# Date 2008-01-16 Time 02:16:24 PST -0800 (1200478584.25 s)
#phil __OFF__

Command line arguments: "../764.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16455
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 764

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.4607, 86.39, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 1.9825
Completeness in resolution range: 0.965451
Completeness with d_max=infinity: 0.962463

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0485
                             d_min =   1.9825

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 1.9825
Completeness in resolution range: 0.965451
Completeness with d_max=infinity: 0.962463

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0489 -  4.2423 [2126/2150]  1913   213  10.0%
  bin  2:  4.2423 -  3.3798 [2042/2062]  1838   204  10.0%
  bin  3:  3.3798 -  2.9562 [2028/2047]  1825   203  10.0%
  bin  4:  2.9562 -  2.6876 [2005/2035]  1808   197   9.8%
  bin  5:  2.6876 -  2.4959 [2002/2021]  1803   199   9.9%
  bin  6:  2.4959 -  2.3493 [1965/1990]  1763   202  10.3%
  bin  7:  2.3493 -  2.2321 [1966/1994]  1766   200  10.2%
  bin  8:  2.2321 -  2.1352 [1975/2011]  1780   195   9.9%
  bin  9:  2.1352 -  2.0532 [1958/2000]  1765   193   9.9%
  bin 10:  2.0532 -  1.9825 [1522/1980]  1369   153  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_764/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 15
        2.42 -     3.04: 2196
        3.04 -     3.66: 4693
        3.66 -     4.28: 9094
        4.28 -     4.90: 12323
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " O   HOH Z 280 " - " O   HOH Z 438 "  2.318 3.040 -x,y-1/2,-z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.330 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28316 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_764/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_764/model_refine_001.geo

CPU time processing inputs: 9.73


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.4607 86.39 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 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4327   r_free= 0.4181   ksol= 0.00   Bsol= 0.00   scale= 0.824    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.225660                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7317 0.99   1385  155 0.3676 0.3530      6.5277      6.4938|
|  2:  4.7317 -  3.7752 0.99   1334  147 0.3251 0.3171      6.6502      6.6075|
|  3:  3.7752 -  3.3037 0.99   1306  143 0.3639 0.3373      6.5416      6.5584|
|  4:  3.3037 -  3.0043 0.99   1293  146 0.4081 0.3694      6.4573      6.3756|
|  5:  3.0043 -  2.7904 0.99   1288  145 0.4585 0.4406      6.3136       6.336|
|  6:  2.7904 -  2.6268 0.99   1297  139 0.4534 0.5028      6.2352      6.1647|
|  7:  2.6268 -  2.4959 0.99   1284  141 0.4842 0.4541       6.207      6.2073|
|  8:  2.4959 -  2.3877 0.98   1261  145 0.4904 0.4412      6.1532      6.1344|
|  9:  2.3877 -  2.2961 0.98   1269  140 0.4642 0.4773      6.0734      6.0713|
| 10:  2.2961 -  2.2171 1.00   1261  142 0.4947 0.4675      6.0996      6.0793|
| 11:  2.2171 -  2.1480 0.98   1269  139 0.5009 0.4482      6.0241      5.9876|
| 12:  2.1480 -  2.0868 0.98   1245  142 0.4895 0.4993      5.9635      5.9894|
| 13:  2.0868 -  2.0320 0.99   1284  138 0.5018 0.4967      5.8728      5.8335|
| 14:  2.0320 -  1.9825 0.67    854   97 0.5141 0.5139      5.8516      5.7618|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7317  1385   155  0.73  31.42   0.81     0.77      60368.58|
|  2:  4.7317 -  3.7752  1334   147  0.79  27.57   0.91     0.84      71563.69|
|  3:  3.7752 -  3.3037  1306   143  0.72  33.78   0.88     0.82      73281.18|
|  4:  3.3037 -  3.0043  1293   146  0.66  38.56   0.83     0.73      66549.64|
|  5:  3.0043 -  2.7904  1288   145  0.56  47.42   0.78     0.64      60492.23|
|  6:  2.7904 -  2.6268  1297   139  0.53  49.98   0.76     0.58      56401.90|
|  7:  2.6268 -  2.4959  1284   141  0.49  53.05   0.76     0.55      53738.78|
|  8:  2.4959 -  2.3877  1261   145  0.48  53.64   0.76     0.55      48939.28|
|  9:  2.3877 -  2.2961  1269   140  0.52  50.94   0.75     0.57      42139.69|
| 10:  2.2961 -  2.2171  1261   142  0.51  51.62   0.79     0.59      37134.09|
| 11:  2.2171 -  2.1480  1269   139  0.49  52.91   0.77     0.58      36114.81|
| 12:  2.1480 -  2.0868  1245   142  0.44  56.87   0.80     0.53      36802.83|
| 13:  2.0868 -  2.0320  1284   138  0.40  60.01   0.75     0.48      33198.12|
| 14:  2.0320 -  1.9825   854    97  0.44  56.68   0.73     0.46      25130.73|
|alpha:            min =        0.46 max =            0.84 mean =         0.63|
|beta:             min =    25130.73 max =        73281.18 mean =     50972.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.99 mean =        47.03|
