# Date 2008-01-16 Time 01:32:52 PST -0800 (1200475972.41 s)
#phil __OFF__

Command line arguments: "../460.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30806
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 460

-------------------------------------------------------------------------------
  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, 47.6339, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.98083
Completeness in resolution range: 0.935527
Completeness with d_max=infinity: 0.932676

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9620
                             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, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.98083
Completeness in resolution range: 0.935527
Completeness with d_max=infinity: 0.932676

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9625 -  4.2383 [2206/2234]  1983   223  10.1%
  bin  2:  4.2383 -  3.3767 [2100/2123]  1889   211  10.0%
  bin  3:  3.3767 -  2.9536 [2069/2091]  1867   202   9.8%
  bin  4:  2.9536 -  2.6853 [2087/2106]  1876   211  10.1%
  bin  5:  2.6853 -  2.4938 [2027/2056]  1821   206  10.2%
  bin  6:  2.4938 -  2.3473 [2063/2105]  1857   206  10.0%
  bin  7:  2.3473 -  2.2302 [2023/2059]  1825   198   9.8%
  bin  8:  2.2302 -  2.1334 [2024/2062]  1816   208  10.3%
  bin  9:  2.1334 -  2.0515 [2028/2059]  1833   195   9.6%
  bin 10:  2.0515 -  1.9808 [ 962/2044]   863    99  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_460/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:
        1.62 -     2.28: 18
        2.28 -     2.93: 1540
        2.93 -     3.59: 4424
        3.59 -     4.24: 9088
        4.24 -     4.90: 12913
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.623 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.711 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.886 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.887 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27978 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_460/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_460/model_refine_001.geo

CPU time processing inputs: 9.05


============================ 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 47.63395 88.1178 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 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4945   r_free= 0.4806   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.294181                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7270 0.99   1429  158 0.3962 0.3886      6.6098       6.609|
|  2:  4.7270 -  3.7718 0.99   1386  154 0.4208 0.4694      6.8012      6.9263|
|  3:  3.7718 -  3.3008 0.99   1336  149 0.4618 0.4249      6.6957      6.6591|
|  4:  3.3008 -  3.0017 0.99   1343  145 0.4863 0.4553      6.5318      6.4921|
|  5:  3.0017 -  2.7880 0.99   1313  152 0.5291 0.4868      6.3744      6.3929|
|  6:  2.7880 -  2.6246 0.98   1335  143 0.5216 0.5415      6.2907      6.2014|
|  7:  2.6246 -  2.4938 0.99   1294  152 0.5114 0.4735      6.2353      6.1463|
|  8:  2.4938 -  2.3857 0.99   1340  140 0.5498 0.4595      6.2019      6.1462|
|  9:  2.3857 -  2.2941 0.98   1312  147 0.5372 0.5859      6.1291       6.171|
| 10:  2.2941 -  2.2152 0.98   1306  145 0.5544 0.4846      6.1048      6.1049|
| 11:  2.2152 -  2.1462 0.98   1285  151 0.5336 0.5672      6.0247      6.0573|
| 12:  2.1462 -  2.0850 0.99   1305  140 0.5451 0.5103      5.9573      5.9575|
| 13:  2.0850 -  2.0302 0.95   1269  128 0.5448 0.5406      5.8937      5.8407|
| 14:  2.0302 -  1.9808 0.30    377   55 0.5397 0.4515      5.8902       5.726|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.7270  1429   158  0.69  35.49   0.79     0.69      74302.82|
|  2:  4.7270 -  3.7718  1386   154  0.67  37.83   0.87     0.72     117186.28|
|  3:  3.7718 -  3.3008  1336   149  0.57  46.22   0.80     0.68     122590.27|
|  4:  3.3008 -  3.0017  1343   145  0.48  53.43   0.78     0.57     103883.23|
|  5:  3.0017 -  2.7880  1313   152  0.41  58.87   0.71     0.49      81938.94|
|  6:  2.7880 -  2.6246  1335   143  0.39  60.79   0.71     0.45      72159.42|
|  7:  2.6246 -  2.4938  1294   152  0.40  59.75   0.73     0.46      63227.31|
|  8:  2.4938 -  2.3857  1340   140  0.41  58.89   0.70     0.48      54023.24|
|  9:  2.3857 -  2.2941  1312   147  0.39  60.55   0.70     0.47      51733.99|
| 10:  2.2941 -  2.2152  1306   145  0.35  64.08   0.71     0.41      49306.40|
| 11:  2.2152 -  2.1462  1285   151  0.28  69.18   0.74     0.36      50469.63|
| 12:  2.1462 -  2.0850  1305   140  0.27  69.91   0.72     0.35      45859.95|
| 13:  2.0850 -  2.0302  1269   128  0.27  69.57   0.72     0.35      39591.30|
| 14:  2.0302 -  1.9808   377    55  0.33  65.39   0.74     0.35      29397.27|
|alpha:            min =        0.35 max =            0.72 mean =         0.50|
|beta:             min =    29397.27 max =       122590.27 mean =     70806.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.98 mean =        57.15|
|phase err.(test): min =        0.00 max =           89.95 mean =        57.47|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.918909             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.171   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.376988              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.739   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      687 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1497 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2590 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3874 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5001 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6512 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7655 |
|-----------------------------------------------------------------------------|
|-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 |       54.203 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.882 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    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 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4996   r_free= 0.4844   ksol= 0.00   Bsol= 0.00   scale= 0.748    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.295525                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4853   r_free= 0.4759   ksol= 0.31   Bsol= 2.95   scale= 0.990    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.78,10.22,11.04,0.00,0.00,0.00); trace/3= 9.35                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.286338                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.365392             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.443   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.298761              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.143   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4853      final r-factor (work) = 0.4062          |
| start r-factor (free) = 0.4759      final r-factor (free) = 0.4287          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 99.4020 = 14.37 * 0.50 * 6.2927 + 1.00 * 54.2031                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.7517 = 14.37 * 0.50 * 6.2092 + 1.00 * 0.1530                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4062      final r-factor (work) = 0.3614          |
| start r-factor (free) = 0.4287      final r-factor (free) = 0.4182          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0786 = 1.30 * 1.00 * 6.2092 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9796 = 1.30 * 1.00 * 6.1292 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.91   14.32    None  None   None       |
|    all(noH): 2823   0      0.00    83.91   14.32    None  None   None       |
|    Sol.    : 438    0      0.00    83.91   26.42    None  None   None       |
|    Mac.    : 2385   0      0.00    73.69   12.10    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 -   8.391: 1128   |   5:    41.954 -  50.345:   62        |
|      1:     8.391 -  16.782:  773   |   6:    50.345 -  58.736:   34        |
|      2:    16.782 -  25.173:  450   |   7:    58.736 -  67.127:    9        |
|      3:    25.173 -  33.564:  233   |   8:    67.127 -  75.518:    7        |
