# Date 2008-01-16 Time 01:27:30 PST -0800 (1200475650.14 s)
#phil __OFF__

Command line arguments: "../428.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7071
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 428

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.93, 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: 2.77, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98082
Completeness in resolution range: 0.944594
Completeness with d_max=infinity: 0.941688

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9810
                             d_min =   1.9808

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98082
Completeness in resolution range: 0.944594
Completeness with d_max=infinity: 0.941688

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9814 -  4.2384 [2183/2210]  1963   220  10.1%
  bin  2:  4.2384 -  3.3768 [2088/2104]  1879   209  10.0%
  bin  3:  3.3768 -  2.9536 [2063/2082]  1859   204   9.9%
  bin  4:  2.9536 -  2.6853 [2051/2081]  1843   208  10.1%
  bin  5:  2.6853 -  2.4938 [2029/2048]  1827   202  10.0%
  bin  6:  2.4938 -  2.3473 [2018/2043]  1815   203  10.1%
  bin  7:  2.3473 -  2.2302 [2019/2053]  1825   194   9.6%
  bin  8:  2.2302 -  2.1334 [2010/2040]  1798   212  10.5%
  bin  9:  2.1334 -  2.0514 [1994/2036]  1799   195   9.8%
  bin 10:  2.0514 -  1.9808 [1134/2041]  1022   112   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_428/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:
        1.32 -     2.04: 12
        2.04 -     2.75: 350
        2.75 -     3.47: 4550
        3.47 -     4.18: 9306
        4.18 -     4.90: 13914
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.324 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.427 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.574 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.751 3.040 -x+1,y+1/2,-z+1/2
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.756 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 28127 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_428/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_428/model_refine_001.geo