|phase err.(test): min =        0.00 max =           89.98 mean =        47.23|
|-----------------------------------------------------------------------------|

============================== 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 = 7.513596              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.922   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.680476              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.410   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      683 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1505 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2646 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3930 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5076 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6586 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7700 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.721 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.704 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    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 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4407   r_free= 0.4246   ksol= 0.00   Bsol= 0.00   scale= 0.792    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.231667                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4243   r_free= 0.4040   ksol= 0.35   Bsol= 16.55   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.51,9.36,8.03,0.00,0.00,0.00); trace/3= 8.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.221186                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.912992              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.901   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.658485              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.538   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4243      final r-factor (work) = 0.3170          |
| start r-factor (free) = 0.4040      final r-factor (free) = 0.3369          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.2780 = 6.91 * 0.50 * 6.2368 + 1.00 * 53.7205                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0982 = 6.91 * 0.50 * 6.0705 + 1.00 * 0.1154                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3170      final r-factor (work) = 0.2526          |
| start r-factor (free) = 0.3369      final r-factor (free) = 0.2911          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0121 = 0.66 * 1.00 * 6.0705 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8914 = 0.66 * 1.00 * 5.8911 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.59   10.93    None  None   None       |
|    all(noH): 2823   0      0.00    66.59   10.93    None  None   None       |
|    Sol.    : 438    0      0.00    66.59   27.78    None  None   None       |
|    Mac.    : 2385   0      0.00    65.30   7.83     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.659: 1338   |   5:    33.295 -  39.954:   81        |
|      1:     6.659 -  13.318:  726   |   6:    39.954 -  46.613:   60        |
|      2:    13.318 -  19.977:  279   |   7:    46.613 -  53.272:   16        |
|      3:    19.977 -  26.636:  173   |   8:    53.272 -  59.931:   12        |
|      4:    26.636 -  33.295:  133   |   9:    59.931 -  66.589:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2526 r_free = 0.2911             target_work(ml) = 5.828         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2521 r_free = 0.2912             target_work(ml) = 5.827         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2521   r_free= 0.2912   ksol= 0.35   Bsol= 16.55   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.51,9.36,8.03,0.00,0.00,0.00); trace/3= 8.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.826692                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2465   r_free= 0.2842   ksol= 0.34   Bsol= 39.26   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.99,4.87,4.85,0.00,0.00,0.00); trace/3= 4.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.823087                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.737515              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.328   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.360384              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.494  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2465      final r-factor (work) = 0.1647          |
| start r-factor (free) = 0.2842      final r-factor (free) = 0.2077          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1424 = 3.74 * 0.50 * 5.9010 + 1.00 * 0.1150                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5899 = 3.74 * 0.50 * 5.6322 + 1.00 * 0.0646                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1647      final r-factor (work) = 0.1471          |