|      4:    33.564 -  41.954:  122   |   9:    75.518 -  83.909:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3614 r_free = 0.4182             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3609 r_free = 0.4183             target_work(ml) = 6.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3609   r_free= 0.4183   ksol= 0.31   Bsol= 2.95   scale= 1.113    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.78,10.22,11.04,0.00,0.00,0.00); trace/3= 9.35                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.114327                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3574   r_free= 0.4118   ksol= 0.30   Bsol= 32.59   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.93,5.90,6.82,0.00,0.00,0.00); trace/3= 5.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.114894                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.724400              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.794   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.512873              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.526  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3574      final r-factor (work) = 0.2704          |
| start r-factor (free) = 0.4118      final r-factor (free) = 0.3237          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.8743 = 8.72 * 0.50 * 6.1256 + 1.00 * 0.1530                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.2553 = 8.72 * 0.50 * 5.9967 + 1.00 * 0.0967                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2704      final r-factor (work) = 0.2469          |
| start r-factor (free) = 0.3237      final r-factor (free) = 0.3004          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0953 = 0.51 * 1.00 * 5.9967 + 1.00 * 0.0197                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0275 = 0.51 * 1.00 * 5.8428 + 1.00 * 0.0309                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    130.21  13.86    None  None   None       |
|    all(noH): 2823   0      0.00    130.21  13.86    None  None   None       |
|    Sol.    : 438    0      0.00    81.56   30.98    None  None   None       |
|    Mac.    : 2385   0      0.00    130.21  10.72    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 -  13.021: 1746   |   5:    65.106 -  78.128:   10        |
|      1:    13.021 -  26.043:  654   |   6:    78.128 -  91.149:    2        |
|      2:    26.043 -  39.064:  281   |   7:    91.149 - 104.170:    0        |
|      3:    39.064 -  52.085:   98   |   8:   104.170 - 117.191:    0        |
|      4:    52.085 -  65.106:   31   |   9:   117.191 - 130.213:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2469 r_free = 0.3004             target_work(ml) = 5.813         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2463 r_free = 0.3006             target_work(ml) = 5.812         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2463   r_free= 0.3006   ksol= 0.30   Bsol= 32.59   scale= 1.060   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.93,5.90,6.82,0.00,0.00,0.00); trace/3= 5.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.812295                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2435   r_free= 0.3008   ksol= 0.30   Bsol= 54.58   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.18,3.19,3.91,0.00,0.00,0.00); trace/3= 2.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.812433                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.136148              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.169   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.265311              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.184   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2435      final r-factor (work) = 0.1808          |
| start r-factor (free) = 0.3008      final r-factor (free) = 0.2278          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1136 = 5.14 * 0.50 * 5.8475 + 1.00 * 0.0967                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7148 = 5.14 * 0.50 * 5.7007 + 1.00 * 0.0751                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1808      final r-factor (work) = 0.1641          |
| start r-factor (free) = 0.2278      final r-factor (free) = 0.2085          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5579 = 0.27 * 1.00 * 5.7007 + 1.00 * 0.0455                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4704 = 0.27 * 1.00 * 5.5062 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.45   13.59    None  None   None       |
|    all(noH): 2823   0      0.00    91.45   13.59    None  None   None       |
|    Sol.    : 438    0      2.72    77.27   34.43    None  None   None       |
|    Mac.    : 2385   0      0.00    91.45   9.76     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.145: 1484   |   5:    45.724 -  54.869:   77        |
|      1:     9.145 -  18.290:  731   |   6:    54.869 -  64.013:   21        |
|      2:    18.290 -  27.434:  204   |   7:    64.013 -  73.158:    6        |
|      3:    27.434 -  36.579:  164   |   8:    73.158 -  82.303:    3        |
|      4:    36.579 -  45.724:  131   |   9:    82.303 -  91.448:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1641 r_free = 0.2085             target_work(ml) = 5.462         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1640 r_free = 0.2085             target_work(ml) = 5.461         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1640   r_free= 0.2085   ksol= 0.30   Bsol= 54.58   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.18,3.19,3.91,0.00,0.00,0.00); trace/3= 2.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.461480                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1632   r_free= 0.2077   ksol= 0.33   Bsol= 54.58   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.45,1.89,2.99,0.00,0.00,0.00); trace/3= 1.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.459754                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.831477              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.223  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.626432              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.386  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1632      final r-factor (work) = 0.1429          |
| start r-factor (free) = 0.2077      final r-factor (free) = 0.1843          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1209 = 1.83 * 0.50 * 5.5101 + 1.00 * 0.0751                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0061 = 1.83 * 0.50 * 5.4042 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1429      final r-factor (work) = 0.1374          |
| start r-factor (free) = 0.1843      final r-factor (free) = 0.1817          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3950 = 0.63 * 1.00 * 5.4042 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3470 = 0.63 * 1.00 * 5.3239 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.73   13.60    None  None   None       |
|    all(noH): 2823   0      0.00    86.73   13.60    None  None   None       |
|    Sol.    : 438    0      1.83    76.26   35.59    None  None   None       |
|    Mac.    : 2385   0      0.00    86.73   9.56     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 -   8.673: 1416   |   5:    43.366 -  52.040:  105        |
|      1:     8.673 -  17.347:  778   |   6:    52.040 -  60.713:   49        |
|      2:    17.347 -  26.020:  193   |   7:    60.713 -  69.386:    8        |
|      3:    26.020 -  34.693:  134   |   8:    69.386 -  78.059:    5        |
|      4:    34.693 -  43.366:  133   |   9:    78.059 -  86.732:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1374 r_free = 0.1817             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1373 r_free = 0.1817             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1373   r_free= 0.1817   ksol= 0.33   Bsol= 54.58   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.45,1.89,2.99,0.00,0.00,0.00); trace/3= 1.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.319264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1374   r_free= 0.1820   ksol= 0.33   Bsol= 54.58   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.47,1.67,2.87,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.319875                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.497144              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.141  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.285091              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.315  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1374      final r-factor (work) = 0.1250          |