CPU time processing inputs: 7.94


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.93 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: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4706   r_free= 0.4568   ksol= 0.00   Bsol= 0.00   scale= 0.794    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.274688                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1415  157 0.3841 0.3588      6.5918      6.5287|
|  2:  4.7272 -  3.7718 0.99   1364  151 0.3774 0.4322      6.7387      6.8891|
|  3:  3.7718 -  3.3008 0.99   1331  149 0.4344 0.3972      6.6665      6.6183|
|  4:  3.3008 -  3.0017 0.99   1331  144 0.4644 0.4497      6.5105      6.4678|
|  5:  3.0017 -  2.7880 0.99   1311  151 0.4931 0.4683      6.3527      6.3623|
|  6:  2.7880 -  2.6246 0.99   1328  145 0.4948 0.5699      6.2732       6.241|
|  7:  2.6246 -  2.4938 0.99   1291  146 0.4993 0.4604      6.2234      6.1363|
|  8:  2.4938 -  2.3856 0.98   1295  141 0.5316 0.4543      6.1947      6.1516|
|  9:  2.3856 -  2.2941 0.98   1317  146 0.5176 0.5024      6.1058      6.1413|
| 10:  2.2941 -  2.2152 0.98   1280  139 0.5283 0.4635      6.1161      6.0627|
| 11:  2.2152 -  2.1462 0.99   1294  154 0.5152 0.5409       6.019      6.0466|
| 12:  2.1462 -  2.0850 0.97   1281  131 0.5181 0.4639       5.952      5.9857|
| 13:  2.0850 -  2.0302 0.95   1255  136 0.5313 0.5057      5.8996      5.8414|
| 14:  2.0302 -  1.9808 0.42    537   69 0.4894 0.4208      5.8891       5.716|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7272  1415   157  0.72  32.36   0.80     0.74      64197.03|
|  2:  4.7272 -  3.7718  1364   151  0.72  33.64   0.88     0.78      98464.57|
|  3:  3.7718 -  3.3008  1331   149  0.63  41.27   0.83     0.74     103947.78|
|  4:  3.3008 -  3.0017  1331   144  0.53  49.28   0.79     0.61      94239.17|
|  5:  3.0017 -  2.7880  1311   151  0.42  57.91   0.74     0.49      80256.78|
|  6:  2.7880 -  2.6246  1328   145  0.35  63.57   0.72     0.41      76019.16|
|  7:  2.6246 -  2.4938  1291   146  0.37  62.37   0.74     0.42      66122.96|
|  8:  2.4938 -  2.3856  1295   141  0.41  59.38   0.72     0.48      54990.80|
|  9:  2.3856 -  2.2941  1317   146  0.44  56.88   0.71     0.52      48247.53|
| 10:  2.2941 -  2.2152  1280   139  0.43  57.89   0.74     0.49      43370.26|
| 11:  2.2152 -  2.1462  1294   154  0.37  62.09   0.75     0.47      45416.17|
| 12:  2.1462 -  2.0850  1281   131  0.37  62.13   0.75     0.46      40234.06|
| 13:  2.0850 -  2.0302  1255   136  0.39  60.86   0.73     0.49      34432.69|
| 14:  2.0302 -  1.9808   537    69  0.50  52.19   0.77     0.52      23630.96|
|alpha:            min =        0.41 max =            0.78 mean =         0.55|
|beta:             min =    23630.96 max =       103947.78 mean =     64489.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.51|
|phase err.(test): min =        0.00 max =           89.96 mean =        53.79|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.867471             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.742   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.947256              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.005   (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 |  1.125 -  1.503:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.503 -  1.880:       17 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.880 -  2.258:      139 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.258 -  2.635:      620 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.635 -  3.013:     1428 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.013 -  3.390:     2510 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.390 -  3.768:     3914 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.768 -  4.145:     5113 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.145 -  4.522:     6595 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.522 -  4.900:     7792 |
|-----------------------------------------------------------------------------|
|-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 |       54.025 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.125 |       1.981 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    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: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4775   r_free= 0.4612   ksol= 0.00   Bsol= 0.00   scale= 0.764    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.278082                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4605   r_free= 0.4476   ksol= 0.34   Bsol= 14.86   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.90,7.35,12.50,0.00,0.00,0.00); trace/3= 8.92                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.266399                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.429371             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.771   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.924866              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.992   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4605      final r-factor (work) = 0.3762          |
| start r-factor (free) = 0.4476      final r-factor (free) = 0.3953          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.7415 = 10.43 * 0.50 * 6.2739 + 1.00 * 54.0254                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.3246 = 10.43 * 0.50 * 6.1731 + 1.00 * 0.1336                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3762      final r-factor (work) = 0.3288          |
| start r-factor (free) = 0.3953      final r-factor (free) = 0.3736          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7237 = 0.92 * 1.00 * 6.1731 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6282 = 0.92 * 1.00 * 6.0699 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.58   12.84    None  None   None       |
|    all(noH): 2823   0      0.00    68.58   12.84    None  None   None       |
|    Sol.    : 438    0      0.00    68.58   26.52    None  None   None       |
|    Mac.    : 2385   0      0.00    57.47   10.33    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 -   6.858: 1058   |   5:    34.292 -  41.150:   87        |
|      1:     6.858 -  13.717:  763   |   6:    41.150 -  48.008:   52        |
|      2:    13.717 -  20.575:  438   |   7:    48.008 -  54.867:   31        |
|      3:    20.575 -  27.433:  227   |   8:    54.867 -  61.725:    7        |
|      4:    27.433 -  34.292:  156   |   9:    61.725 -  68.584:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3288 r_free = 0.3736             target_work(ml) = 6.046         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3282 r_free = 0.3747             target_work(ml) = 6.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3282   r_free= 0.3747   ksol= 0.34   Bsol= 14.86   scale= 1.105   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.90,7.35,12.50,0.00,0.00,0.00); trace/3= 8.92                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.045060                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3245   r_free= 0.3710   ksol= 0.34   Bsol= 46.95   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.22,3.63,8.62,0.00,0.00,0.00); trace/3= 5.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.045835                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.044562              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.976   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.450610              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.864  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3245      final r-factor (work) = 0.2343          |
| start r-factor (free) = 0.3710      final r-factor (free) = 0.2838          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.5390 = 8.04 * 0.50 * 6.0676 + 1.00 * 0.1336                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.8300 = 8.04 * 0.50 * 5.9013 + 1.00 * 0.0935                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2343      final r-factor (work) = 0.2087          |
| start r-factor (free) = 0.2838      final r-factor (free) = 0.2613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6735 = 0.45 * 1.00 * 5.9013 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5824 = 0.45 * 1.00 * 5.7059 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.77   12.77    None  None   None       |
|    all(noH): 2823   0      0.00    67.77   12.77    None  None   None       |
|    Sol.    : 438    0      0.00    67.77   32.70    None  None   None       |
|    Mac.    : 2385   0      0.00    62.92   9.11     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 -   6.777: 1149   |   5:    33.885 -  40.662:  121        |
|      1:     6.777 -  13.554:  812   |   6:    40.662 -  47.439:   82        |
|      2:    13.554 -  20.331:  341   |   7:    47.439 -  54.215:   34        |
|      3:    20.331 -  27.108:  128   |   8:    54.215 -  60.992:   17        |
|      4:    27.108 -  33.885:  130   |   9:    60.992 -  67.769:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2087 r_free = 0.2613             target_work(ml) = 5.668         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2086 r_free = 0.2613             target_work(ml) = 5.668         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2086   r_free= 0.2613   ksol= 0.34   Bsol= 46.95   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.22,3.63,8.62,0.00,0.00,0.00); trace/3= 5.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.668095                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2059   r_free= 0.2617   ksol= 0.32   Bsol= 56.91   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,2.47,5.20,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.667744                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.720756              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.401  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.581378              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.369  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2059      final r-factor (work) = 0.1558          |
| start r-factor (free) = 0.2617      final r-factor (free) = 0.2083          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7264 = 3.72 * 0.50 * 5.7155 + 1.00 * 0.0935                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4035 = 3.72 * 0.50 * 5.5543 + 1.00 * 0.0705                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1558      final r-factor (work) = 0.1433          |
| start r-factor (free) = 0.2083      final r-factor (free) = 0.1953          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2404 = 0.58 * 1.00 * 5.5543 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1441 = 0.58 * 1.00 * 5.3862 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.39   13.06    None  None   None       |
|    all(noH): 2823   0      0.00    76.39   13.06    None  None   None       |
|    Sol.    : 438    0      1.43    76.39   36.38    None  None   None       |
|    Mac.    : 2385   0      0.00    71.22   8.78     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.639: 1402   |   5:    38.193 -  45.831:  110        |
|      1:     7.639 -  15.277:  731   |   6:    45.831 -  53.470:   93        |
|      2:    15.277 -  22.916:  228   |   7:    53.470 -  61.108:   35        |
|      3:    22.916 -  30.554:   98   |   8:    61.108 -  68.747:   14        |