| start r-factor (free) = 0.2077      final r-factor (free) = 0.1922          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0418 = 0.36 * 1.00 * 5.6322 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9590 = 0.36 * 1.00 * 5.4055 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.11   11.22    None  None   None       |
|    all(noH): 2823   0      0.00    69.11   11.22    None  None   None       |
|    Sol.    : 438    0      0.66    69.11   32.24    None  None   None       |
|    Mac.    : 2385   0      0.00    68.45   7.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.911: 1538   |   5:    34.557 -  41.468:  113        |
|      1:     6.911 -  13.823:  627   |   6:    41.468 -  48.379:   83        |
|      2:    13.823 -  20.734:  198   |   7:    48.379 -  55.290:   39        |
|      3:    20.734 -  27.645:  106   |   8:    55.290 -  62.202:   14        |
|      4:    27.645 -  34.557:  101   |   9:    62.202 -  69.113:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1471 r_free = 0.1922             target_work(ml) = 5.368         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1470 r_free = 0.1921             target_work(ml) = 5.367         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1470   r_free= 0.1921   ksol= 0.34   Bsol= 39.26   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.99,4.87,4.85,0.00,0.00,0.00); trace/3= 4.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.367028                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1468   r_free= 0.1911   ksol= 0.33   Bsol= 45.65   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.29,3.44,4.43,0.00,0.00,0.00); trace/3= 3.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.365789                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.728390              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.007  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.538367              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.637  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1468      final r-factor (work) = 0.1266          |
| start r-factor (free) = 0.1911      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7393 = 1.73 * 0.50 * 5.4093 + 1.00 * 0.0646                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6340 = 1.73 * 0.50 * 5.2986 + 1.00 * 0.0549                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1266      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1694      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1621 = 1.54 * 1.00 * 5.2986 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0427 = 1.54 * 1.00 * 5.2189 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.86   11.97    None  None   None       |
|    all(noH): 2823   0      0.00    80.86   11.97    None  None   None       |
|    Sol.    : 438    0      0.75    76.94   35.90    None  None   None       |
|    Mac.    : 2385   0      0.00    80.86   7.58     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 -   8.086: 1688   |   5:    40.431 -  48.517:   89        |
|      1:     8.086 -  16.172:  553   |   6:    48.517 -  56.603:   72        |
|      2:    16.172 -  24.259:  153   |   7:    56.603 -  64.689:   34        |
|      3:    24.259 -  32.345:  105   |   8:    64.689 -  72.776:   19        |
|      4:    32.345 -  40.431:  105   |   9:    72.776 -  80.862:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1218 r_free = 0.1659             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1217 r_free = 0.1659             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1659   ksol= 0.33   Bsol= 45.65   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.29,3.44,4.43,0.00,0.00,0.00); trace/3= 3.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.208141                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1658   ksol= 0.33   Bsol= 45.65   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,3.17,4.35,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.207902                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.702741              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.513  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.218430              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.033  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4978 = 1.70 * 0.50 * 5.2185 + 1.00 * 0.0549                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4719 = 1.70 * 0.50 * 5.1860 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1609      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1468 = 0.22 * 1.00 * 5.1860 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1422 = 0.22 * 1.00 * 5.1769 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.79   11.68    None  None   None       |