| start r-factor (free) = 0.1820      final r-factor (free) = 0.1716          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7047 = 2.50 * 0.50 * 5.3240 + 1.00 * 0.0573                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6591 = 2.50 * 0.50 * 5.2772 + 1.00 * 0.0702                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1250      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1716      final r-factor (free) = 0.1704          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.3477 = 3.29 * 1.00 * 5.2772 + 1.00 * 0.0117                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.2052 = 3.29 * 1.00 * 5.2329 + 1.00 * 0.0148                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.70   14.19    None  None   None       |
|    all(noH): 2823   0      0.00    88.70   14.19    None  None   None       |
|    Sol.    : 438    0      2.15    88.70   39.38    None  None   None       |
|    Mac.    : 2385   0      0.00    84.19   9.57     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 -   8.870: 1486   |   5:    44.352 -  53.222:   90        |
|      1:     8.870 -  17.741:  722   |   6:    53.222 -  62.093:   62        |
|      2:    17.741 -  26.611:  178   |   7:    62.093 -  70.963:   42        |
|      3:    26.611 -  35.482:  121   |   8:    70.963 -  79.834:   22        |
|      4:    35.482 -  44.352:   96   |   9:    79.834 -  88.704:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1217 r_free = 0.1704             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1217 r_free = 0.1704             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1704   ksol= 0.33   Bsol= 54.58   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.47,1.67,2.87,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.230052                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7270 0.99   1429  158 0.0997 0.1324      5.4167      5.5689|
|  2:  4.7270 -  3.7718 0.99   1386  154 0.0870 0.1073      5.4457      5.6452|
|  3:  3.7718 -  3.3008 0.99   1336  149 0.1121 0.1569      5.5126      5.8853|
|  4:  3.3008 -  3.0017 0.99   1343  145 0.1309 0.1770      5.5099      5.6852|
|  5:  3.0017 -  2.7880 0.99   1313  152 0.1500 0.1752      5.4316      5.5764|
|  6:  2.7880 -  2.6246 0.98   1335  143 0.1387 0.2337      5.3142      5.6275|
|  7:  2.6246 -  2.4938 0.99   1294  152 0.1423 0.1743      5.2764      5.4423|
|  8:  2.4938 -  2.3857 0.99   1340  140 0.1280 0.1855      5.1774      5.3958|
|  9:  2.3857 -  2.2941 0.98   1312  147 0.1327 0.2187      5.1249      5.4474|
| 10:  2.2941 -  2.2152 0.98   1306  145 0.1253 0.1798      5.0535      5.2407|
| 11:  2.2152 -  2.1462 0.98   1285  151 0.1277 0.2040      5.0094      5.3754|
| 12:  2.1462 -  2.0850 0.99   1305  140 0.1213 0.1688      4.9388      5.1571|
| 13:  2.0850 -  2.0302 0.95   1269  128 0.1196 0.1849      4.8505      5.0766|
| 14:  2.0302 -  1.9808 0.30    377   55 0.1111 0.1961      4.7748      5.0315|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.7270  1429   158  0.94   9.65   0.97     0.94       8024.56|
|  2:  4.7270 -  3.7718  1386   154  0.95   8.41   1.01     0.99       9378.29|
|  3:  3.7718 -  3.3008  1336   149  0.93  11.81   1.02     1.02      11010.37|
|  4:  3.3008 -  3.0017  1343   145  0.91  15.17   1.00     0.99      11726.93|
|  5:  3.0017 -  2.7880  1313   152  0.88  18.01   0.99     0.97      10336.93|
|  6:  2.7880 -  2.6246  1335   143  0.88  18.81   0.97     0.93       8944.54|
|  7:  2.6246 -  2.4938  1294   152  0.89  17.87   0.98     0.94       7811.51|
|  8:  2.4938 -  2.3857  1340   140  0.89  17.88   0.98     0.95       6980.00|
|  9:  2.3857 -  2.2941  1312   147  0.88  18.18   0.99     0.95       6140.23|
| 10:  2.2941 -  2.2152  1306   145  0.88  18.00   0.98     0.93       5568.86|
| 11:  2.2152 -  2.1462  1285   151  0.88  18.47   0.98     0.93       5160.39|
| 12:  2.1462 -  2.0850  1305   140  0.89  17.62   0.98     0.97       4633.83|
| 13:  2.0850 -  2.0302  1269   128  0.89  17.86   0.97     0.94       3918.98|
| 14:  2.0302 -  1.9808   377    55  0.90  16.56   0.94     0.90       3225.95|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     3225.95 max =        11726.93 mean =      7606.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.91|
|phase err.(test): min =        0.00 max =           89.57 mean =        15.32|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1701   ksol= 0.32   Bsol= 61.37   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.05,1.15,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.229850                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1701   ksol= 0.32   Bsol= 61.37   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.05,1.15,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.229850                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7270 0.99   1429  158 0.0996 0.1322      5.4148      5.5705|
|  2:  4.7270 -  3.7718 0.99   1386  154 0.0876 0.1077      5.4497      5.6505|
|  3:  3.7718 -  3.3008 0.99   1336  149 0.1121 0.1572      5.5148      5.8855|
|  4:  3.3008 -  3.0017 0.99   1343  145 0.1306 0.1768      5.5085      5.6846|
|  5:  3.0017 -  2.7880 0.99   1313  152 0.1498 0.1747      5.4297      5.5739|
|  6:  2.7880 -  2.6246 0.98   1335  143 0.1385 0.2333      5.3127      5.6258|
|  7:  2.6246 -  2.4938 0.99   1294  152 0.1420 0.1745      5.2753      5.4423|
|  8:  2.4938 -  2.3857 0.99   1340  140 0.1279 0.1852      5.1775      5.3953|
|  9:  2.3857 -  2.2941 0.98   1312  147 0.1326 0.2190      5.1247      5.4478|
| 10:  2.2941 -  2.2152 0.98   1306  145 0.1253 0.1797      5.0534      5.2403|
| 11:  2.2152 -  2.1462 0.98   1285  151 0.1278 0.2036       5.009      5.3748|
| 12:  2.1462 -  2.0850 0.99   1305  140 0.1213 0.1687      4.9385      5.1567|
| 13:  2.0850 -  2.0302 0.95   1269  128 0.1195 0.1847        4.85      5.0756|
| 14:  2.0302 -  1.9808 0.30    377   55 0.1111 0.1960       4.776      5.0315|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.7270  1429   158  0.94   9.64   0.97     0.94       7988.83|
|  2:  4.7270 -  3.7718  1386   154  0.95   8.48   1.01     0.99       9440.24|
|  3:  3.7718 -  3.3008  1336   149  0.93  11.90   1.03     1.02      11118.00|
|  4:  3.3008 -  3.0017  1343   145  0.91  15.18   1.01     1.00      11716.41|
|  5:  3.0017 -  2.7880  1313   152  0.88  17.98   1.00     0.97      10298.61|
|  6:  2.7880 -  2.6246  1335   143  0.88  18.78   0.98     0.94       8911.66|
|  7:  2.6246 -  2.4938  1294   152  0.89  17.85   0.99     0.95       7796.21|
|  8:  2.4938 -  2.3857  1340   140  0.89  17.88   0.99     0.96       6978.40|
|  9:  2.3857 -  2.2941  1312   147  0.88  18.18   1.00     0.96       6138.87|
| 10:  2.2941 -  2.2152  1306   145  0.88  17.99   0.99     0.95       5564.25|
| 11:  2.2152 -  2.1462  1285   151  0.88  18.45   0.99     0.94       5149.31|
| 12:  2.1462 -  2.0850  1305   140  0.89  17.60   1.00     0.99       4629.42|
| 13:  2.0850 -  2.0302  1269   128  0.89  17.84   0.98     0.96       3912.04|
| 14:  2.0302 -  1.9808   377    55  0.90  16.56   0.96     0.91       3220.14|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3220.14 max =        11716.41 mean =      7606.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.91|
|phase err.(test): min =        0.00 max =           89.59 mean =        15.31|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.93    90.64   16.13    None  None   None       |
|    all(noH): 2823   0      1.93    90.64   16.13    None  None   None       |
|    Sol.    : 438    0      4.08    90.64   41.31    None  None   None       |
|    Mac.    : 2385   0      1.93    86.12   11.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.934 -  10.804: 1486   |   5:    46.286 -  55.156:   90        |
|      1:    10.804 -  19.675:  722   |   6:    55.156 -  64.027:   62        |
|      2:    19.675 -  28.545:  178   |   7:    64.027 -  72.897:   42        |
|      3:    28.545 -  37.415:  121   |   8:    72.897 -  81.767:   22        |
|      4:    37.415 -  46.286:   96   |   9:    81.767 -  90.638:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.166 - 5.194
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 317
   mapped sites are within: 0.724 - 5.194

peak=   10.227 closest distance to " CB  VAL A 230 " =    1.437
peak=    6.047 closest distance to " CG1 VAL A 296 " =    1.189
peak=    5.991 closest distance to " CD1AILE A 234 " =    1.074
peak=    5.910 closest distance to " O   HOH Z 210 " =    1.259
peak=    5.538 closest distance to " CG  LEU A   5 " =    1.212
peak=    5.405 closest distance to " NH2 ARG A  56 " =    2.147
peak=    5.150 closest distance to " CB  GLN A 223 " =    1.458
peak=    5.079 closest distance to " O   HOH Z 248 " =    1.502
peak=    5.076 closest distance to " O   HOH Z 403 " =    1.921
peak=    4.937 closest distance to " CG  PRO A  54 " =    1.319
peak=    4.875 closest distance to " CA  TYR A  30 " =    0.939
peak=    4.829 closest distance to " CD2 LEU A   5 " =    1.136