|      4:    30.554 -  38.193:  105   |   9:    68.747 -  76.385:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1433 r_free = 0.1953             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1431 r_free = 0.1949             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1431   r_free= 0.1949   ksol= 0.32   Bsol= 56.91   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,2.47,5.20,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.356307                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1428   r_free= 0.1946   ksol= 0.33   Bsol= 56.91   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.27,2.00,4.21,0.00,0.00,0.00); trace/3= 2.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.355574                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.933093              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.321  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.230376              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.351  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1428      final r-factor (work) = 0.1304          |
| start r-factor (free) = 0.1946      final r-factor (free) = 0.1766          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2788 = 1.93 * 0.50 * 5.3886 + 1.00 * 0.0705                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1991 = 1.93 * 0.50 * 5.3187 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1304      final r-factor (work) = 0.1271          |
| start r-factor (free) = 0.1766      final r-factor (free) = 0.1749          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5617 = 1.23 * 1.00 * 5.3187 + 1.00 * 0.0177                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5721 = 1.23 * 1.00 * 5.2630 + 1.00 * 0.0966                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.14   13.26    None  None   None       |
|    all(noH): 2823   0      0.00    83.14   13.26    None  None   None       |
|    Sol.    : 438    0      1.22    83.14   37.80    None  None   None       |
|    Mac.    : 2385   0      0.00    76.83   8.75     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.314: 1536   |   5:    41.569 -  49.883:   98        |
|      1:     8.314 -  16.628:  654   |   6:    49.883 -  58.197:   78        |
|      2:    16.628 -  24.942:  192   |   7:    58.197 -  66.511:   35        |
|      3:    24.942 -  33.255:  102   |   8:    66.511 -  74.825:   15        |
|      4:    33.255 -  41.569:  107   |   9:    74.825 -  83.139:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1271 r_free = 0.1749             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1269 r_free = 0.1750             target_work(ml) = 5.259         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1269   r_free= 0.1750   ksol= 0.33   Bsol= 56.91   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.27,2.00,4.21,0.00,0.00,0.00); trace/3= 2.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.259420                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1269   r_free= 0.1750   ksol= 0.33   Bsol= 56.91   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.49,2.17,4.11,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.259610                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.983290              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.663  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 14.266525             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.771   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1269      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1750      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9085 = 2.98 * 0.50 * 5.2628 + 1.00 * 0.0583                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8716 = 2.98 * 0.50 * 5.2266 + 1.00 * 0.0754                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 74.5851 = 14.27 * 1.00 * 5.2266 + 1.00 * 0.0201                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 74.1453 = 14.27 * 1.00 * 5.1959 + 1.00 * 0.0178                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.31  13.44    None  None   None       |
|    all(noH): 2823   0      0.00    102.31  13.44    None  None   None       |
|    Sol.    : 438    0      1.12    102.31  39.14    None  None   None       |
|    Mac.    : 2385   0      0.00    90.41   8.72     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.231: 1808   |   5:    51.154 -  61.385:   79        |
|      1:    10.231 -  20.462:  489   |   6:    61.385 -  71.616:   41        |
|      2:    20.462 -  30.693:  160   |   7:    71.616 -  81.847:   20        |
|      3:    30.693 -  40.924:  123   |   8:    81.847 -  92.078:    8        |
|      4:    40.924 -  51.154:   93   |   9:    92.078 - 102.309:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1667             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1156 r_free = 0.1666             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1666   ksol= 0.33   Bsol= 56.91   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.49,2.17,4.11,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.195917                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1415  157 0.1006 0.1367      5.4282      5.5931|
|  2:  4.7272 -  3.7718 0.99   1364  151 0.0833 0.1124      5.4495      5.6679|
|  3:  3.7718 -  3.3008 0.99   1331  149 0.1093 0.1589      5.5042       5.871|
|  4:  3.3008 -  3.0017 0.99   1331  144 0.1233 0.1694      5.4667      5.6627|
|  5:  3.0017 -  2.7880 0.99   1311  151 0.1361 0.1629       5.366       5.542|
|  6:  2.7880 -  2.6246 0.99   1328  145 0.1293 0.2174      5.2592      5.5786|
|  7:  2.6246 -  2.4938 0.99   1291  146 0.1339 0.1752      5.2407       5.385|
|  8:  2.4938 -  2.3856 0.98   1295  141 0.1204 0.1773      5.1418      5.3962|
|  9:  2.3856 -  2.2941 0.98   1317  146 0.1252 0.2087      5.0879      5.4331|
| 10:  2.2941 -  2.2152 0.98   1280  139 0.1163 0.1618       5.015      5.1945|
| 11:  2.2152 -  2.1462 0.99   1294  154 0.1205 0.2084      4.9914       5.379|
| 12:  2.1462 -  2.0850 0.97   1281  131 0.1242 0.1641      4.9474      5.1703|
| 13:  2.0850 -  2.0302 0.95   1255  136 0.1108 0.1816      4.8064      5.0423|
| 14:  2.0302 -  1.9808 0.42    537   69 0.0920 0.1713      4.6475      4.9582|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7272  1415   157  0.93  10.09   0.97     0.94       8390.11|
|  2:  4.7272 -  3.7718  1364   151  0.95   8.62   1.01     0.99      10012.23|
|  3:  3.7718 -  3.3008  1331   149  0.93  12.19   1.03     1.03      11206.03|
|  4:  3.3008 -  3.0017  1331   144  0.92  14.03   1.01     1.00      10833.44|
|  5:  3.0017 -  2.7880  1311   151  0.90  16.67   1.00     0.97       9172.90|
|  6:  2.7880 -  2.6246  1328   145  0.88  17.89   0.97     0.94       8100.94|
|  7:  2.6246 -  2.4938  1291   146  0.89  17.06   0.98     0.93       7305.21|
|  8:  2.4938 -  2.3856  1295   141  0.89  16.96   0.99     0.96       6465.75|
|  9:  2.3856 -  2.2941  1317   146  0.89  17.33   0.99     0.95       5781.10|
| 10:  2.2941 -  2.2152  1280   139  0.89  17.25   0.99     0.95       5155.46|
| 11:  2.2152 -  2.1462  1294   154  0.88  18.10   0.98     0.94       5103.76|
| 12:  2.1462 -  2.0850  1281   131  0.89  17.52   0.99     0.98       4622.29|
| 13:  2.0850 -  2.0302  1255   136  0.90  16.88   0.98     0.95       3591.62|
| 14:  2.0302 -  1.9808   537    69  0.92  13.53   0.97     0.93       2560.49|
|alpha:            min =        0.93 max =            1.03 mean =         0.96|
|beta:             min =     2560.49 max =        11206.03 mean =      7264.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.30|
|phase err.(test): min =        0.00 max =           89.95 mean =        14.78|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1662   ksol= 0.33   Bsol= 62.81   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.04,-0.42,1.47,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.194668                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1662   ksol= 0.33   Bsol= 62.81   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.04,-0.42,1.47,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.194668                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1415  157 0.0982 0.1362      5.4135      5.5821|
|  2:  4.7272 -  3.7718 0.99   1364  151 0.0847 0.1118      5.4554       5.671|
|  3:  3.7718 -  3.3008 0.99   1331  149 0.1098 0.1586      5.5061       5.867|
|  4:  3.3008 -  3.0017 0.99   1331  144 0.1232 0.1700      5.4651      5.6649|
|  5:  3.0017 -  2.7880 0.99   1311  151 0.1358 0.1621      5.3647      5.5375|
|  6:  2.7880 -  2.6246 0.99   1328  145 0.1290 0.2175      5.2563      5.5773|
|  7:  2.6246 -  2.4938 0.99   1291  146 0.1338 0.1752        5.24      5.3829|
|  8:  2.4938 -  2.3856 0.98   1295  141 0.1202 0.1774       5.141      5.3965|
|  9:  2.3856 -  2.2941 0.98   1317  146 0.1251 0.2088      5.0879      5.4329|
| 10:  2.2941 -  2.2152 0.98   1280  139 0.1162 0.1617      5.0148      5.1947|
| 11:  2.2152 -  2.1462 0.99   1294  154 0.1204 0.2080      4.9909      5.3782|
| 12:  2.1462 -  2.0850 0.97   1281  131 0.1241 0.1640       4.947      5.1701|
| 13:  2.0850 -  2.0302 0.95   1255  136 0.1108 0.1817      4.8061      5.0425|
| 14:  2.0302 -  1.9808 0.42    537   69 0.0920 0.1710      4.6473      4.9568|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7272  1415   157  0.93  10.08   0.97     0.94       8343.19|
|  2:  4.7272 -  3.7718  1364   151  0.95   8.60   1.01     1.00       9938.90|
|  3:  3.7718 -  3.3008  1331   149  0.93  12.16   1.03     1.03      11181.12|
|  4:  3.3008 -  3.0017  1331   144  0.92  14.00   1.02     1.01      10799.01|
|  5:  3.0017 -  2.7880  1311   151  0.90  16.64   1.01     0.98       9157.66|
|  6:  2.7880 -  2.6246  1328   145  0.88  17.83   0.98     0.95       8046.12|
|  7:  2.6246 -  2.4938  1291   146  0.89  17.05   0.99     0.94       7289.09|
|  8:  2.4938 -  2.3856  1295   141  0.89  16.95   1.00     0.97       6464.37|
|  9:  2.3856 -  2.2941  1317   146  0.89  17.34   1.00     0.96       5789.08|
| 10:  2.2941 -  2.2152  1280   139  0.89  17.24   1.00     0.96       5152.63|
| 11:  2.2152 -  2.1462  1294   154  0.88  18.08   0.99     0.95       5097.27|
| 12:  2.1462 -  2.0850  1281   131  0.89  17.52   1.00     0.99       4619.62|
| 13:  2.0850 -  2.0302  1255   136  0.90  16.87   0.99     0.96       3586.52|
| 14:  2.0302 -  1.9808   537    69  0.92  13.52   0.98     0.94       2556.30|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2556.30 max =        11181.12 mean =      7243.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.28|
|phase err.(test): min =        0.00 max =           89.83 mean =        14.76|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.77    105.08  16.21    None  None   None       |
|    all(noH): 2823   0      2.77    105.08  16.21    None  None   None       |
|    Sol.    : 438    0      3.89    105.08  41.91    None  None   None       |
|    Mac.    : 2385   0      2.77    93.18   11.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.771 -  13.002: 1808   |   5:    53.925 -  64.156:   79        |
|      1:    13.002 -  23.233:  489   |   6:    64.156 -  74.387:   41        |
|      2:    23.233 -  33.464:  160   |   7:    74.387 -  84.618:   20        |
|      3:    33.464 -  43.695:  123   |   8:    84.618 -  94.849:    8        |
|      4:    43.695 -  53.925:   93   |   9:    94.849 - 105.080:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.138 - 5.605
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 313
   mapped sites are within: 0.713 - 5.605