|    all(noH): 2823   0      0.00    80.79   11.68    None  None   None       |
|    Sol.    : 438    0      1.20    75.76   34.80    None  None   None       |
|    Mac.    : 2385   0      0.00    80.79   7.43     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 -   8.079: 1735   |   5:    40.396 -  48.475:   88        |
|      1:     8.079 -  16.158:  532   |   6:    48.475 -  56.554:   65        |
|      2:    16.158 -  24.237:  141   |   7:    56.554 -  64.633:   34        |
|      3:    24.237 -  32.316:  111   |   8:    64.633 -  72.712:   14        |
|      4:    32.316 -  40.396:   99   |   9:    72.712 -  80.791:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1160 r_free = 0.1585             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1159 r_free = 0.1584             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1584   ksol= 0.33   Bsol= 45.65   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,3.17,4.35,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.166153                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1587   ksol= 0.32   Bsol= 45.65   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,3.17,4.35,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.166450                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.105180              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.464  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.888820              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.647  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0934 = 3.11 * 0.50 * 5.1763 + 1.00 * 0.0568                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0541 = 3.11 * 0.50 * 5.1424 + 1.00 * 0.0701                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.0092 = 3.89 * 1.00 * 5.1424 + 1.00 * 0.0113                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.9415 = 3.89 * 1.00 * 5.1243 + 1.00 * 0.0138                              |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.45   11.72    None  None   None       |
|    all(noH): 2823   0      0.00    83.45   11.72    None  None   None       |
|    Sol.    : 438    0      0.86    76.81   35.16    None  None   None       |
|    Mac.    : 2385   0      0.00    83.45   7.42     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 -   8.345: 1749   |   5:    41.727 -  50.072:   83        |
|      1:     8.345 -  16.691:  508   |   6:    50.072 -  58.417:   65        |
|      2:    16.691 -  25.036:  155   |   7:    58.417 -  66.763:   23        |
|      3:    25.036 -  33.381:  115   |   8:    66.763 -  75.108:   15        |
|      4:    33.381 -  41.727:  106   |   9:    75.108 -  83.453:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1087 r_free = 0.1568             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1087 r_free = 0.1568             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1568   ksol= 0.32   Bsol= 45.65   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,3.17,4.35,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131018                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7317 0.99   1385  155 0.0962 0.1262      5.3685      5.5151|
|  2:  4.7317 -  3.7752 0.99   1334  147 0.0833 0.1133      5.4175      5.6164|
|  3:  3.7752 -  3.3037 0.99   1306  143 0.1040 0.1474      5.4606      5.8354|
|  4:  3.3037 -  3.0043 0.99   1293  146 0.1172 0.1675      5.4339      5.6014|
|  5:  3.0043 -  2.7904 0.99   1288  145 0.1291 0.1683      5.3148      5.5539|
|  6:  2.7904 -  2.6268 0.99   1297  139 0.1145 0.1886      5.1866      5.4606|
|  7:  2.6268 -  2.4959 0.99   1284  141 0.1258 0.1530      5.1612      5.3253|
|  8:  2.4959 -  2.3877 0.98   1261  145 0.1128 0.1749      5.0565      5.3542|
|  9:  2.3877 -  2.2961 0.98   1269  140 0.1155 0.1786      5.0374      5.2862|
| 10:  2.2961 -  2.2171 1.00   1261  142 0.1067 0.1740      4.9424      5.2625|
| 11:  2.2171 -  2.1480 0.98   1269  139 0.1102 0.1773      4.9366       5.288|
| 12:  2.1480 -  2.0868 0.98   1245  142 0.1081 0.1629      4.8648      5.1395|
| 13:  2.0868 -  2.0320 0.99   1284  138 0.1106 0.1737      4.7802       5.049|
| 14:  2.0320 -  1.9825 0.67    854   97 0.0996 0.1640      4.6609      4.8897|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7317  1385   155  0.94   9.11   0.98     0.95       7052.32|
|  2:  4.7317 -  3.7752  1334   147  0.95   7.68   1.02     1.01       8820.12|
|  3:  3.7752 -  3.3037  1306   143  0.94  11.08   1.03     1.02      10071.15|
|  4:  3.3037 -  3.0043  1293   146  0.92  13.55   1.01     0.99      10164.32|
|  5:  3.0043 -  2.7904  1288   145  0.90  15.89   1.00     0.97       8307.08|
|  6:  2.7904 -  2.6268  1297   139  0.90  15.56   0.99     0.96       6968.32|