peak=    4.812 closest distance to " CB  VAL A 296 " =    1.077
peak=    4.682 closest distance to " CG  LEU A 228 " =    1.197
peak=    4.677 closest distance to " NE2 GLN A  11 " =    1.089
peak=    4.657 closest distance to " CB  ARG A 275 " =    0.925
peak=    4.643 closest distance to " O   HOH Z 128 " =    1.699
peak=    4.640 closest distance to " O   HOH Z 232 " =    2.313
peak=    4.640 closest distance to " O   HOH Z 251 " =    1.711
peak=    4.522 closest distance to " CB  SER A  63 " =    1.153
peak=    4.518 closest distance to " O   HOH Z 142 " =    1.731
peak=    4.448 closest distance to " O   HOH Z 238 " =    1.265
peak=    4.426 closest distance to " O   HOH Z 402 " =    1.491
peak=    4.412 closest distance to " O   HOH Z 130 " =    2.520
peak=    4.400 closest distance to " CA  ALA A  51 " =    0.988
peak=    4.392 closest distance to " CB  VAL A 230 " =    1.174
peak=    4.390 closest distance to " CG  PRO A 280 " =    0.918
peak=    4.382 closest distance to " CB  PRO A  54 " =    0.967
peak=    4.316 closest distance to " O   HOH Z  76 " =    1.132
peak=    4.293 closest distance to " CD2 LEU A 228 " =    1.297
peak=    4.292 closest distance to " CB  TRP A 179 " =    1.358
peak=    4.286 closest distance to " O   HOH Z 209 " =    2.352
peak=    4.282 closest distance to " O   HOH Z 154 " =    1.772
peak=    4.280 closest distance to " CB  GLN A 183 " =    1.284
peak=    4.231 closest distance to " CB  ARG A 190 " =    1.782
peak=    4.229 closest distance to " CD2 TRP A 179 " =    1.292
peak=    4.214 closest distance to " CB  ARG A  79 " =    1.497
peak=    4.211 closest distance to " O   SER A  87 " =    2.366
peak=    4.209 closest distance to " O   PRO A 198 " =    1.505
peak=    4.209 closest distance to " O   HOH Z 404 " =    1.352
peak=    4.188 closest distance to " O   ASP A 124 " =    1.330
peak=    4.179 closest distance to " CB  GLU A 277 " =    3.753
peak=    4.169 closest distance to " O   HOH Z 126 " =    1.592
peak=    4.158 closest distance to " O   HOH Z  49 " =    1.381
peak=    4.144 closest distance to " CG2 VAL A 296 " =    0.958
peak=    4.140 closest distance to " O   HOH Z 359 " =    1.929
peak=    4.135 closest distance to " O   HOH Z  43 " =    2.107
peak=    4.125 closest distance to " CG  PRO A 243 " =    1.153
peak=    4.124 closest distance to " CZ  PHE A 218 " =    1.170
peak=    4.114 closest distance to " O   HOH Z 412 " =    3.801
peak=    4.101 closest distance to " O   HOH Z 214 " =    1.427
peak=    4.071 closest distance to " O   HOH Z 124 " =    1.217
peak=    4.039 closest distance to " CZ3 TRP A 266 " =    1.051
peak=    4.032 closest distance to " O   ASN A  74 " =    2.094
peak=    4.030 closest distance to " O   ALA A 165 " =    1.306
peak=    4.020 closest distance to " O   HOH Z 365 " =    2.335
peak=    4.017 closest distance to " O   HOH Z 265 " =    1.902
peak=    4.013 closest distance to " O   HOH Z  40 " =    1.973
peak=    4.005 closest distance to " CG2 ILE A 234 " =    1.135
peak=    3.996 closest distance to " O   HOH Z 193 " =    1.715
peak=    3.987 closest distance to " O   HOH Z 425 " =    1.480
peak=    3.982 closest distance to " OG BSER A 164 " =    2.204
peak=    3.979 closest distance to " O   HOH Z 346 " =    1.480
peak=    3.969 closest distance to " CB  ASN A 148 " =    1.365
peak=    3.961 closest distance to " CB  ASN A 142 " =    1.239
peak=    3.953 closest distance to " O   HOH Z 422 " =    2.615
peak=    3.947 closest distance to " O   HOH Z 214 " =    2.549
peak=    3.946 closest distance to " O   HOH Z 126 " =    1.917
peak=    3.936 closest distance to " O   HOH Z  85 " =    1.436
peak=    3.931 closest distance to " CG  PRO A 213 " =    1.182
peak=    3.918 closest distance to " CE  LYS A  76 " =    0.901
peak=    3.903 closest distance to " O   HOH Z 189 " =    2.943
peak=    3.877 closest distance to " O   HOH Z 284 " =    2.958
peak=    3.867 closest distance to " CD1 LEU A  96 " =    0.842
peak=    3.854 closest distance to " O   HOH Z  63 " =    2.045
peak=    3.849 closest distance to " CA  ALA A 295 " =    1.040
peak=    3.838 closest distance to " O   HOH Z 427 " =    2.835
peak=    3.837 closest distance to " CA  ARG A  36 " =    1.007
peak=    3.829 closest distance to " CB BVAL A  41 " =    1.336
peak=    3.814 closest distance to " CA  ARG A 195 " =    1.156
peak=    3.812 closest distance to " O   HOH Z 234 " =    3.630
peak=    3.807 closest distance to " CB  SER A  26 " =    1.790
peak=    3.791 closest distance to " CA  TYR A 116 " =    1.421
peak=    3.791 closest distance to " O   HOH Z 298 " =    1.824
peak=    3.790 closest distance to " O   HOH Z 369 " =    2.223
peak=    3.782 closest distance to " CG  MET A 185 " =    1.152
peak=    3.780 closest distance to " CB  GLU A 152 " =    1.150
peak=    3.774 closest distance to " CZ  PHE A  38 " =    1.200
peak=    3.768 closest distance to " O   HOH Z 247 " =    1.315
peak=    3.767 closest distance to " CD  ARG A 269 " =    1.101
peak=    3.762 closest distance to " O   HOH Z  80 " =    1.950
peak=    3.757 closest distance to " CG  PHE A 204 " =    0.854
peak=    3.756 closest distance to " CG  PRO A 198 " =    1.236
peak=    3.755 closest distance to " CA  VAL A  41 " =    0.807
peak=    3.747 closest distance to " CD  ARG A 159 " =    0.770
peak=    3.732 closest distance to " O   HOH Z 261 " =    2.559
peak=    3.718 closest distance to " CB  TRP A 266 " =    1.056
peak=    3.706 closest distance to " CA  ALA A 160 " =    0.968
peak=    3.705 closest distance to " O   HOH Z 371 " =    2.734
peak=    3.698 closest distance to " CB  THR A  52 " =    0.832
peak=    3.697 closest distance to " O   HOH Z 287 " =    1.754
peak=    3.696 closest distance to " O   HOH Z 431 " =    1.191
peak=    3.690 closest distance to " CD  LYS A 166 " =    1.444
peak=    3.686 closest distance to " O   HOH Z 199 " =    1.583
peak=    3.667 closest distance to " O   HOH Z  97 " =    2.061
peak=    3.664 closest distance to " CA  VAL A 125 " =    1.278
peak=    3.659 closest distance to " CA  LYS A 117 " =    1.296
peak=    3.656 closest distance to " CB  ASP A 124 " =    0.724
peak=    3.652 closest distance to " CB  GLU A 128 " =    1.163
peak=    3.647 closest distance to " CA  ALA A  21 " =    1.228
peak=    3.647 closest distance to " O   HOH Z 203 " =    1.394
peak=    3.641 closest distance to " O   ASN A  74 " =    1.722
peak=    3.641 closest distance to " NH1AARG A 145 " =    1.338
peak=    3.640 closest distance to " CB  PHE A 204 " =    0.961
peak=    3.617 closest distance to " O   HOH Z 366 " =    2.722
peak=    3.611 closest distance to " O   HOH Z 316 " =    3.122
peak=    3.603 closest distance to " O   HOH Z 337 " =    1.894
peak=    3.598 closest distance to " O   HOH Z 406 " =    1.493
peak=    3.596 closest distance to " CB  SER A   3 " =    1.341
peak=    3.595 closest distance to " N   ASN A  39 " =    1.242
peak=    3.593 closest distance to " O   HOH Z 423 " =    1.786
peak=    3.583 closest distance to " O   HOH Z 303 " =    2.236
peak=    3.583 closest distance to " O   HOH Z 394 " =    1.536
peak=    3.582 closest distance to " CB  VAL A 265 " =    1.227
peak=    3.581 closest distance to " O   HOH Z 134 " =    1.302
peak=    3.566 closest distance to " CB  PRO A  90 " =    1.172
peak=    3.566 closest distance to " O   HOH Z   4 " =    1.643
peak=    3.563 closest distance to " CB  SER A 141 " =    1.186
peak=    3.561 closest distance to " NZ  LYS A  48 " =    1.212
peak=    3.557 closest distance to " CZ3 TRP A  85 " =    0.913
peak=    3.556 closest distance to " CB  ASN A  39 " =    0.832
peak=    3.555 closest distance to " CD  LYS A 119 " =    1.936
peak=    3.555 closest distance to " O   ASP A 200 " =    1.513
peak=    3.550 closest distance to " O   HOH Z 162 " =    1.606
peak=    3.537 closest distance to " O   HOH Z 154 " =    2.189
peak=    3.532 closest distance to " O   HOH Z 272 " =    1.875
peak=    3.522 closest distance to " O   HOH Z 433 " =    1.530
peak=    3.521 closest distance to " CB  GLU A  46 " =    0.967
peak=    3.520 closest distance to " CA  ASN A 217 " =    1.132
peak=    3.518 closest distance to " O   HOH Z 368 " =    3.474
peak=    3.513 closest distance to " OG  SER A 245 " =    1.560
peak=    3.513 closest distance to " O   HOH Z 189 " =    2.803
peak=    3.507 closest distance to " CB  ARG A 190 " =    1.189
peak=    3.503 closest distance to " O   HOH Z 313 " =    1.684
peak=    3.499 closest distance to " CG1 ILE A  33 " =    1.217
peak=    3.499 closest distance to " CG AARG A 275 " =    1.204
peak=    3.497 closest distance to " O   HOH Z 353 " =    2.773
peak=    3.493 closest distance to " CB  TYR A 169 " =    0.791