peak=   10.595 closest distance to " CB  VAL A 230 " =    1.433
peak=    5.793 closest distance to " NE2 GLN A  11 " =    1.153
peak=    5.605 closest distance to " CD2 LEU A   5 " =    1.168
peak=    5.565 closest distance to " CB  VAL A 296 " =    1.031
peak=    5.565 closest distance to " CG  LEU A   5 " =    1.189
peak=    5.464 closest distance to " NH2 ARG A  56 " =    2.060
peak=    5.412 closest distance to " CG  LEU A 228 " =    1.196
peak=    5.339 closest distance to " CG  PRO A  54 " =    1.322
peak=    5.194 closest distance to " CB  GLN A 223 " =    1.514
peak=    5.079 closest distance to " O   HOH Z 142 " =    1.835
peak=    4.789 closest distance to " O   HOH Z 265 " =    2.054
peak=    4.750 closest distance to " O   HOH Z 248 " =    1.443
peak=    4.731 closest distance to " O   HOH Z 126 " =    1.620
peak=    4.684 closest distance to " CG2 VAL A 296 " =    1.032
peak=    4.679 closest distance to " CB  GLN A 183 " =    1.241
peak=    4.629 closest distance to " O   HOH Z 232 " =    2.304
peak=    4.609 closest distance to " O   HOH Z 313 " =    2.074
peak=    4.559 closest distance to " O   SER A  87 " =    2.431
peak=    4.546 closest distance to " O   HOH Z   9 " =    1.437
peak=    4.534 closest distance to " O   HOH Z 369 " =    2.301
peak=    4.529 closest distance to " O   HOH Z 251 " =    1.705
peak=    4.520 closest distance to " O   HOH Z 406 " =    1.602
peak=    4.456 closest distance to " O   HOH Z 425 " =    1.466
peak=    4.427 closest distance to " O   HOH Z 427 " =    2.980
peak=    4.420 closest distance to " CB  ASN A 142 " =    1.178
peak=    4.391 closest distance to " CB  ARG A 275 " =    0.977
peak=    4.364 closest distance to " CB  ARG A 190 " =    1.592
peak=    4.356 closest distance to " CA  TYR A  30 " =    0.959
peak=    4.320 closest distance to " CB  ASN A 148 " =    1.507
peak=    4.307 closest distance to " CZ  PHE A 218 " =    1.140
peak=    4.303 closest distance to " CB  PRO A  54 " =    0.900
peak=    4.302 closest distance to " O   HOH Z 193 " =    1.469
peak=    4.300 closest distance to " CB  GLU A 277 " =    3.691
peak=    4.280 closest distance to " O   HOH Z  76 " =    1.151
peak=    4.277 closest distance to " CG1 VAL A 296 " =    1.208
peak=    4.255 closest distance to " CG  PRO A 243 " =    1.079
peak=    4.201 closest distance to " CZ3 TRP A 266 " =    1.135
peak=    4.189 closest distance to " O   PRO A 198 " =    1.604
peak=    4.180 closest distance to " O   HOH Z 368 " =    2.368
peak=    4.161 closest distance to " ND2 ASN A 187 " =    1.558
peak=    4.121 closest distance to " O   HOH Z 261 " =    2.299
peak=    4.111 closest distance to " NH2AARG A 145 " =    1.157
peak=    4.108 closest distance to " CG  GLN A  58 " =    0.884
peak=    4.103 closest distance to " CD2 TRP A 179 " =    1.298
peak=    4.096 closest distance to " O  BHOH Z 338 " =    2.306
peak=    4.094 closest distance to " O   HOH Z  78 " =    1.606
peak=    4.084 closest distance to " O   HOH Z 287 " =    1.905
peak=    4.070 closest distance to " CG  PRO A 213 " =    1.150
peak=    4.054 closest distance to " O   HOH Z 303 " =    2.080
peak=    4.048 closest distance to " O   HOH Z 128 " =    1.114
peak=    4.030 closest distance to " CB  SER A  63 " =    1.139
peak=    4.029 closest distance to " CE  LYS A  76 " =    0.875
peak=    4.020 closest distance to " O   HOH Z 290 " =    1.015
peak=    4.017 closest distance to " O   HOH Z 359 " =    1.797
peak=    4.017 closest distance to " CG2 ILE A 234 " =    1.099
peak=    4.013 closest distance to " CB  VAL A 230 " =    1.132
peak=    4.012 closest distance to " O   HOH Z 214 " =    2.532
peak=    4.011 closest distance to " CB  VAL A 265 " =    1.278
peak=    4.004 closest distance to " O   HOH Z 422 " =    2.643
peak=    3.986 closest distance to " O   HOH Z 346 " =    1.511
peak=    3.986 closest distance to " CB  ARG A  79 " =    1.506
peak=    3.970 closest distance to " CA  ARG A 195 " =    1.138
peak=    3.958 closest distance to " CA  VAL A 125 " =    1.153
peak=    3.941 closest distance to " CA  ALA A  51 " =    0.907
peak=    3.941 closest distance to " CD2 LEU A 228 " =    1.184
peak=    3.936 closest distance to " CB  PRO A  90 " =    1.108
peak=    3.935 closest distance to " CB  TYR A 169 " =    0.760
peak=    3.926 closest distance to " O   HOH Z  43 " =    1.979
peak=    3.872 closest distance to " O   HOH Z 353 " =    2.714
peak=    3.872 closest distance to " N   ASN A  39 " =    1.282
peak=    3.866 closest distance to " O   HOH Z 203 " =    1.637
peak=    3.856 closest distance to " O   HOH Z 214 " =    1.300
peak=    3.840 closest distance to " O   HOH Z 188 " =    2.851
peak=    3.840 closest distance to " CB  THR A  52 " =    0.801
peak=    3.832 closest distance to " O   HOH Z 193 " =    1.722
peak=    3.826 closest distance to " CG  MET A 185 " =    1.334
peak=    3.812 closest distance to " CB  VAL A 202 " =    1.560
peak=    3.807 closest distance to " NH1AARG A 145 " =    1.232
peak=    3.807 closest distance to " O   HOH Z  59 " =    2.165
peak=    3.792 closest distance to " ND2 ASN A 249 " =    0.906
peak=    3.789 closest distance to " CA  ALA A 160 " =    0.908
peak=    3.779 closest distance to " CB  ASP A 124 " =    0.852
peak=    3.779 closest distance to " O   HOH Z 207 " =    1.127
peak=    3.775 closest distance to " CB  ASP A 140 " =    1.241
peak=    3.775 closest distance to " O   HOH Z 299 " =    4.269
peak=    3.768 closest distance to " O   HOH Z   3 " =    1.979
peak=    3.757 closest distance to " O   HOH Z 126 " =    2.070
peak=    3.753 closest distance to " CB  GLU A 152 " =    1.186
peak=    3.750 closest distance to " O   HOH Z   4 " =    1.483
peak=    3.737 closest distance to " O   HOH Z  80 " =    1.769
peak=    3.734 closest distance to " O   HOH Z 411 " =    4.032
peak=    3.725 closest distance to " O   HOH Z 298 " =    1.810
peak=    3.724 closest distance to " O   HOH Z 193 " =    1.560
peak=    3.721 closest distance to " O   HOH Z  88 " =    3.592
peak=    3.716 closest distance to " CB  TRP A 266 " =    1.093
peak=    3.713 closest distance to " O   HOH Z 365 " =    2.702
peak=    3.708 closest distance to " CG AARG A 275 " =    1.281
peak=    3.706 closest distance to " O   HOH Z 403 " =    1.567
peak=    3.702 closest distance to " CB  LYS A 117 " =    1.229
peak=    3.702 closest distance to " CD  ARG A 269 " =    0.973
peak=    3.696 closest distance to " O   HOH Z  61 " =    1.808
peak=    3.685 closest distance to " CZ  PHE A  38 " =    1.151
peak=    3.675 closest distance to " CG  LEU A 167 " =    1.257
peak=    3.675 closest distance to " O   HOH Z 402 " =    1.334
peak=    3.667 closest distance to " O   HOH Z  85 " =    1.255
peak=    3.656 closest distance to " CB  SER A  26 " =    1.846
peak=    3.647 closest distance to " CG  PRO A 198 " =    1.245
peak=    3.647 closest distance to " CG2 VAL A 257 " =    0.736
peak=    3.646 closest distance to " O   HOH Z 258 " =    1.193
peak=    3.644 closest distance to " CA  ARG A  36 " =    1.044
peak=    3.642 closest distance to " O   HOH Z 423 " =    1.835
peak=    3.640 closest distance to " O   HOH Z  92 " =    2.090
peak=    3.634 closest distance to " OG BSER A 164 " =    2.264
peak=    3.629 closest distance to " O   HOH Z 371 " =    2.671
peak=    3.624 closest distance to " O   HOH Z 258 " =    1.832
peak=    3.618 closest distance to " OD1 ASN A  69 " =    2.519
peak=    3.617 closest distance to " O   HOH Z 128 " =    2.074
peak=    3.617 closest distance to " O   HOH Z 316 " =    3.081
peak=    3.615 closest distance to " O   HOH Z 280 " =    2.990
peak=    3.609 closest distance to " O   HOH Z 263 " =    1.724
peak=    3.608 closest distance to " CG  ARG A  66 " =    2.521
peak=    3.608 closest distance to " O   HOH Z  66 " =    2.273
peak=    3.607 closest distance to " CD  ARG A 159 " =    0.735
peak=    3.593 closest distance to " CB  GLN A  89 " =    1.341
peak=    3.580 closest distance to " O   ASP A 124 " =    1.155
peak=    3.580 closest distance to " O   HOH Z 188 " =    1.439
peak=    3.575 closest distance to " CB  ARG A  79 " =    0.928
peak=    3.573 closest distance to " O   HOH Z  40 " =    1.683
peak=    3.571 closest distance to " CD  LYS A  76 " =    1.933
peak=    3.571 closest distance to " CA  ALA A 295 " =    1.038
peak=    3.565 closest distance to " CD  LYS A 166 " =    1.318
peak=    3.564 closest distance to " OE2 GLU A  53 " =    1.923
peak=    3.562 closest distance to " O   HOH Z 303 " =    3.051
peak=    3.555 closest distance to " NZ  LYS A  48 " =    1.133
peak=    3.553 closest distance to " CB  TRP A 179 " =    1.501
peak=    3.543 closest distance to " NE2 HIS A 207 " =    1.206
peak=    3.541 closest distance to " CB  GLU A 128 " =    1.005
peak=    3.532 closest distance to " CB  THR A  31 " =    1.624
peak=    3.526 closest distance to " CG AARG A 102 " =    1.189
peak=    3.521 closest distance to " O   HOH Z 272 " =    1.785
peak=    3.515 closest distance to " O   HOH Z 109 " =    1.163
peak=    3.510 closest distance to " O   HOH Z  49 " =    1.084
peak=    3.504 closest distance to " CG  LEU A   5 " =    0.754
peak=    3.504 closest distance to " CE3 TRP A 150 " =    1.149
peak=    3.494 closest distance to " O   HOH Z 286 " =    2.464
peak=    3.488 closest distance to " O   HOH Z 148 " =    3.470
peak=    3.484 closest distance to " CB  SER A 212 " =    1.273
peak=    3.482 closest distance to " CB  ASN A  39 " =    0.925
peak=    3.478 closest distance to " O   HOH Z  85 " =    1.517
peak=    3.476 closest distance to " CA  ILE A 234 " =    1.016
peak=    3.475 closest distance to " CB  SER A   3 " =    1.380
peak=    3.471 closest distance to " O   HOH Z 213 " =    1.867