|  7:  2.6268 -  2.4959  1284   141  0.90  15.65   0.99     0.96       6156.39|
|  8:  2.4959 -  2.3877  1261   145  0.91  15.15   0.99     0.97       5219.02|
|  9:  2.3877 -  2.2961  1269   140  0.91  15.45   1.01     0.98       5120.74|
| 10:  2.2961 -  2.2171  1261   142  0.90  15.43   1.00     0.97       4357.03|
| 11:  2.2171 -  2.1480  1269   139  0.90  16.33   0.99     0.95       4387.51|
| 12:  2.1480 -  2.0868  1245   142  0.91  14.93   1.02     1.01       3911.49|
| 13:  2.0868 -  2.0320  1284   138  0.90  16.27   1.00     0.98       3344.72|
| 14:  2.0320 -  1.9825   854    97  0.92  14.39   0.99     0.96       2633.12|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2633.12 max =        10164.32 mean =      6297.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.97|
|phase err.(test): min =        0.00 max =           89.96 mean =        13.49|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1568   ksol= 0.32   Bsol= 49.27   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,-0.45,0.83,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130981                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1568   ksol= 0.32   Bsol= 49.27   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,-0.45,0.83,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130981                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7317 0.99   1385  155 0.0962 0.1263      5.3688      5.5157|
|  2:  4.7317 -  3.7752 0.99   1334  147 0.0833 0.1133      5.4178      5.6166|
|  3:  3.7752 -  3.3037 0.99   1306  143 0.1040 0.1475      5.4607      5.8355|
|  4:  3.3037 -  3.0043 0.99   1293  146 0.1172 0.1675      5.4338      5.6015|
|  5:  3.0043 -  2.7904 0.99   1288  145 0.1291 0.1683      5.3145      5.5536|
|  6:  2.7904 -  2.6268 0.99   1297  139 0.1145 0.1885      5.1863      5.4599|
|  7:  2.6268 -  2.4959 0.99   1284  141 0.1258 0.1531       5.161      5.3257|
|  8:  2.4959 -  2.3877 0.98   1261  145 0.1128 0.1748      5.0565      5.3538|
|  9:  2.3877 -  2.2961 0.98   1269  140 0.1155 0.1785      5.0373      5.2856|
| 10:  2.2961 -  2.2171 1.00   1261  142 0.1066 0.1742      4.9425      5.2636|
| 11:  2.2171 -  2.1480 0.98   1269  139 0.1102 0.1773      4.9367      5.2882|
| 12:  2.1480 -  2.0868 0.98   1245  142 0.1081 0.1629       4.865      5.1398|
| 13:  2.0868 -  2.0320 0.99   1284  138 0.1105 0.1734      4.7799      5.0485|
| 14:  2.0320 -  1.9825 0.67    854   97 0.0997 0.1637      4.6601      4.8882|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.7317  1385   155  0.94   9.11   0.98     0.95       7058.08|
|  2:  4.7317 -  3.7752  1334   147  0.95   7.69   1.02     1.01       8826.42|
|  3:  3.7752 -  3.3037  1306   143  0.94  11.08   1.03     1.02      10076.40|
|  4:  3.3037 -  3.0043  1293   146  0.92  13.55   1.01     0.99      10162.23|
|  5:  3.0043 -  2.7904  1288   145  0.90  15.88   1.00     0.98       8298.75|
|  6:  2.7904 -  2.6268  1297   139  0.90  15.56   0.99     0.96       6964.19|
|  7:  2.6268 -  2.4959  1284   141  0.90  15.65   0.99     0.96       6153.41|
|  8:  2.4959 -  2.3877  1261   145  0.91  15.15   0.99     0.97       5217.19|
|  9:  2.3877 -  2.2961  1269   140  0.91  15.45   1.01     0.98       5119.29|
| 10:  2.2961 -  2.2171  1261   142  0.90  15.44   1.01     0.97       4360.44|
| 11:  2.2171 -  2.1480  1269   139  0.90  16.34   1.00     0.96       4390.69|
| 12:  2.1480 -  2.0868  1245   142  0.91  14.94   1.02     1.01       3914.81|
| 13:  2.0868 -  2.0320  1284   138  0.90  16.26   1.01     0.98       3342.47|
| 14:  2.0320 -  1.9825   854    97  0.92  14.36   0.99     0.96       2626.98|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2626.98 max =        10162.23 mean =      6297.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.97|
|phase err.(test): min =        0.00 max =           89.96 mean =        13.49|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.62    87.07   15.34    None  None   None       |
|    all(noH): 2823   0      3.62    87.07   15.34    None  None   None       |
|    Sol.    : 438    0      4.47    80.43   38.78    None  None   None       |
|    Mac.    : 2385   0      3.62    87.07   11.04    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:     3.616 -  11.962: 1749   |   5:    45.343 -  53.688:   83        |
|      1:    11.962 -  20.307:  508   |   6:    53.688 -  62.034:   65        |
|      2:    20.307 -  28.652:  155   |   7:    62.034 -  70.379:   23        |
|      3:    28.652 -  36.998:  115   |   8:    70.379 -  78.724:   15        |
|      4:    36.998 -  45.343:  106   |   9:    78.724 -  87.070:    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)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.331 - 4.761
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 302