peak=    3.492 closest distance to " CG1 ILE A  49 " =    1.635
peak=    3.492 closest distance to " CB  VAL A 202 " =    1.453
peak=    3.474 closest distance to " O   HOH Z  78 " =    1.689
peak=    3.471 closest distance to " O   HOH Z 128 " =    2.344
peak=    3.464 closest distance to " CA  ILE A 106 " =    0.790
peak=    3.461 closest distance to " O   HOH Z  19 " =    1.909
peak=    3.460 closest distance to " CD1 ILE A 199 " =    1.048
peak=    3.459 closest distance to " OH  TYR A 169 " =    0.969
peak=    3.449 closest distance to " CA  GLY A 267 " =    0.957
peak=    3.446 closest distance to " O   HOH Z 299 " =    4.278
peak=    3.446 closest distance to " O   HOH Z 146 " =    1.569
peak=    3.437 closest distance to " O   HOH Z   3 " =    1.882
peak=    3.436 closest distance to " O   HOH Z 155 " =    3.296
peak=    3.435 closest distance to " ND2 ASN A 249 " =    1.971
peak=    3.435 closest distance to " O   HOH Z 420 " =    5.194
peak=    3.432 closest distance to " O   HOH Z 285 " =    2.246
peak=    3.425 closest distance to " CA  ASN A 127 " =    1.161
peak=    3.423 closest distance to " CA  ARG A 275 " =    1.647
peak=    3.409 closest distance to " O   HOH Z 393 " =    3.366
peak=    3.402 closest distance to " O   HOH Z 130 " =    1.127
peak=    3.402 closest distance to " NH2 ARG A 156 " =    1.009
peak=    3.400 closest distance to " O   HOH Z 414 " =    1.543
peak=    3.398 closest distance to " O   HOH Z  61 " =    1.620
peak=    3.395 closest distance to " O   HOH Z 391 " =    3.036
peak=    3.395 closest distance to " O  BHOH Z  74 " =    1.294
peak=    3.391 closest distance to " O   HOH Z 144 " =    1.681
peak=    3.383 closest distance to " CG1 VAL A 153 " =    1.002
peak=    3.383 closest distance to " CE1 TYR A 186 " =    1.261
peak=    3.382 closest distance to " O   HOH Z 285 " =    2.127
peak=    3.378 closest distance to " O   HOH Z 383 " =    2.001
peak=    3.372 closest distance to " CB  MET A 105 " =    1.100
peak=    3.369 closest distance to " CB  SER A  62 " =    0.963
peak=    3.365 closest distance to " CA  ALA A 291 " =    0.846
peak=    3.361 closest distance to " CB  ALA A 248 " =    1.406
peak=    3.358 closest distance to " CG2AVAL A 121 " =    2.128
peak=    3.348 closest distance to " CB  ALA A   9 " =    1.632
peak=    3.347 closest distance to " O   THR A 220 " =    1.260
peak=    3.346 closest distance to " O   HOH Z 298 " =    4.331
peak=    3.340 closest distance to " O   HOH Z 148 " =    3.334
peak=    3.339 closest distance to " O   HOH Z 236 " =    1.648
peak=    3.335 closest distance to " ND2 ASN A 187 " =    1.711
peak=    3.334 closest distance to " O   HOH Z 361 " =    2.672
peak=    3.334 closest distance to " CA  MET A 105 " =    1.096
peak=    3.330 closest distance to " CG  GLN A  58 " =    2.982
peak=    3.328 closest distance to " N   SER A 164 " =    0.901
peak=    3.327 closest distance to " O   HOH Z 273 " =    2.976
peak=    3.327 closest distance to " CG2 ILE A  20 " =    1.371
peak=    3.323 closest distance to " OG  SER A  62 " =    2.830
peak=    3.322 closest distance to " O   HOH Z 417 " =    3.212
peak=    3.320 closest distance to " CA  ARG A 139 " =    1.209
peak=    3.319 closest distance to " CD  ARG A 195 " =    1.041
peak=    3.317 closest distance to " CD2 TYR A 186 " =    1.077
peak=    3.313 closest distance to " O   HOH Z  35 " =    2.336
peak=    3.310 closest distance to " CA  SER A  87 " =    1.044
peak=    3.307 closest distance to " CB  THR A 235 " =    1.324
peak=    3.306 closest distance to " O  BHOH Z 338 " =    2.175
peak=    3.305 closest distance to " CA  ASP A 191 " =    1.206
peak=    3.304 closest distance to " CB  ASN A 110 " =    1.116
peak=    3.303 closest distance to " O   HOH Z  83 " =    1.486
peak=    3.302 closest distance to " CB  ASP A 298 " =    1.205
peak=    3.302 closest distance to " O   ASP A 191 " =    1.597
peak=    3.300 closest distance to " CB  THR A  31 " =    1.357
peak=    3.297 closest distance to " CG  GLU A  37 " =    0.912
peak=    3.294 closest distance to " O   HOH Z 132 " =    2.939
peak=    3.294 closest distance to " CB  ASN A 215 " =    1.245
peak=    3.294 closest distance to " O   HOH Z 327 " =    2.755
peak=    3.292 closest distance to " OD1 ASN A  69 " =    2.439
peak=    3.288 closest distance to " O   HOH Z 437 " =    1.722
peak=    3.285 closest distance to " O   HOH Z 329 " =    4.131
peak=    3.285 closest distance to " CG  LEU A 167 " =    1.146
peak=    3.285 closest distance to " CG2 THR A 221 " =    1.221
peak=    3.281 closest distance to " NZ  LYS A 117 " =    2.964
peak=    3.280 closest distance to " ND2 ASN A 249 " =    0.886
peak=    3.276 closest distance to " O   HOH Z 293 " =    1.982
peak=    3.272 closest distance to " CA  GLU A 152 " =    0.900
peak=    3.271 closest distance to " O   HOH Z 345 " =    3.292
peak=    3.271 closest distance to " CB  LYS A 117 " =    1.187
peak=    3.270 closest distance to " O   HOH Z 102 " =    1.322
peak=    3.259 closest distance to " O   GLY A  91 " =    1.256
peak=    3.259 closest distance to " O   HOH Z 313 " =    1.609
peak=    3.256 closest distance to " CG  GLN A  58 " =    0.970
peak=    3.256 closest distance to " N   VAL A 126 " =    1.596
peak=    3.249 closest distance to " O   HOH Z 109 " =    2.242
peak=    3.248 closest distance to " CB  GLN A  89 " =    1.212
peak=    3.244 closest distance to " O   HOH Z 193 " =    1.440
peak=    3.244 closest distance to " O   HOH Z 193 " =    1.786
peak=    3.240 closest distance to " O   LEU A 228 " =    1.728
peak=    3.240 closest distance to " OG BSER A 134 " =    2.755
peak=    3.239 closest distance to " CE3 TRP A 274 " =    1.167
peak=    3.234 closest distance to " O   HOH Z 407 " =    2.672
peak=    3.234 closest distance to " O   HOH Z 117 " =    0.987
peak=    3.232 closest distance to " O   HOH Z 366 " =    2.445
peak=    3.231 closest distance to " CG2AVAL A  72 " =    1.825
peak=    3.228 closest distance to " O   HOH Z 158 " =    3.194
peak=    3.224 closest distance to " CB  LYS A 119 " =    1.329
peak=    3.223 closest distance to " CB  ASN A 285 " =    0.979
peak=    3.223 closest distance to " CB  PRO A 243 " =    1.082
peak=    3.222 closest distance to " O   HOH Z   1 " =    2.161
peak=    3.222 closest distance to " O   HOH Z 299 " =    4.238
peak=    3.221 closest distance to " O   HOH Z 117 " =    1.962
peak=    3.220 closest distance to " CG2 ILE A 120 " =    1.427
peak=    3.219 closest distance to " O   HOH Z 393 " =    3.731
peak=    3.211 closest distance to " OG1 THR A 294 " =    4.004
peak=    3.209 closest distance to " CA  ALA A 100 " =    0.886
peak=    3.204 closest distance to " CB  PHE A 283 " =    0.867
peak=    3.203 closest distance to " CA  LEU A 282 " =    1.261
peak=    3.202 closest distance to " O   HOH Z 133 " =    2.679
peak=    3.199 closest distance to " O   HOH Z 271 " =    2.394
peak=    3.198 closest distance to " CA  ALA A 158 " =    1.366
peak=    3.198 closest distance to " O   HOH Z 406 " =    1.935
peak=    3.196 closest distance to " O   HOH Z 404 " =    2.063
peak=    3.194 closest distance to " NE  ARG A  14 " =    1.254
peak=    3.194 closest distance to " CG1 ILE A  20 " =    1.308
peak=    3.194 closest distance to " O   GLU A   2 " =    1.531
peak=    3.192 closest distance to " CB  ARG A 145 " =    0.776
peak=    3.191 closest distance to " O   HOH Z 403 " =    1.455
peak=    3.190 closest distance to " CE3 TRP A  85 " =    1.137
peak=    3.190 closest distance to " O   HOH Z 279 " =    2.193
peak=    3.190 closest distance to " O   HOH Z 213 " =    1.711
peak=    3.183 closest distance to " O   HOH Z 394 " =    3.659
peak=    3.181 closest distance to " CD2 LEU A 297 " =    0.819
peak=    3.172 closest distance to " O   HOH Z 166 " =    3.821
peak=    3.171 closest distance to " O   HOH Z 185 " =    1.673
peak=    3.168 closest distance to " O   HOH Z 258 " =    2.015
peak=    3.165 closest distance to " O   ASN A 284 " =    1.814
peak=    3.163 closest distance to " O   GLN A  88 " =    1.643
peak=    3.162 closest distance to " O   HOH Z  68 " =    1.782
peak=    3.157 closest distance to " O   HOH Z 151 " =    1.723
peak=    3.156 closest distance to " O   HOH Z 438 " =    2.664
peak=    3.155 closest distance to " O   HOH Z  54 " =    1.685
peak=    3.150 closest distance to " OG  SER A  22 " =    2.728
peak=    3.147 closest distance to " O   HOH Z 294 " =    1.576
peak=    3.140 closest distance to " O   HOH Z 142 " =    1.813
peak=    3.140 closest distance to " CA  ASP A 162 " =    1.018
peak=    3.134 closest distance to " CB  GLN A 103 " =    0.986
peak=    3.134 closest distance to " O   HOH Z 327 " =    1.582