peak=    3.470 closest distance to " CD1 ILE A 199 " =    1.140
peak=    3.462 closest distance to " O   HOH Z  63 " =    1.718
peak=    3.459 closest distance to " O   HOH Z 368 " =    3.371
peak=    3.459 closest distance to " O   HOH Z 329 " =    4.233
peak=    3.458 closest distance to " CG  GLU A  37 " =    0.944
peak=    3.456 closest distance to " O   HOH Z 234 " =    3.511
peak=    3.452 closest distance to " CB  ALA A 248 " =    1.404
peak=    3.452 closest distance to " O   HOH Z  44 " =    1.589
peak=    3.452 closest distance to " O   HOH Z 133 " =    2.770
peak=    3.442 closest distance to " CG1 ILE A  49 " =    1.531
peak=    3.440 closest distance to " CB  ASP A 298 " =    1.159
peak=    3.438 closest distance to " CB  ASN A 215 " =    1.200
peak=    3.432 closest distance to " O   HOH Z 244 " =    1.694
peak=    3.430 closest distance to " O   HOH Z 380 " =    1.795
peak=    3.427 closest distance to " CA  ALA A 291 " =    0.858
peak=    3.426 closest distance to " O   HOH Z 172 " =    3.842
peak=    3.424 closest distance to " CA  ALA A 158 " =    1.334
peak=    3.420 closest distance to " CB  ASN A 110 " =    1.171
peak=    3.417 closest distance to " OG BSER A 164 " =    2.199
peak=    3.414 closest distance to " O   HOH Z 199 " =    1.638
peak=    3.414 closest distance to " CA  ASN A 127 " =    0.991
peak=    3.412 closest distance to " O   ASN A  74 " =    1.376
peak=    3.406 closest distance to " CA  LYS A 117 " =    1.307
peak=    3.404 closest distance to " N   ASP A 162 " =    1.177
peak=    3.396 closest distance to " OG  SER A  22 " =    2.749
peak=    3.395 closest distance to " O   HOH Z 361 " =    3.665
peak=    3.393 closest distance to " CA  LEU A  83 " =    1.113
peak=    3.389 closest distance to " NZ  LYS A 117 " =    3.197
peak=    3.388 closest distance to " O   HOH Z 337 " =    2.048
peak=    3.387 closest distance to " O   HOH Z  30 " =    1.380
peak=    3.384 closest distance to " O   HOH Z   1 " =    1.849
peak=    3.384 closest distance to " CB  GLU A  46 " =    0.999
peak=    3.384 closest distance to " O   HOH Z 438 " =    2.881
peak=    3.381 closest distance to " CG2 ILE A  20 " =    1.467
peak=    3.373 closest distance to " CA  TYR A 116 " =    1.440
peak=    3.370 closest distance to " O   HOH Z 325 " =    2.206
peak=    3.367 closest distance to " N   ALA A 256 " =    1.082
peak=    3.366 closest distance to " O   HOH Z 128 " =    0.976
peak=    3.360 closest distance to " CE1 TYR A 186 " =    1.271
peak=    3.357 closest distance to " CA  MET A 105 " =    1.013
peak=    3.355 closest distance to " O   ALA A 165 " =    1.460
peak=    3.353 closest distance to " CB AVAL A  41 " =    1.117
peak=    3.351 closest distance to " O   HOH Z 158 " =    3.138
peak=    3.338 closest distance to " O   HOH Z 417 " =    3.373
peak=    3.333 closest distance to " O   HOH Z 171 " =    3.968
peak=    3.327 closest distance to " CA  ARG A 102 " =    1.152
peak=    3.324 closest distance to " CB  GLN A 205 " =    1.030
peak=    3.321 closest distance to " CB  GLN A  88 " =    1.287
peak=    3.321 closest distance to " O   HOH Z 345 " =    3.351
peak=    3.320 closest distance to " CA  ARG A 139 " =    1.079
peak=    3.319 closest distance to " C   ILE A 106 " =    1.895
peak=    3.319 closest distance to " NH2 ARG A  56 " =    1.117
peak=    3.313 closest distance to " CG2 ILE A 120 " =    1.163
peak=    3.313 closest distance to " CA  ALA A 129 " =    1.476
peak=    3.311 closest distance to " O   HOH Z 385 " =    3.957
peak=    3.310 closest distance to " O   HOH Z 305 " =    3.400
peak=    3.302 closest distance to " CB  SER A  62 " =    0.975
peak=    3.301 closest distance to " CD1 ILE A  33 " =    1.745
peak=    3.300 closest distance to " CB  ALA A   9 " =    1.602
peak=    3.292 closest distance to " CA  ALA A 154 " =    1.059
peak=    3.286 closest distance to " CB  TYR A  30 " =    1.149
peak=    3.286 closest distance to " CD BLYS A 290 " =    1.101
peak=    3.285 closest distance to " O   HOH Z 227 " =    1.746
peak=    3.278 closest distance to " O   HOH Z 285 " =    2.206
peak=    3.277 closest distance to " O   HOH Z 180 " =    2.152
peak=    3.277 closest distance to " CB  SER A  97 " =    0.895
peak=    3.276 closest distance to " CG  PHE A 204 " =    0.910
peak=    3.274 closest distance to " CA  ASP A 191 " =    1.317
peak=    3.271 closest distance to " CA  ASN A 217 " =    1.169
peak=    3.270 closest distance to " CG1BVAL A  72 " =    1.818
peak=    3.269 closest distance to " O   HOH Z 162 " =    1.421
peak=    3.269 closest distance to " CA  LEU A 282 " =    1.161
peak=    3.269 closest distance to " CB  THR A 235 " =    1.624
peak=    3.268 closest distance to " CA  SER A 146 " =    1.819
peak=    3.267 closest distance to " CB  LEU A  83 " =    0.713
peak=    3.266 closest distance to " O   HOH Z 394 " =    3.601
peak=    3.262 closest distance to " O   HOH Z 250 " =    1.244
peak=    3.260 closest distance to " O   HOH Z  10 " =    1.708
peak=    3.257 closest distance to " O   HOH Z 209 " =    2.222
peak=    3.255 closest distance to " CE  LYS A  48 " =    1.142
peak=    3.253 closest distance to " ND2BASN A 224 " =    0.733
peak=    3.247 closest distance to " O   THR A 182 " =    1.413
peak=    3.245 closest distance to " CB  HIS A 108 " =    0.835
peak=    3.245 closest distance to " O   HOH Z 403 " =    1.955
peak=    3.243 closest distance to " O   HOH Z 141 " =    1.588
peak=    3.242 closest distance to " O   HOH Z 117 " =    2.073
peak=    3.240 closest distance to " O   HOH Z  32 " =    2.032
peak=    3.236 closest distance to " CB  ARG A 145 " =    0.892
peak=    3.233 closest distance to " CG BARG A 102 " =    1.836
peak=    3.228 closest distance to " NE2 GLN A  77 " =    3.294
peak=    3.227 closest distance to " N   TYR A 247 " =    1.365
peak=    3.227 closest distance to " O   GLN A  88 " =    1.635
peak=    3.226 closest distance to " O   HOH Z 124 " =    1.165
peak=    3.226 closest distance to " CA  THR A 264 " =    0.879
peak=    3.224 closest distance to " O   HOH Z   1 " =    1.500
peak=    3.219 closest distance to " CG1 ILE A  20 " =    1.316
peak=    3.219 closest distance to " O   HOH Z 246 " =    1.248
peak=    3.216 closest distance to " O   HOH Z  94 " =    2.361
peak=    3.216 closest distance to " OG1 THR A 264 " =    0.730
peak=    3.215 closest distance to " CA  LYS A 290 " =    1.219
peak=    3.215 closest distance to " CB  PHE A 204 " =    0.956
peak=    3.213 closest distance to " CG  GLN A  55 " =    2.525
peak=    3.213 closest distance to " O   HOH Z  88 " =    2.907
peak=    3.211 closest distance to " CA  ALA A  21 " =    1.101
peak=    3.204 closest distance to " O   HOH Z 106 " =    1.885
peak=    3.202 closest distance to " CB  ARG A 156 " =    1.139
peak=    3.202 closest distance to " O   HOH Z 189 " =    2.900
peak=    3.200 closest distance to " N   PHE A 130 " =    1.302
peak=    3.195 closest distance to " O   HOH Z 430 " =    5.605
peak=    3.190 closest distance to " CG2BVAL A 121 " =    0.743
peak=    3.185 closest distance to " OG  SER A  62 " =    2.848
peak=    3.183 closest distance to " O   PHE A 192 " =    1.402
peak=    3.183 closest distance to " CG1 VAL A 153 " =    0.945
peak=    3.182 closest distance to " O   HOH Z 187 " =    2.290
peak=    3.181 closest distance to " CD  ARG A  66 " =    2.492
peak=    3.174 closest distance to " NH1 ARG A 138 " =    1.019
peak=    3.173 closest distance to " O   ASN A 284 " =    1.723
peak=    3.172 closest distance to " CB  SER A 288 " =    1.488
peak=    3.171 closest distance to " O   HOH Z 200 " =    2.102
peak=    3.163 closest distance to " CD2 LEU A 297 " =    0.886
peak=    3.160 closest distance to " CA  GLY A 267 " =    0.959
peak=    3.158 closest distance to " O   LEU A 228 " =    1.883
peak=    3.146 closest distance to " O   HOH Z 410 " =    3.036
peak=    3.146 closest distance to " CA  ASP A 162 " =    0.998
peak=    3.144 closest distance to " O   HOH Z 148 " =    2.088
peak=    3.136 closest distance to " O   HOH Z 293 " =    1.822
peak=    3.132 closest distance to " CB  ARG A 139 " =    0.988
peak=    3.131 closest distance to " CE  LYS A 119 " =    1.067
peak=    3.122 closest distance to " OG BSER A  99 " =    2.279
peak=    3.118 closest distance to " O   HOH Z 357 " =    2.157
peak=    3.117 closest distance to " CB  LEU A 300 " =    0.894
peak=    3.116 closest distance to " CB  ARG A 219 " =    0.972
peak=    3.109 closest distance to " O   HOH Z 417 " =    2.430
peak=    3.105 closest distance to " CA  SER A  87 " =    1.073
peak=    3.104 closest distance to " CD1 ILE A 263 " =    1.108
peak=    3.095 closest distance to " CD2 TYR A 186 " =    1.071
peak=    3.093 closest distance to " CD  LYS A 119 " =    2.014
peak=    3.078 closest distance to " O   SER A 164 " =    1.184
peak=    3.077 closest distance to " CG  LEU A 281 " =    0.989
peak=    3.072 closest distance to " CB  ALA A 227 " =    1.039
peak=    3.071 closest distance to " CB  PRO A 243 " =    1.326
peak=    3.067 closest distance to " CD1 LEU A 261 " =    1.186
peak=    3.065 closest distance to " O   HOH Z 238 " =    1.278
peak=    3.063 closest distance to " CA  GLN A  94 " =    0.799
peak=    3.059 closest distance to " O   HOH Z 371 " =    1.347
peak=    3.041 closest distance to " O   HOH Z 371 " =    3.351
peak=    3.039 closest distance to " NH2BARG A 190 " =    2.080
peak=    3.035 closest distance to " O   HOH Z 327 " =    2.314
peak=    3.033 closest distance to " CG  LYS A 289 " =    1.340
peak=    3.031 closest distance to " O   HOH Z 357 " =    2.515
peak=    2.912 closest distance to " O   HOH Z 371 " =    1.697

