   8.371  0.063  0.312 89.852  0.041  2.269   5.6944e-02
   4_occ:   8.371  0.063  0.312 89.852  0.041  2.269   5.6944e-02
   5_bss:   8.371  0.063  0.312 89.852  0.041  2.269   5.6944e-02
   5_xyz:   9.791  0.087  0.472 82.683  0.036  2.299   7.1127e-02
   5_adp:   9.791  0.087  0.472 82.683  0.036  2.299   7.1127e-02
   5_occ:   9.791  0.087  0.472 82.683  0.036  2.299   7.1127e-02
   5_bss:   9.791  0.087  0.472 82.683  0.036  2.299   7.1127e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  87.27   0.00  16.56  87.27   0.00  14.18  84.66   0.00  29.56
   1_occ:  87.27   0.00  16.56  87.27   0.00  14.18  84.66   0.00  29.56
   2_bss:  87.27   0.00  16.56  87.27   0.00  14.18  84.66   0.00  29.56
   2_xyz:  87.27   0.00  16.56  87.27   0.00  14.18  84.66   0.00  29.56
   2_adp:  84.81   0.00  15.56  84.25   0.00  12.18  84.81   0.00  33.96
   2_occ:  84.81   0.00  15.56  84.25   0.00  12.18  84.81   0.00  33.96
   3_bss:  84.81   0.00  15.56  84.25   0.00  12.18  84.81   0.00  33.96
   3_xyz:  84.81   0.00  15.56  84.25   0.00  12.18  84.81   0.00  33.96
   3_adp: 112.93   0.00  16.79 112.93   0.00  11.59 109.49   0.00  45.09
   3_occ: 112.93   0.00  16.79 112.93   0.00  11.59 109.49   0.00  45.09
   4_bss: 112.93   0.00  16.79 112.93   0.00  11.59 109.49   0.00  45.09
   4_xyz: 112.93   0.00  16.79 112.93   0.00  11.59 109.49   0.00  45.09
   4_adp:  91.62   0.00  14.96  90.07   0.00  10.34  91.62   2.68  40.10
   4_occ:  91.62   0.00  14.96  90.07   0.00  10.34  91.62   2.68  40.10
   5_bss:  91.62   0.00  14.96  90.07   0.00  10.34  91.62   2.68  40.10
   5_xyz:  91.62   0.00  14.96  90.07   0.00  10.34  91.62   2.68  40.10
   5_adp:  86.87   0.00  14.46  77.48   0.00  10.12  86.87   3.17  38.11
   5_occ:  86.87   0.00  14.46  77.48   0.00  10.12  86.87   3.17  38.11
   5_bss:  88.03   1.16  15.62  78.64   1.16  11.28  88.03   4.33  39.27
------------------------------------------------------------------------
 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:    1.253    0.009    0.414
   1_adp:    1.253    0.009    0.414
   1_occ:    1.253    0.009    0.414
   2_bss:    1.253    0.009    0.414
   2_xyz:    1.695    0.033    0.605
   2_adp:    1.695    0.033    0.605
   2_occ:    1.695    0.033    0.605
   3_bss:    1.695    0.033    0.605
   3_xyz:    1.702    0.016    0.700
   3_adp:    1.702    0.016    0.700
   3_occ:    1.702    0.016    0.700
   4_bss:    1.702    0.016    0.700
   4_xyz:    1.835    0.060    0.774
   4_adp:    1.835    0.060    0.774
   4_occ:    1.835    0.060    0.774
   5_bss:    1.835    0.060    0.774
   5_xyz:    1.832    0.076    0.809
   5_adp:    1.832    0.076    0.809
   5_occ:    1.832    0.076    0.809
   5_bss:    1.832    0.076    0.809
------------------------------------------------------------------------

CPU time actual refinement: 346.63


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1264/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_1264/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1264/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1264/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1264/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.47 
  Macro-tasks:
    bulk solvent and scale       = 47.15  
    individual site refinement   = 138.19 
    weights calculation          = 31.87  
    collect and process          = 6.46   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 223.78 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 107.46 
    alpha_beta                      = 8.46   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 115.59 
    fmodel                         = 7.79   
    r_factors                      = 0.31   
    phase_errors                   = 10.37  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 253.89 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.942 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    627 calls, 107.10 s
gradients_fft:          573 calls, 103.12 s

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

# Date 2008-01-16 Time 03:36:35 PST -0800 (1200483395.54 s)
Start R-work = 0.5002, R-free = 0.4932 (no bulk solvent and anisotropic scale)
Final R-work = 0.1469, R-free = 0.1967 (no bulk solvent and anisotropic scale)

Start R-work = 0.4928, R-free = 0.4859
Final R-work = 0.1301, R-free = 0.1800