peak=    3.129 closest distance to " O   HOH Z 120 " =    2.583
peak=    3.128 closest distance to " CB  ASN A  74 " =    1.495
peak=    3.122 closest distance to " CE  MET A  40 " =    1.133
peak=    3.121 closest distance to " CA  GLY A 133 " =    3.755
peak=    3.121 closest distance to " NH1 ARG A 269 " =    0.791
peak=    3.120 closest distance to " CB  GLN A  88 " =    1.249
peak=    3.119 closest distance to " O   THR A 182 " =    1.513
peak=    3.115 closest distance to " O   HOH Z 299 " =    2.418
peak=    3.112 closest distance to " O   HOH Z 172 " =    3.756
peak=    3.109 closest distance to " CA  ASP A 149 " =    1.192
peak=    3.102 closest distance to " CA  LEU A  83 " =    1.201
peak=    3.100 closest distance to " CZ3 TRP A 274 " =    4.424
peak=    3.096 closest distance to " CD1 LEU A   5 " =    1.465
peak=    3.094 closest distance to " CB  SER A 210 " =    0.840
peak=    3.091 closest distance to " CA  ASN A 176 " =    1.202
peak=    3.087 closest distance to " NH2AARG A 275 " =    2.934
peak=    3.084 closest distance to " CB  LEU A  83 " =    0.730
peak=    3.081 closest distance to " CB  TYR A 247 " =    1.055
peak=    3.075 closest distance to " O   ALA A 292 " =    0.935
peak=    3.074 closest distance to " O   HOH Z 420 " =    1.809
peak=    3.073 closest distance to " CE3 TRP A 150 " =    1.119
peak=    3.063 closest distance to " O   HOH Z 387 " =    2.826
peak=    3.061 closest distance to " CA  LEU A 101 " =    1.605
peak=    3.047 closest distance to " O   HOH Z 197 " =    2.065
peak=    3.044 closest distance to " CA  LYS A 290 " =    1.062
peak=    3.044 closest distance to " CB  ALA A  43 " =    0.844
peak=    3.037 closest distance to " CG2 VAL A 197 " =    1.069
peak=    3.030 closest distance to " N   ASP A 162 " =    1.354

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.794 - 5.889
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 211
   mapped sites are within: 0.794 - 5.889

peak=   -4.746 closest distance to " CG2 VAL A 230 " =    0.794
peak=   -4.642 closest distance to " SG  CYS A 254 " =    3.267
peak=   -4.438 closest distance to " CG1 VAL A 296 " =    0.988
peak=   -4.390 closest distance to " CD  GLN A  58 " =    1.070
peak=   -4.302 closest distance to " CZ2 TRP A  92 " =    2.871
peak=   -4.269 closest distance to " CD2 LEU A 237 " =    2.720
peak=   -4.243 closest distance to " CA  ASP A 298 " =    1.075
peak=   -4.235 closest distance to " CE2 TYR A  30 " =    2.732
peak=   -4.221 closest distance to " CG1 VAL A 112 " =    2.579
peak=   -4.212 closest distance to " CD  ARG A 156 " =    2.040
peak=   -4.197 closest distance to " O   HOH Z 196 " =    2.302
peak=   -4.109 closest distance to " CD2 TYR A 293 " =    1.883
peak=   -4.084 closest distance to " O   SER A 271 " =    2.117
peak=   -4.063 closest distance to " O   HOH Z 266 " =    5.621
peak=   -4.047 closest distance to " O   HOH Z 193 " =    1.017
peak=   -4.038 closest distance to " O   HOH Z 285 " =    1.936
peak=   -4.038 closest distance to " OXT GLY A 302 " =    2.957
peak=   -4.022 closest distance to " OG BSER A 134 " =    1.410
peak=   -3.988 closest distance to " C   HIS A 108 " =    1.165
peak=   -3.986 closest distance to " O   HOH Z  13 " =    1.726
peak=   -3.964 closest distance to " O   HOH Z 166 " =    1.588
peak=   -3.961 closest distance to " CG2BVAL A  41 " =    2.816
peak=   -3.949 closest distance to " O   HOH Z 231 " =    2.192
peak=   -3.909 closest distance to " O   PRO A 198 " =    1.332
peak=   -3.894 closest distance to " CD1 LEU A 101 " =    2.378
peak=   -3.861 closest distance to " CG  PRO A 243 " =    1.684
peak=   -3.848 closest distance to " CG2 VAL A 189 " =    2.084
peak=   -3.818 closest distance to " CE3 TRP A 150 " =    2.358
peak=   -3.809 closest distance to " O   HOH Z 394 " =    1.716
peak=   -3.804 closest distance to " O   HOH Z 348 " =    2.349
peak=   -3.779 closest distance to " CB  ALA A 248 " =    2.217
peak=   -3.769 closest distance to " O   PRO A 163 " =    2.102
peak=   -3.756 closest distance to " O   HOH Z 119 " =    2.120
peak=   -3.753 closest distance to " CD1 PHE A  59 " =    2.045
peak=   -3.750 closest distance to " CG  GLN A  11 " =    1.641
peak=   -3.741 closest distance to " O   HOH Z 283 " =    2.374
peak=   -3.740 closest distance to " O   HOH Z 154 " =    1.389
peak=   -3.737 closest distance to " O   HOH Z 423 " =    2.387
peak=   -3.732 closest distance to " CG  ARG A 269 " =    2.254
peak=   -3.726 closest distance to " CE2 PHE A  61 " =    2.671
peak=   -3.723 closest distance to " O   HOH Z 431 " =    2.224
peak=   -3.704 closest distance to " O   HOH Z  10 " =    1.576
peak=   -3.686 closest distance to " CA  GLY A 203 " =    2.433
peak=   -3.686 closest distance to " OE1 GLN A 223 " =    2.434
peak=   -3.686 closest distance to " CG  GLU A 277 " =    1.244
peak=   -3.682 closest distance to " CZ  TYR A 169 " =    1.860
peak=   -3.673 closest distance to " O   HOH Z  37 " =    1.846
peak=   -3.646 closest distance to " ND2BASN A 224 " =    1.922
peak=   -3.644 closest distance to " N   SER A 276 " =    1.438
peak=   -3.639 closest distance to " O   HOH Z 384 " =    2.159
peak=   -3.632 closest distance to " CE2 TRP A  70 " =    2.195
peak=   -3.626 closest distance to " O   HOH Z 387 " =    2.663
peak=   -3.616 closest distance to " OG  SER A  97 " =    2.346
peak=   -3.612 closest distance to " O   HOH Z 131 " =    4.172
peak=   -3.599 closest distance to " CB  ALA A 161 " =    2.511
peak=   -3.594 closest distance to " ND2 ASN A 187 " =    1.543
peak=   -3.593 closest distance to " CG  GLU A  53 " =    1.529
peak=   -3.574 closest distance to " O   HOH Z  68 " =    1.766
peak=   -3.566 closest distance to " O   HOH Z 174 " =    2.182
peak=   -3.564 closest distance to " O   HOH Z 114 " =    3.314
peak=   -3.564 closest distance to " O   HOH Z 107 " =    0.950
peak=   -3.555 closest distance to " O   HOH Z 136 " =    2.630
peak=   -3.552 closest distance to " CG  ASP A 286 " =    1.545
peak=   -3.546 closest distance to " CD  LYS A 289 " =    2.433
peak=   -3.546 closest distance to " O   HOH Z 102 " =    1.619
peak=   -3.544 closest distance to " O   HOH Z 128 " =    2.611
peak=   -3.542 closest distance to " O   HOH Z 166 " =    1.658
peak=   -3.537 closest distance to " O   HOH Z 340 " =    1.617
peak=   -3.521 closest distance to " O   HOH Z 301 " =    2.569
peak=   -3.519 closest distance to " CG  GLN A 103 " =    2.510
peak=   -3.515 closest distance to " ND2 ASN A  45 " =    1.224
peak=   -3.506 closest distance to " O   HOH Z 216 " =    1.172
peak=   -3.501 closest distance to " O   HOH Z 351 " =    1.644
peak=   -3.498 closest distance to " O   GLY A  80 " =    2.702
peak=   -3.485 closest distance to " O   HOH Z 165 " =    1.947
peak=   -3.484 closest distance to " CE3 TRP A 274 " =    2.424
peak=   -3.481 closest distance to " ND2 ASN A  69 " =    1.939
peak=   -3.478 closest distance to " O   HOH Z 133 " =    1.132
peak=   -3.473 closest distance to " CG  LEU A  83 " =    2.133
peak=   -3.468 closest distance to " CG2 ILE A  20 " =    2.957
peak=   -3.447 closest distance to " OE2 GLU A 152 " =    1.445
peak=   -3.442 closest distance to " O   SER A 210 " =    1.704
peak=   -3.439 closest distance to " SD BMET A  47 " =    1.412
peak=   -3.432 closest distance to " CB  VAL A 230 " =    1.096
peak=   -3.430 closest distance to " CH2 TRP A 179 " =    1.234
peak=   -3.421 closest distance to " O   ARG A  24 " =    2.129
peak=   -3.417 closest distance to " CD  PRO A 243 " =    1.968
peak=   -3.415 closest distance to " O   SER A 276 " =    1.599
peak=   -3.414 closest distance to " OD1 ASN A 148 " =    1.405
peak=   -3.412 closest distance to " CB  HIS A  86 " =    1.245
peak=   -3.411 closest distance to " ND2 ASN A 249 " =    2.310
peak=   -3.409 closest distance to " O   HOH Z 137 " =    1.673
peak=   -3.407 closest distance to " O   HOH Z   6 " =    1.757
peak=   -3.401 closest distance to " C   ILE A 239 " =    2.163
peak=   -3.398 closest distance to " CD2 HIS A 207 " =    2.472
peak=   -3.398 closest distance to " O   GLY A  17 " =    1.097
peak=   -3.396 closest distance to " OD1 ASN A 173 " =    1.410
peak=   -3.386 closest distance to " N   ALA A  43 " =    2.730
peak=   -3.386 closest distance to " CB  ALA A  51 " =    1.928
peak=   -3.384 closest distance to " NE  ARG A  66 " =    4.369
peak=   -3.383 closest distance to " O   HOH Z  19 " =    2.379
peak=   -3.383 closest distance to " CD2 LEU A 167 " =    1.811
peak=   -3.378 closest distance to " CB  ALA A  10 " =    2.208
peak=   -3.375 closest distance to " O   PHE A 218 " =    1.426
peak=   -3.367 closest distance to " CG  MET A 105 " =    0.972