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.829 - 5.653
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 202
   mapped sites are within: 0.829 - 5.653

peak=   -4.922 closest distance to " CD  ARG A  14 " =    3.307
peak=   -4.400 closest distance to " CZ2 TRP A  92 " =    2.846
peak=   -4.372 closest distance to " CB  PRO A 243 " =    2.760
peak=   -4.326 closest distance to " OG BSER A 134 " =    1.410
peak=   -4.323 closest distance to " OE1 GLN A 223 " =    2.350
peak=   -4.321 closest distance to " C   HIS A 108 " =    1.187
peak=   -4.289 closest distance to " O   HOH Z 211 " =    1.038
peak=   -4.219 closest distance to " O   HOH Z 267 " =    5.589
peak=   -4.212 closest distance to " CA  ASP A 298 " =    1.104
peak=   -4.189 closest distance to " O   VAL A  67 " =    2.608
peak=   -4.182 closest distance to " CG  GLN A  58 " =    1.049
peak=   -4.174 closest distance to " O   HOH Z 193 " =    0.831
peak=   -4.078 closest distance to " CG2 VAL A 230 " =    0.829
peak=   -4.036 closest distance to " CD  ARG A 156 " =    2.044
peak=   -4.010 closest distance to " CB  PHE A 192 " =    1.999
peak=   -4.006 closest distance to " CG1 VAL A 250 " =    2.708
peak=   -3.993 closest distance to " O   HOH Z 100 " =    0.918
peak=   -3.965 closest distance to " O   PRO A 198 " =    1.250
peak=   -3.962 closest distance to " O   HOH Z 231 " =    2.201
peak=   -3.959 closest distance to " O   HOH Z 359 " =    2.852
peak=   -3.947 closest distance to " O   HOH Z 394 " =    1.613
peak=   -3.911 closest distance to " O   HOH Z 103 " =    1.718
peak=   -3.910 closest distance to " CE BMET A  47 " =    1.289
peak=   -3.901 closest distance to " O   HOH Z  73 " =    2.448
peak=   -3.890 closest distance to " O   HOH Z  69 " =    1.658
peak=   -3.890 closest distance to " OG  SER A  97 " =    2.392
peak=   -3.848 closest distance to " O   HOH Z 166 " =    2.234
peak=   -3.842 closest distance to " CG1 VAL A 112 " =    2.756
peak=   -3.825 closest distance to " CA  VAL A  67 " =    3.032
peak=   -3.811 closest distance to " CG2 THR A  18 " =    2.883
peak=   -3.795 closest distance to " O   HOH Z 131 " =    4.050
peak=   -3.791 closest distance to " CE2 TYR A  30 " =    2.603
peak=   -3.788 closest distance to " O   HOH Z 133 " =    1.163
peak=   -3.785 closest distance to " CE3 TRP A 150 " =    2.369
peak=   -3.783 closest distance to " CD1 LEU A 101 " =    2.360
peak=   -3.769 closest distance to " O   PRO A 163 " =    2.109
peak=   -3.767 closest distance to " O   ALA A 227 " =    1.327
peak=   -3.760 closest distance to " NE2 GLN A  11 " =    1.790
peak=   -3.739 closest distance to " O   HOH Z  11 " =    2.238
peak=   -3.718 closest distance to " CD1 ILE A 199 " =    2.414
peak=   -3.712 closest distance to " CG2 VAL A 296 " =    1.247
peak=   -3.706 closest distance to " CB  ALA A 161 " =    2.515
peak=   -3.703 closest distance to " O   HOH Z 216 " =    1.255
peak=   -3.692 closest distance to " CB  ALA A  43 " =    2.628
peak=   -3.690 closest distance to " CG1 VAL A 296 " =    1.092
peak=   -3.667 closest distance to " CB  HIS A  86 " =    1.136
peak=   -3.662 closest distance to " O   HOH Z 115 " =    1.822
peak=   -3.655 closest distance to " OXT GLY A 302 " =    3.068
peak=   -3.650 closest distance to " O   HOH Z 198 " =    1.849
peak=   -3.649 closest distance to " CD2 TYR A 293 " =    1.980
peak=   -3.647 closest distance to " ND2 ASN A 249 " =    2.360
peak=   -3.631 closest distance to " CE2 PHE A  61 " =    2.659
peak=   -3.628 closest distance to " O   SER A 271 " =    2.047
peak=   -3.627 closest distance to " CG2 VAL A 189 " =    1.996
peak=   -3.621 closest distance to " N   THR A  52 " =    1.695
peak=   -3.616 closest distance to " CB  PRO A 280 " =    2.150
peak=   -3.597 closest distance to " CG2 THR A 178 " =    2.376
peak=   -3.596 closest distance to " CG  GLU A 277 " =    1.253
peak=   -3.593 closest distance to " O   HOH Z 128 " =    1.038
peak=   -3.568 closest distance to " O   HOH Z 295 " =    1.679
peak=   -3.563 closest distance to " O   HOH Z 191 " =    5.653
peak=   -3.558 closest distance to " CE  MET A 105 " =    2.375
peak=   -3.558 closest distance to " O   HOH Z  68 " =    1.288
peak=   -3.552 closest distance to " O   HOH Z 149 " =    1.956
peak=   -3.534 closest distance to " O   HOH Z 166 " =    1.844
peak=   -3.533 closest distance to " OG  SER A  62 " =    4.234
peak=   -3.523 closest distance to " O   HOH Z 238 " =    0.877
peak=   -3.511 closest distance to " CG  ARG A 269 " =    2.245
peak=   -3.501 closest distance to " ND2 ASN A  45 " =    1.277
peak=   -3.491 closest distance to " CA  GLY A 241 " =    2.416
peak=   -3.490 closest distance to " CE2 TRP A  70 " =    2.124
peak=   -3.489 closest distance to " CG2 VAL A 202 " =    2.813
peak=   -3.483 closest distance to " CA  ASP A  27 " =    2.466
peak=   -3.482 closest distance to " O   HOH Z 429 " =    1.767
peak=   -3.475 closest distance to " O   HOH Z 285 " =    1.999
peak=   -3.472 closest distance to " O   LYS A  76 " =    1.703
peak=   -3.470 closest distance to " CD2 PHE A 225 " =    1.144
peak=   -3.465 closest distance to " O   HOH Z 371 " =    2.393
peak=   -3.464 closest distance to " CG1 VAL A 112 " =    2.658
peak=   -3.464 closest distance to " CD1 LEU A 255 " =    2.833
peak=   -3.454 closest distance to " O   ASN A 252 " =    1.367
peak=   -3.452 closest distance to " O   HOH Z 275 " =    1.544
peak=   -3.451 closest distance to " O   SER A 210 " =    1.747
peak=   -3.450 closest distance to " C   ALA A 158 " =    1.139
peak=   -3.450 closest distance to " O   HOH Z 351 " =    1.644
peak=   -3.448 closest distance to " CG1 VAL A 125 " =    1.920
peak=   -3.442 closest distance to " CA  GLY A 203 " =    2.546
peak=   -3.441 closest distance to " O   HOH Z 127 " =    1.118
peak=   -3.426 closest distance to " O   HOH Z 110 " =    1.422
peak=   -3.418 closest distance to " O   ASP A  27 " =    1.932
peak=   -3.412 closest distance to " O   HOH Z 236 " =    1.370
peak=   -3.410 closest distance to " CG  ASP A 286 " =    1.711
peak=   -3.405 closest distance to " O   HOH Z 286 " =    1.962
peak=   -3.401 closest distance to " O   HOH Z 128 " =    2.253
peak=   -3.400 closest distance to " O   HOH Z 364 " =    2.825
peak=   -3.397 closest distance to " O   HOH Z   9 " =    1.511
peak=   -3.397 closest distance to " O   HOH Z 174 " =    2.400
peak=   -3.385 closest distance to " CB  ALA A 248 " =    2.287
peak=   -3.384 closest distance to " O   HOH Z 106 " =    1.664