peak=   -3.367 closest distance to " CG1 VAL A 112 " =    2.693
peak=   -3.366 closest distance to " CA  GLY A 133 " =    2.384
peak=   -3.366 closest distance to " O   HOH Z 111 " =    1.747
peak=   -3.362 closest distance to " O   ALA A 227 " =    1.311
peak=   -3.362 closest distance to " O   HOH Z 210 " =    0.911
peak=   -3.354 closest distance to " O   HOH Z 252 " =    3.426
peak=   -3.347 closest distance to " O   HOH Z 198 " =    1.869
peak=   -3.346 closest distance to " O   SER A 273 " =    1.207
peak=   -3.342 closest distance to " O   HOH Z 185 " =    2.405
peak=   -3.341 closest distance to " OH  TYR A 169 " =    0.918
peak=   -3.339 closest distance to " CE BMET A  47 " =    1.467
peak=   -3.338 closest distance to " CD1 ILE A 109 " =    2.720
peak=   -3.338 closest distance to " OXT GLY A 302 " =    3.510
peak=   -3.336 closest distance to " CH2 TRP A 150 " =    1.071
peak=   -3.335 closest distance to " O   HOH Z 191 " =    5.661
peak=   -3.324 closest distance to " O   HOH Z 435 " =    2.646
peak=   -3.316 closest distance to " O   HOH Z 251 " =    4.969
peak=   -3.315 closest distance to " CG  GLN A  58 " =    1.135
peak=   -3.314 closest distance to " CA  GLY A 241 " =    2.390
peak=   -3.313 closest distance to " O   HOH Z  60 " =    2.123
peak=   -3.310 closest distance to " CD2 PHE A 192 " =    2.110
peak=   -3.310 closest distance to " O   HOH Z 244 " =    1.939
peak=   -3.309 closest distance to " O   HOH Z 264 " =    1.845
peak=   -3.308 closest distance to " O   HOH Z 421 " =    3.857
peak=   -3.307 closest distance to " CB  SER A 210 " =    1.119
peak=   -3.307 closest distance to " CG1 VAL A  78 " =    2.488
peak=   -3.307 closest distance to " O   GLN A 240 " =    2.469
peak=   -3.306 closest distance to " O   ALA A 299 " =    2.234
peak=   -3.301 closest distance to " CG2 VAL A 202 " =    2.739
peak=   -3.300 closest distance to " CG2 ILE A 263 " =    2.276
peak=   -3.298 closest distance to " CZ  PHE A  38 " =    2.362
peak=   -3.293 closest distance to " C   THR A 279 " =    1.235
peak=   -3.287 closest distance to " OH  TYR A 172 " =    1.915
peak=   -3.287 closest distance to " O   HOH Z 378 " =    1.465
peak=   -3.281 closest distance to " O   TYR A 186 " =    1.733
peak=   -3.278 closest distance to " O   HOH Z 374 " =    2.051
peak=   -3.274 closest distance to " CB  TRP A  85 " =    2.674
peak=   -3.273 closest distance to " O   GLY A  75 " =    2.028
peak=   -3.272 closest distance to " O   TRP A  92 " =    2.042
peak=   -3.270 closest distance to " NE2 GLN A 223 " =    1.548
peak=   -3.266 closest distance to " O   HOH Z 211 " =    1.350
peak=   -3.264 closest distance to " ND2 ASN A  45 " =    2.100
peak=   -3.264 closest distance to " O   TRP A  70 " =    1.622
peak=   -3.263 closest distance to " CB  ASP A 171 " =    2.233
peak=   -3.260 closest distance to " O   HOH Z 145 " =    2.539
peak=   -3.260 closest distance to " NH2 ARG A  79 " =    2.251
peak=   -3.255 closest distance to " CE  LYS A  76 " =    2.611
peak=   -3.251 closest distance to " C   ASN A 285 " =    2.276
peak=   -3.250 closest distance to " CB  ALA A  43 " =    2.544
peak=   -3.250 closest distance to " O   HOH Z  52 " =    1.856
peak=   -3.242 closest distance to " CD  GLN A  73 " =    0.878
peak=   -3.241 closest distance to " O   SER A 206 " =    1.450
peak=   -3.241 closest distance to " CE  MET A  93 " =    1.540
peak=   -3.238 closest distance to " O   HOH Z 357 " =    2.149
peak=   -3.235 closest distance to " CD2 PHE A 225 " =    1.162
peak=   -3.234 closest distance to " O   HOH Z 177 " =    1.822
peak=   -3.226 closest distance to " O   HOH Z 275 " =    1.546
peak=   -3.225 closest distance to " NH2 ARG A  66 " =    5.889
peak=   -3.223 closest distance to " O   HOH Z 149 " =    2.022
peak=   -3.220 closest distance to " O   HOH Z 407 " =    2.860
peak=   -3.218 closest distance to " CD  GLN A 223 " =    1.438
peak=   -3.218 closest distance to " OG BSER A 210 " =    1.324
peak=   -3.212 closest distance to " CB  PRO A 163 " =    2.508
peak=   -3.209 closest distance to " OD1 ASP A 171 " =    1.519
peak=   -3.208 closest distance to " N   ALA A 226 " =    2.007
peak=   -3.198 closest distance to " O   HOH Z  78 " =    1.866
peak=   -3.198 closest distance to " CA  ASN A 127 " =    1.080
peak=   -3.198 closest distance to " CG  LEU A   5 " =    1.034
peak=   -3.197 closest distance to " OE1 GLN A  88 " =    0.875
peak=   -3.195 closest distance to " CA  VAL A 197 " =    0.949
peak=   -3.193 closest distance to " O   GLY A 203 " =    2.355
peak=   -3.187 closest distance to " O   HOH Z 426 " =    1.727
peak=   -3.185 closest distance to " O   HOH Z 250 " =    1.853
peak=   -3.179 closest distance to " NE2 GLN A  88 " =    1.094
peak=   -3.172 closest distance to " CE1 TYR A 247 " =    2.662
peak=   -3.169 closest distance to " CG1BVAL A  72 " =    2.486
peak=   -3.166 closest distance to " OD2 ASP A 171 " =    1.839
peak=   -3.161 closest distance to " O   HOH Z 101 " =    1.542
peak=   -3.159 closest distance to " O   HOH Z 200 " =    1.507
peak=   -3.155 closest distance to " O   ALA A  34 " =    2.040
peak=   -3.148 closest distance to " CG2 THR A 178 " =    2.441
peak=   -3.147 closest distance to " O   MET A 113 " =    2.779
peak=   -3.145 closest distance to " O   HOH Z 106 " =    1.873
peak=   -3.144 closest distance to " O   HOH Z 156 " =    3.593
peak=   -3.144 closest distance to " NH2 ARG A  24 " =    1.994
peak=   -3.143 closest distance to " CG  TRP A 266 " =    1.883
peak=   -3.142 closest distance to " O   ALA A   1 " =    1.631
peak=   -3.140 closest distance to " O   HOH Z 118 " =    4.665
peak=   -3.137 closest distance to " OG  SER A  63 " =    1.184
peak=   -3.134 closest distance to " CG2 VAL A 296 " =    1.360
peak=   -3.129 closest distance to " O   HOH Z  11 " =    1.807
peak=   -3.126 closest distance to " CG2 THR A  18 " =    2.914
peak=   -3.123 closest distance to " O   HOH Z 231 " =    2.111
peak=   -3.121 closest distance to " O   HOH Z 109 " =    1.159
peak=   -3.119 closest distance to " CA  LYS A 166 " =    2.113
peak=   -3.116 closest distance to " CD2 LEU A 237 " =    2.557
peak=   -3.111 closest distance to " O   HOH Z   2 " =    2.393
peak=   -3.110 closest distance to " O   HOH Z 265 " =    2.507
peak=   -3.107 closest distance to " O   HOH Z 150 " =    2.101
peak=   -3.103 closest distance to " CD2 TYR A 172 " =    2.065
peak=   -3.095 closest distance to " O   ASN A 187 " =    1.638
peak=   -3.086 closest distance to " CD  ARG A 195 " =    5.061
peak=   -3.082 closest distance to " O   HOH Z 105 " =    2.218
peak=   -3.053 closest distance to " O   HOH Z  64 " =    1.795
peak=   -3.007 closest distance to " O   HOH Z 429 " =    1.740

================= 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    :  0.4945 0.4806   6.294181e+00   6.279358e+00
   1_bss:  0.4853 0.4759   6.286338e+00   6.276455e+00
   1_xyz:  0.4062 0.4287   6.185286e+00   6.213591e+00
   1_adp:  0.3614 0.4182   6.114669e+00   6.192206e+00
   1_occ:  0.3609 0.4183   6.114327e+00   6.192934e+00
   2_bss:  0.3574 0.4118   6.114894e+00   6.191741e+00
   2_xyz:  0.2704 0.3237   5.883500e+00   6.029512e+00
   2_adp:  0.2469 0.3004   5.813159e+00   5.974191e+00
   2_occ:  0.2463 0.3006   5.812295e+00   5.975013e+00
   3_bss:  0.2435 0.3008   5.812433e+00   5.974618e+00
   3_xyz:  0.1808 0.2278   5.549997e+00   5.743921e+00
   3_adp:  0.1641 0.2085   5.462008e+00   5.659181e+00
   3_occ:  0.1640 0.2085   5.461480e+00   5.659109e+00
   4_bss:  0.1632 0.2077   5.459754e+00   5.656419e+00
   4_xyz:  0.1429 0.1843   5.344016e+00   5.540115e+00
   4_adp:  0.1374 0.1817   5.319669e+00   5.527317e+00
   4_occ:  0.1373 0.1817   5.319264e+00   5.526961e+00
   5_bss:  0.1374 0.1820   5.319875e+00   5.527377e+00
   5_xyz:  0.1250 0.1716   5.245762e+00   5.472523e+00
   5_adp:  0.1217 0.1704   5.230337e+00   5.465540e+00
   5_occ:  0.1217 0.1704   5.230052e+00   5.465230e+00
   5_bss:  0.1215 0.1701   5.229850e+00   5.465244e+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:  0.314   2.946   6.784  10.221  11.042   0.000   0.000   0.000
   1_xyz:  0.314   2.946   6.784  10.221  11.042   0.000   0.000   0.000
   1_adp:  0.314   2.946   6.784  10.221  11.042   0.000   0.000   0.000
   1_occ:  0.314   2.946   6.784  10.221  11.042   0.000   0.000   0.000
   2_bss:  0.298  32.591   2.930   5.899   6.823   0.000   0.000   0.000
   2_xyz:  0.298  32.591   2.930   5.899   6.823   0.000   0.000   0.000
   2_adp:  0.298  32.591   2.930   5.899   6.823   0.000   0.000   0.000
   2_occ:  0.298  32.591   2.930   5.899   6.823   0.000   0.000   0.000
   3_bss:  0.303  54.581   1.175   3.194   3.906   0.000   0.000   0.000