peak=   -3.377 closest distance to " CG  TRP A 266 " =    1.810
peak=   -3.370 closest distance to " CG  PRO A 243 " =    1.681
peak=   -3.364 closest distance to " O   HOH Z 345 " =    2.205
peak=   -3.362 closest distance to " O   SER A 141 " =    1.831
peak=   -3.357 closest distance to " O   HOH Z 265 " =    2.420
peak=   -3.354 closest distance to " CE3 TRP A 274 " =    2.284
peak=   -3.352 closest distance to " O   HOH Z 252 " =    3.769
peak=   -3.350 closest distance to " CA  GLY A 133 " =    2.272
peak=   -3.349 closest distance to " CD2 LEU A 237 " =    2.734
peak=   -3.347 closest distance to " OD1 ASN A 148 " =    1.369
peak=   -3.343 closest distance to " O   HOH Z 421 " =    3.122
peak=   -3.335 closest distance to " OE1 GLN A 223 " =    2.240
peak=   -3.334 closest distance to " OH  TYR A 172 " =    1.820
peak=   -3.331 closest distance to " N   ALA A 226 " =    1.996
peak=   -3.330 closest distance to " O   TYR A 186 " =    1.795
peak=   -3.330 closest distance to " CB  ALA A 248 " =    2.188
peak=   -3.325 closest distance to " NE  ARG A  66 " =    4.262
peak=   -3.316 closest distance to " O   HOH Z 251 " =    5.084
peak=   -3.313 closest distance to " O   HOH Z 250 " =    1.828
peak=   -3.313 closest distance to " O   HOH Z 111 " =    1.620
peak=   -3.309 closest distance to " ND2 ASN A  69 " =    1.966
peak=   -3.302 closest distance to " CD  LYS A 289 " =    2.407
peak=   -3.301 closest distance to " O   HOH Z  52 " =    1.595
peak=   -3.298 closest distance to " O   HOH Z 119 " =    2.172
peak=   -3.298 closest distance to " CB  ALA A  10 " =    2.312
peak=   -3.297 closest distance to " O   HOH Z  11 " =    1.869
peak=   -3.294 closest distance to " O   HOH Z 431 " =    1.960
peak=   -3.292 closest distance to " NE2 GLN A 278 " =    1.850
peak=   -3.289 closest distance to " O   HOH Z 137 " =    1.681
peak=   -3.278 closest distance to " O   LYS A 289 " =    3.080
peak=   -3.275 closest distance to " O   HOH Z 165 " =    1.990
peak=   -3.272 closest distance to " CZ  PHE A  38 " =    2.433
peak=   -3.271 closest distance to " CD  PRO A 243 " =    1.887
peak=   -3.268 closest distance to " O   HOH Z 276 " =    1.644
peak=   -3.267 closest distance to " NE2 GLN A  88 " =    1.202
peak=   -3.265 closest distance to " O   PHE A 218 " =    1.461
peak=   -3.265 closest distance to " O   HOH Z 116 " =    1.928
peak=   -3.258 closest distance to " N   ALA A  43 " =    2.745
peak=   -3.255 closest distance to " O   GLN A  94 " =    2.280
peak=   -3.246 closest distance to " N   SER A 276 " =    1.434
peak=   -3.244 closest distance to " O   HOH Z 102 " =    1.580
peak=   -3.244 closest distance to " CB  PRO A 163 " =    2.448
peak=   -3.232 closest distance to " CZ2 TRP A 274 " =    1.029
peak=   -3.232 closest distance to " CB  TRP A  85 " =    2.661
peak=   -3.229 closest distance to " O   HOH Z 114 " =    3.046
peak=   -3.224 closest distance to " O   HOH Z 307 " =    2.091
peak=   -3.221 closest distance to " C   ASN A 285 " =    2.215
peak=   -3.220 closest distance to " O   VAL A 189 " =    2.768
peak=   -3.215 closest distance to " CE3 TRP A  70 " =    1.687
peak=   -3.209 closest distance to " ND2 ASN A  45 " =    1.630
peak=   -3.209 closest distance to " O   HOH Z  20 " =    1.286
peak=   -3.208 closest distance to " O   HOH Z 262 " =    2.513
peak=   -3.208 closest distance to " OXT GLY A 302 " =    3.492
peak=   -3.207 closest distance to " OD1 ASN A 249 " =    2.520
peak=   -3.206 closest distance to " O   HOH Z 407 " =    2.867
peak=   -3.202 closest distance to " CZ  TYR A 169 " =    1.843
peak=   -3.201 closest distance to " C   MET A 188 " =    1.441
peak=   -3.200 closest distance to " CD1 TYR A 247 " =    2.482
peak=   -3.198 closest distance to " O   TRP A  70 " =    1.615
peak=   -3.197 closest distance to " CB  ALA A 114 " =    2.503
peak=   -3.195 closest distance to " OD1 ASN A  39 " =    2.101
peak=   -3.195 closest distance to " O   HOH Z 350 " =    2.214
peak=   -3.195 closest distance to " O   HOH Z 162 " =    3.039
peak=   -3.191 closest distance to " O   HOH Z 348 " =    2.195
peak=   -3.191 closest distance to " ND2 ASN A 187 " =    1.576
peak=   -3.188 closest distance to " O   SER A 135 " =    1.498
peak=   -3.187 closest distance to " CA  GLY A 241 " =    3.186
peak=   -3.185 closest distance to " O   HOH Z  43 " =    1.712
peak=   -3.178 closest distance to " CB  ASN A  39 " =    2.292
peak=   -3.176 closest distance to " O   ILE A 234 " =    1.176
peak=   -3.176 closest distance to " O   HOH Z 185 " =    2.341
peak=   -3.173 closest distance to " O   ALA A 180 " =    1.426
peak=   -3.171 closest distance to " N   ALA A 248 " =    1.799
peak=   -3.165 closest distance to " O   GLY A  80 " =    2.634
peak=   -3.158 closest distance to " CB  ASP A 171 " =    2.183
peak=   -3.149 closest distance to " CE1 TYR A 247 " =    2.603
peak=   -3.145 closest distance to " CD1 LEU A 228 " =    2.239
peak=   -3.144 closest distance to " CG2 ILE A 263 " =    2.318
peak=   -3.137 closest distance to " O   ASN A 187 " =    1.586
peak=   -3.136 closest distance to " OD1 ASP A 171 " =    1.579
peak=   -3.136 closest distance to " CD2 HIS A 207 " =    2.224
peak=   -3.133 closest distance to " O   HOH Z  64 " =    1.507
peak=   -3.127 closest distance to " O   HOH Z 155 " =    2.261
peak=   -3.118 closest distance to " O   LYS A 117 " =    1.698
peak=   -3.115 closest distance to " CB  ALA A 129 " =    2.459
peak=   -3.103 closest distance to " O   HOH Z  89 " =    2.776
peak=   -3.103 closest distance to " O   HOH Z 139 " =    3.133
peak=   -3.101 closest distance to " CE1 TYR A 186 " =    2.342
peak=   -3.096 closest distance to " N   ALA A 248 " =    2.333
peak=   -3.090 closest distance to " CB  ASN A 148 " =    1.754
peak=   -3.090 closest distance to " CG1 VAL A 197 " =    2.251
peak=   -3.084 closest distance to " OD1 ASP A 200 " =    1.630
peak=   -3.082 closest distance to " CD  GLN A 223 " =    1.745
peak=   -3.081 closest distance to " O   PRO A 198 " =    1.413
peak=   -3.071 closest distance to " O   HOH Z   9 " =    2.918
peak=   -3.068 closest distance to " O   ILE A 106 " =    1.901
peak=   -3.050 closest distance to " CG  ARG A 259 " =    2.277
peak=   -3.038 closest distance to " O   HOH Z   6 " =    1.658
peak=   -3.037 closest distance to " OD1 ASN A 173 " =    1.435
peak=   -3.025 closest distance to " O   HOH Z 278 " =    1.239
peak=   -3.016 closest distance to " O   HOH Z 313 " =    1.713

================= 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    :  0.4706 0.4568   6.274688e+00   6.255831e+00
   1_bss:  0.4605 0.4476   6.266399e+00   6.244246e+00
   1_xyz:  0.3762 0.3953   6.143264e+00   6.172533e+00
   1_adp:  0.3288 0.3736   6.045929e+00   6.127296e+00
   1_occ:  0.3282 0.3747   6.045060e+00   6.129132e+00
   2_bss:  0.3245 0.3710   6.045835e+00   6.129533e+00
   2_xyz:  0.2343 0.2838   5.763139e+00   5.916956e+00
   2_adp:  0.2087 0.2613   5.668339e+00   5.846715e+00
   2_occ:  0.2086 0.2613   5.668095e+00   5.846672e+00
   3_bss:  0.2059 0.2617   5.667744e+00   5.848208e+00
   3_xyz:  0.1558 0.2083   5.424502e+00   5.635381e+00
   3_adp:  0.1433 0.1953   5.356914e+00   5.578408e+00
   3_occ:  0.1431 0.1949   5.356307e+00   5.578017e+00
   4_bss:  0.1428 0.1946   5.355574e+00   5.576360e+00
   4_xyz:  0.1304 0.1766   5.274404e+00   5.496750e+00
   4_adp:  0.1271 0.1749   5.259764e+00   5.486879e+00
   4_occ:  0.1269 0.1750   5.259420e+00   5.487322e+00
   5_bss:  0.1269 0.1750   5.259610e+00   5.487816e+00
   5_xyz:  0.1171 0.1669   5.202525e+00   5.447984e+00
   5_adp:  0.1156 0.1667   5.196158e+00   5.444601e+00
   5_occ:  0.1156 0.1666   5.195917e+00   5.444515e+00
   5_bss:  0.1153 0.1662   5.194668e+00   5.443053e+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:  0.336  14.859   6.899   7.355  12.500   0.000   0.000   0.000
   1_xyz:  0.336  14.859   6.899   7.355  12.500   0.000   0.000   0.000
   1_adp:  0.336  14.859   6.899   7.355  12.500   0.000   0.000   0.000
   1_occ:  0.336  14.859   6.899   7.355  12.500   0.000   0.000   0.000
   2_bss:  0.339  46.946   3.219   3.631   8.616   0.000   0.000   0.000
   2_xyz:  0.339  46.946   3.219   3.631   8.616   0.000   0.000   0.000
   2_adp:  0.339  46.946   3.219   3.631   8.616   0.000   0.000   0.000
   2_occ:  0.339  46.946   3.219   3.631   8.616   0.000   0.000   0.000
   3_bss:  0.318  56.913   1.667   2.465   5.198   0.000   0.000   0.000
   3_xyz:  0.318  56.913   1.667   2.465   5.198   0.000   0.000   0.000
   3_adp:  0.318  56.913   1.667   2.465   5.198   0.000   0.000   0.000
   3_occ:  0.318  56.913   1.667   2.465   5.198   0.000   0.000   0.000
   4_bss:  0.329  56.913   1.273   1.999   4.207   0.000   0.000   0.000
   4_xyz:  0.329  56.913   1.273   1.999   4.207   0.000   0.000   0.000
   4_adp:  0.329  56.913   1.273   1.999   4.207   0.000   0.000   0.000
   4_occ:  0.329  56.913   1.273   1.999   4.207   0.000   0.000   0.000
   5_bss:  0.329  56.913   1.493   2.167   4.107   0.000   0.000   0.000
   5_xyz:  0.329  56.913   1.493   2.167   4.107   0.000   0.000   0.000
   5_adp:  0.329  56.913   1.493   2.167   4.107   0.000   0.000   0.000
   5_occ:  0.329  56.913   1.493   2.167   4.107   0.000   0.000   0.000
   5_bss:  0.328  62.810  -1.043  -0.424   1.467   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.533 0.4771  0.5485    64482.722
   1_bss:  53.212 0.4800  0.7210    62722.461
   1_xyz:  44.216 0.5916  0.8602    45201.070
   1_adp:  40.191 0.6408  0.9638    39242.991
   1_occ:  40.270 0.6398  0.9612    39377.834
   2_bss:  40.031 0.6427  0.8470    39180.149
   2_xyz:  29.065 0.7675  0.9839    21187.560
   2_adp:  25.905 0.8022  1.0150    17762.489
   2_occ:  25.920 0.8021  1.0147    17760.227
   3_bss:  25.819 0.8033  0.9447    17804.482
   3_xyz:  19.754 0.8642  0.9818    10958.481
   3_adp:  18.343 0.8777  0.9823     9847.365
   3_occ:  18.334 0.8778  0.9823     9832.826
   4_bss:  18.285 0.8782  0.9614     9790.343
   4_xyz:  16.424 0.8947  0.9696     8167.930
   4_adp:  16.177 0.8971  0.9634     7993.301
   4_occ:  16.186 0.8970  0.9632     8002.900
   5_bss:  16.193 0.8970  0.9666     8011.638
   5_xyz:  15.345 0.9040  0.9712     7330.863
   5_adp:  15.252 0.9050  0.9641     7268.861
   5_occ:  15.248 0.9051  0.9640     7263.554
   5_bss:  15.232 0.9052  0.9701     7242.327
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.4025e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.4025e+01
   1_xyz:   1.641  0.013  0.104 18.108  0.006  4.109   1.3357e-01
   1_adp:   1.641  0.013  0.104 18.108  0.006  4.109   1.3357e-01
   1_occ:   1.641  0.013  0.104 18.108  0.006  4.109   1.3357e-01
   2_bss:   1.641  0.013  0.104 18.108  0.006  4.109   1.3357e-01
   2_xyz:   1.288  0.010  0.087 16.319  0.005  4.111   9.3458e-02
   2_adp:   1.288  0.010  0.087 16.319  0.005  4.111   9.3458e-02
   2_occ:   1.288  0.010  0.087 16.319  0.005  4.111   9.3458e-02
   3_bss:   1.288  0.010  0.087 16.319  0.005  4.111   9.3458e-02
   3_xyz:   1.086  0.008  0.080 16.028  0.004  4.129   7.0457e-02
   3_adp:   1.086  0.008  0.080 16.028  0.004  4.129   7.0457e-02
   3_occ:   1.086  0.008  0.080 16.028  0.004  4.129   7.0457e-02
   4_bss:   1.086  0.008  0.080 16.028  0.004  4.129   7.0457e-02
   4_xyz:   0.956  0.007  0.074 15.645  0.004  4.114   5.8347e-02
   4_adp:   0.956  0.007  0.074 15.645  0.004  4.114   5.8347e-02
   4_occ:   0.956  0.007  0.074 15.645  0.004  4.114   5.8347e-02
   5_bss:   0.956  0.007  0.074 15.645  0.004  4.114   5.8347e-02
   5_xyz:   1.123  0.010  0.088 15.715  0.004  4.119   7.5406e-02
   5_adp:   1.123  0.010  0.088 15.715  0.004  4.119   7.5406e-02
   5_occ:   1.123  0.010  0.088 15.715  0.004  4.119   7.5406e-02
   5_bss:   1.123  0.010  0.088 15.715  0.004  4.119   7.5406e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.125   7.0023e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.125   7.0023e+00
   1_xyz:  13.438  0.160  0.406 88.824  0.044  2.147   9.8138e-02
   1_adp:  13.438  0.160  0.406 88.824  0.044  2.147   9.8138e-02
   1_occ:  13.438  0.160  0.406 88.824  0.044  2.147   9.8138e-02
   2_bss:  13.438  0.160  0.406 88.824  0.044  2.147   9.8138e-02
   2_xyz:   8.112  0.120  0.295 84.348  0.033  2.138   7.2373e-02
   2_adp:   8.112  0.120  0.295 84.348  0.033  2.138   7.2373e-02
   2_occ:   8.112  0.120  0.295 84.348  0.033  2.138   7.2373e-02
   3_bss:   8.112  0.120  0.295 84.348  0.033  2.138   7.2373e-02
   3_xyz:   8.598  0.051  0.313 84.421  0.047  2.240   5.5220e-02
   3_adp:   8.598  0.051  0.313 84.421  0.047  2.240   5.5220e-02
   3_occ:   8.598  0.051  0.313 84.421  0.047  2.240   5.5220e-02
   4_bss:   8.598  0.051  0.313 84.421  0.047  2.240   5.5220e-02
   4_xyz:   5.934  0.040  0.308 87.111  0.037  2.373   3.4189e-02
   4_adp:   5.934  0.040  0.308 87.111  0.037  2.373   3.4189e-02
   4_occ:   5.934  0.040  0.308 87.111  0.037  2.373   3.4189e-02
   5_bss:   5.934  0.040  0.308 87.111  0.037  2.373   3.4189e-02
   5_xyz:   7.305  0.064  0.494 88.109  0.042  2.296   5.3117e-02
   5_adp:   7.305  0.064  0.494 88.109  0.042  2.296   5.3117e-02
   5_occ:   7.305  0.064  0.494 88.109  0.042  2.296   5.3117e-02
   5_bss:   7.305  0.064  0.494 88.109  0.042  2.296   5.3117e-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:  68.58   0.00  12.84  57.47   0.00  10.33  68.58   0.00  26.52
   1_occ:  68.58   0.00  12.84  57.47   0.00  10.33  68.58   0.00  26.52
   2_bss:  68.58   0.00  12.84  57.47   0.00  10.33  68.58   0.00  26.52
   2_xyz:  68.58   0.00  12.84  57.47   0.00  10.33  68.58   0.00  26.52
   2_adp:  67.77   0.00  12.77  62.92   0.00   9.11  67.77   0.00  32.70
   2_occ:  67.77   0.00  12.77  62.92   0.00   9.11  67.77   0.00  32.70
   3_bss:  67.77   0.00  12.77  62.92   0.00   9.11  67.77   0.00  32.70
   3_xyz:  67.77   0.00  12.77  62.92   0.00   9.11  67.77   0.00  32.70
   3_adp:  76.39   0.00  13.06  71.22   0.00   8.78  76.39   1.43  36.38
   3_occ:  76.39   0.00  13.06  71.22   0.00   8.78  76.39   1.43  36.38
   4_bss:  76.39   0.00  13.06  71.22   0.00   8.78  76.39   1.43  36.38
   4_xyz:  76.39   0.00  13.06  71.22   0.00   8.78  76.39   1.43  36.38
   4_adp:  83.14   0.00  13.26  76.83   0.00   8.75  83.14   1.22  37.80
   4_occ:  83.14   0.00  13.26  76.83   0.00   8.75  83.14   1.22  37.80
   5_bss:  83.14   0.00  13.26  76.83   0.00   8.75  83.14   1.22  37.80
   5_xyz:  83.14   0.00  13.26  76.83   0.00   8.75  83.14   1.22  37.80
   5_adp: 102.31   0.00  13.44  90.41   0.00   8.72 102.31   1.12  39.14
   5_occ: 102.31   0.00  13.44  90.41   0.00   8.72 102.31   1.12  39.14
   5_bss: 105.08   2.77  16.21  93.18   2.77  11.49 105.08   3.89  41.91
------------------------------------------------------------------------
 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:    1.262    0.015    0.407
   1_adp:    1.262    0.015    0.407
   1_occ:    1.262    0.015    0.407
   2_bss:    1.262    0.015    0.407
   2_xyz:    1.872    0.024    0.593
   2_adp:    1.872    0.024    0.593
   2_occ:    1.872    0.024    0.593
   3_bss:    1.872    0.024    0.593
   3_xyz:    1.825    0.052    0.647
   3_adp:    1.825    0.052    0.647
   3_occ:    1.825    0.052    0.647
   4_bss:    1.825    0.052    0.647
   4_xyz:    1.944    0.038    0.675
   4_adp:    1.944    0.038    0.675
   4_occ:    1.944    0.038    0.675
   5_bss:    1.944    0.038    0.675
   5_xyz:    1.956    0.040    0.692
   5_adp:    1.956    0.040    0.692
   5_occ:    1.956    0.040    0.692
   5_bss:    1.956    0.040    0.692
------------------------------------------------------------------------

CPU time actual refinement: 268.10


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_428/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_428/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_428/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_428/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_428/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 267.97 
  Macro-tasks:
    bulk solvent and scale       = 33.83  
    individual site refinement   = 108.02 
    weights calculation          = 25.89  
    collect and process          = 5.38   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 173.21 
  Micro-tasks:
    mask                            = 1.95   
    f_calc                          = 81.77  
    alpha_beta                      = 7.00   
    target                          = 0.97   
    gradients_wrt_atomic_parameters = 89.88  
    fmodel                         = 5.80   
    r_factors                      = 0.12   
    phase_errors                   = 8.73   
    foms                           = 0.16   
    TOTAL for micro-tasks          = 196.38 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.815 micro seconds
Total CPU time: 4.66 minutes
from_scatterers_fft:    635 calls, 81.52 s
gradients_fft:          579 calls, 78.82 s

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

# Date 2008-01-16 Time 01:32:09 PST -0800 (1200475929.46 s)
Start R-work = 0.4706, R-free = 0.4568 (no bulk solvent and anisotropic scale)
Final R-work = 0.1331, R-free = 0.1815 (no bulk solvent and anisotropic scale)

Start R-work = 0.4605, R-free = 0.4476
Final R-work = 0.1153, R-free = 0.1662