   3_xyz:  0.303  54.581   1.175   3.194   3.906   0.000   0.000   0.000
   3_adp:  0.303  54.581   1.175   3.194   3.906   0.000   0.000   0.000
   3_occ:  0.303  54.581   1.175   3.194   3.906   0.000   0.000   0.000
   4_bss:  0.328  54.581   0.449   1.887   2.987   0.000   0.000   0.000
   4_xyz:  0.328  54.581   0.449   1.887   2.987   0.000   0.000   0.000
   4_adp:  0.328  54.581   0.449   1.887   2.987   0.000   0.000   0.000
   4_occ:  0.328  54.581   0.449   1.887   2.987   0.000   0.000   0.000
   5_bss:  0.328  54.581   0.471   1.673   2.872   0.000   0.000   0.000
   5_xyz:  0.328  54.581   0.471   1.673   2.872   0.000   0.000   0.000
   5_adp:  0.328  54.581   0.471   1.673   2.872   0.000   0.000   0.000
   5_occ:  0.328  54.581   0.471   1.673   2.872   0.000   0.000   0.000
   5_bss:  0.324  61.373  -1.104  -0.049   1.153   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.182 0.4306  0.4986    70797.777
   1_bss:  57.634 0.4236  0.6439    70667.504
   1_xyz:  49.027 0.5314  0.7902    52809.070
   1_adp:  46.236 0.5665  0.8954    49307.673
   1_occ:  46.322 0.5654  0.8923    49416.361
   2_bss:  45.861 0.5712  0.7870    49020.706
   2_xyz:  34.838 0.7025  0.9451    29034.751
   2_adp:  31.707 0.7388  0.9838    25102.702
   2_occ:  31.710 0.7387  0.9835    25095.921
   3_bss:  31.520 0.7410  0.9054    25011.410
   3_xyz:  23.075 0.8307  0.9758    13964.570
   3_adp:  20.485 0.8572  0.9886    11689.000
   3_occ:  20.474 0.8573  0.9889    11682.832
   4_bss:  20.354 0.8583  0.9560    11544.447
   4_xyz:  17.475 0.8854  0.9674     8928.365
   4_adp:  17.209 0.8879  0.9597     8763.645
   4_occ:  17.198 0.8880  0.9597     8758.764
   5_bss:  17.215 0.8878  0.9562     8782.323
   5_xyz:  16.052 0.8979  0.9627     7776.313
   5_adp:  15.858 0.8997  0.9561     7610.613
   5_occ:  15.849 0.8998  0.9561     7605.326
   5_bss:  15.849 0.8998  0.9650     7605.859
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4203e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4203e+01
   1_xyz:   1.772  0.014  0.111 18.228  0.007  4.111   1.5299e-01
   1_adp:   1.772  0.014  0.111 18.228  0.007  4.111   1.5299e-01
   1_occ:   1.772  0.014  0.111 18.228  0.007  4.111   1.5299e-01
   2_bss:   1.772  0.014  0.111 18.228  0.007  4.111   1.5299e-01
   2_xyz:   1.300  0.010  0.081 16.296  0.005  4.112   9.6716e-02
   2_adp:   1.300  0.010  0.081 16.296  0.005  4.112   9.6716e-02
   2_occ:   1.300  0.010  0.081 16.296  0.005  4.112   9.6716e-02
   3_bss:   1.300  0.010  0.081 16.296  0.005  4.112   9.6716e-02
   3_xyz:   1.118  0.009  0.080 15.756  0.004  4.136   7.5117e-02
   3_adp:   1.118  0.009  0.080 15.756  0.004  4.136   7.5117e-02
   3_occ:   1.118  0.009  0.080 15.756  0.004  4.136   7.5117e-02
   4_bss:   1.118  0.009  0.080 15.756  0.004  4.136   7.5117e-02
   4_xyz:   0.951  0.007  0.071 15.205  0.003  4.118   5.7269e-02
   4_adp:   0.951  0.007  0.071 15.205  0.003  4.118   5.7269e-02
   4_occ:   0.951  0.007  0.071 15.205  0.003  4.118   5.7269e-02
   5_bss:   0.951  0.007  0.071 15.205  0.003  4.118   5.7269e-02
   5_xyz:   1.104  0.009  0.084 15.445  0.003  4.125   7.0159e-02
   5_adp:   1.104  0.009  0.084 15.445  0.003  4.125   7.0159e-02
   5_occ:   1.104  0.009  0.084 15.445  0.003  4.125   7.0159e-02
   5_bss:   1.104  0.009  0.084 15.445  0.003  4.125   7.0159e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0262e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0262e+00
   1_xyz:  16.419  0.173  0.516 86.394  0.051  2.200   1.1091e-01
   1_adp:  16.419  0.173  0.516 86.394  0.051  2.200   1.1091e-01
   1_occ:  16.419  0.173  0.516 86.394  0.051  2.200   1.1091e-01
   2_bss:  16.419  0.173  0.516 86.394  0.051  2.200   1.1091e-01
   2_xyz:   8.918  0.122  0.298 87.777  0.041  2.089   1.1310e-01
   2_adp:   8.918  0.122  0.298 87.777  0.041  2.089   1.1310e-01
   2_occ:   8.918  0.122  0.298 87.777  0.041  2.089   1.1310e-01
   3_bss:   8.918  0.122  0.298 87.777  0.041  2.089   1.1310e-01
   3_xyz:   6.938  0.048  0.281 87.319  0.042  2.275   8.4124e-02
   3_adp:   6.938  0.048  0.281 87.319  0.042  2.275   8.4124e-02
   3_occ:   6.938  0.048  0.281 87.319  0.042  2.275   8.4124e-02
   4_bss:   6.938  0.048  0.281 87.319  0.042  2.275   8.4124e-02
   4_xyz:   6.322  0.039  0.267 85.007  0.032  2.276   7.1566e-02
   4_adp:   6.322  0.039  0.267 85.007  0.032  2.276   7.1566e-02
   4_occ:   6.322  0.039  0.267 85.007  0.032  2.276   7.1566e-02
   5_bss:   6.322  0.039  0.267 85.007  0.032  2.276   7.1566e-02
   5_xyz:   7.653  0.046  0.446 88.346  0.032  2.287   3.9954e-02
   5_adp:   7.653  0.046  0.446 88.346  0.032  2.287   3.9954e-02
   5_occ:   7.653  0.046  0.446 88.346  0.032  2.287   3.9954e-02
   5_bss:   7.653  0.046  0.446 88.346  0.032  2.287   3.9954e-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:  83.91   0.00  14.32  73.69   0.00  12.10  83.91   0.00  26.42
   1_occ:  83.91   0.00  14.32  73.69   0.00  12.10  83.91   0.00  26.42
   2_bss:  83.91   0.00  14.32  73.69   0.00  12.10  83.91   0.00  26.42
   2_xyz:  83.91   0.00  14.32  73.69   0.00  12.10  83.91   0.00  26.42
   2_adp: 130.21   0.00  13.86 130.21   0.00  10.72  81.56   0.00  30.98
   2_occ: 130.21   0.00  13.86 130.21   0.00  10.72  81.56   0.00  30.98
   3_bss: 130.21   0.00  13.86 130.21   0.00  10.72  81.56   0.00  30.98
   3_xyz: 130.21   0.00  13.86 130.21   0.00  10.72  81.56   0.00  30.98
   3_adp:  91.45   0.00  13.59  91.45   0.00   9.76  77.27   2.72  34.43
   3_occ:  91.45   0.00  13.59  91.45   0.00   9.76  77.27   2.72  34.43
   4_bss:  91.45   0.00  13.59  91.45   0.00   9.76  77.27   2.72  34.43
   4_xyz:  91.45   0.00  13.59  91.45   0.00   9.76  77.27   2.72  34.43
   4_adp:  86.73   0.00  13.60  86.73   0.00   9.56  76.26   1.83  35.59
   4_occ:  86.73   0.00  13.60  86.73   0.00   9.56  76.26   1.83  35.59
   5_bss:  86.73   0.00  13.60  86.73   0.00   9.56  76.26   1.83  35.59
   5_xyz:  86.73   0.00  13.60  86.73   0.00   9.56  76.26   1.83  35.59
   5_adp:  88.70   0.00  14.19  84.19   0.00   9.57  88.70   2.15  39.38
   5_occ:  88.70   0.00  14.19  84.19   0.00   9.57  88.70   2.15  39.38
   5_bss:  90.64   1.93  16.13  86.12   1.93  11.50  90.64   4.08  41.31
------------------------------------------------------------------------
 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:    1.289    0.006    0.417
   1_adp:    1.289    0.006    0.417
   1_occ:    1.289    0.006    0.417
   2_bss:    1.289    0.006    0.417
   2_xyz:    1.882    0.032    0.617
   2_adp:    1.882    0.032    0.617
   2_occ:    1.882    0.032    0.617
   3_bss:    1.882    0.032    0.617
   3_xyz:    1.852    0.034    0.705
   3_adp:    1.852    0.034    0.705
   3_occ:    1.852    0.034    0.705
   4_bss:    1.852    0.034    0.705
   4_xyz:    2.048    0.050    0.754
   4_adp:    2.048    0.050    0.754
   4_occ:    2.048    0.050    0.754
   5_bss:    2.048    0.050    0.754
   5_xyz:    2.086    0.055    0.777
   5_adp:    2.086    0.055    0.777
   5_occ:    2.086    0.055    0.777
   5_bss:    2.086    0.055    0.777
------------------------------------------------------------------------

CPU time actual refinement: 344.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_460/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_460/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_460/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_460/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_460/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.21 
  Macro-tasks:
    bulk solvent and scale       = 41.76  
    individual site refinement   = 147.09 
    weights calculation          = 31.85  
    collect and process          = 6.63   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 227.46 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 106.55 
    alpha_beta                      = 8.59   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 118.28 
    fmodel                         = 7.50   
    r_factors                      = 0.24   
    phase_errors                   = 10.54  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 255.62 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.796 micro seconds
Total CPU time: 5.96 minutes
from_scatterers_fft:    648 calls, 106.15 s
gradients_fft:          592 calls, 104.65 s

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

# Date 2008-01-16 Time 01:38:50 PST -0800 (1200476330.03 s)
Start R-work = 0.4945, R-free = 0.4806 (no bulk solvent and anisotropic scale)
Final R-work = 0.1388, R-free = 0.1848 (no bulk solvent and anisotropic scale)

Start R-work = 0.4853, R-free = 0.4759
Final R-work = 0.1215, R-free = 0.1701