   mapped sites are within: 0.709 - 4.761

peak=   11.265 closest distance to " CB  VAL A 230 " =    1.446
peak=    7.713 closest distance to " CG2 VAL A 296 " =    1.120
peak=    6.212 closest distance to " NE2 GLN A  11 " =    1.174
peak=    6.050 closest distance to " CD2 LEU A   5 " =    1.179
peak=    5.948 closest distance to " CG  LEU A   5 " =    1.144
peak=    5.921 closest distance to " NH2 ARG A  56 " =    2.176
peak=    5.686 closest distance to " CG  PRO A  54 " =    1.245
peak=    5.534 closest distance to " O   HOH Z 144 " =    1.910
peak=    5.456 closest distance to " CG  LEU A 228 " =    1.133
peak=    5.124 closest distance to " CB  GLN A 183 " =    1.259
peak=    5.018 closest distance to " O   HOH Z 427 " =    2.829
peak=    4.929 closest distance to " O   HOH Z 232 " =    2.343
peak=    4.849 closest distance to " CB  GLN A 223 " =    1.471
peak=    4.810 closest distance to " CB  SER A  63 " =    1.318
peak=    4.775 closest distance to " CB  VAL A 296 " =    1.061
peak=    4.768 closest distance to " O   HOH Z 126 " =    1.983
peak=    4.672 closest distance to " O   HOH Z 209 " =    2.290
peak=    4.608 closest distance to " O   HOH Z 425 " =    1.436
peak=    4.606 closest distance to " CB  VAL A 230 " =    1.157
peak=    4.586 closest distance to " O   HOH Z 369 " =    2.150
peak=    4.558 closest distance to " CB  PRO A  54 " =    0.950
peak=    4.526 closest distance to " O   HOH Z   9 " =    1.259
peak=    4.492 closest distance to " O   HOH Z  78 " =    1.809
peak=    4.488 closest distance to " O   HOH Z 316 " =    3.068
peak=    4.458 closest distance to " CB  GLU A 152 " =    1.267
peak=    4.458 closest distance to " O   HOH Z 298 " =    1.771
peak=    4.444 closest distance to " C   PRO A 198 " =    1.536
peak=    4.432 closest distance to " CB  ASN A 148 " =    1.313
peak=    4.423 closest distance to " CG  PRO A 213 " =    1.168
peak=    4.423 closest distance to " CB  ARG A  79 " =    1.479
peak=    4.415 closest distance to " CB  SER A   3 " =    1.334
peak=    4.349 closest distance to " CD2 LEU A 228 " =    1.154
peak=    4.348 closest distance to " O   SER A  87 " =    2.337
peak=    4.318 closest distance to " O   HOH Z  61 " =    1.635
peak=    4.296 closest distance to " O   HOH Z 272 " =    1.835
peak=    4.285 closest distance to " O   HOH Z 346 " =    1.605
peak=    4.248 closest distance to " O   HOH Z 193 " =    1.750
peak=    4.201 closest distance to " ND2 ASN A 187 " =    1.449
peak=    4.198 closest distance to " CB  TRP A 266 " =    1.029
peak=    4.167 closest distance to " CB  ARG A 275 " =    0.924
peak=    4.128 closest distance to " O   HOH Z 236 " =    2.072
peak=    4.117 closest distance to " OD1 ASN A  69 " =    2.661
peak=    4.107 closest distance to " O   HOH Z 203 " =    1.734
peak=    4.093 closest distance to " O   HOH Z 126 " =    1.595
peak=    4.092 closest distance to " CD  ARG A  66 " =    2.765
peak=    4.065 closest distance to " CB  VAL A 265 " =    1.339
peak=    4.027 closest distance to " O   HOH Z 303 " =    2.177
peak=    4.016 closest distance to " O   HOH Z 234 " =    3.662
peak=    4.013 closest distance to " O   HOH Z 261 " =    2.233
peak=    4.012 closest distance to " O   HOH Z 158 " =    3.140
peak=    3.993 closest distance to " CA  TYR A  30 " =    0.985
peak=    3.990 closest distance to " O   HOH Z  54 " =    2.490
peak=    3.981 closest distance to " O   HOH Z 411 " =    3.729
peak=    3.938 closest distance to " O   HOH Z 403 " =    1.664
peak=    3.917 closest distance to " O   HOH Z 193 " =    1.678
peak=    3.916 closest distance to " CB  SER A 216 " =    0.838
peak=    3.915 closest distance to " CB  ASN A 142 " =    1.037
peak=    3.913 closest distance to " O   HOH Z 189 " =    2.900
peak=    3.913 closest distance to " NH2AARG A 190 " =    1.820
peak=    3.873 closest distance to " CB  TRP A 179 " =    1.426
peak=    3.870 closest distance to " O   HOH Z  30 " =    1.511
peak=    3.869 closest distance to " CG  LEU A 167 " =    1.198
peak=    3.868 closest distance to " CB  TYR A 169 " =    0.727
peak=    3.865 closest distance to " O   HOH Z 368 " =    2.097
peak=    3.855 closest distance to " CG  PRO A 198 " =    1.167
peak=    3.850 closest distance to " NZ  LYS A 117 " =    3.068
peak=    3.849 closest distance to " O   HOH Z  43 " =    1.991
peak=    3.846 closest distance to " CB  GLU A 128 " =    1.024
peak=    3.843 closest distance to " CB  VAL A 202 " =    1.624
peak=    3.826 closest distance to " O   HOH Z  59 " =    1.794
peak=    3.818 closest distance to " O   HOH Z   9 " =    1.906
peak=    3.810 closest distance to " CB  ASP A 140 " =    0.930
peak=    3.788 closest distance to " CD BLYS A 290 " =    1.137
peak=    3.763 closest distance to " CD2 TRP A 179 " =    1.350
peak=    3.761 closest distance to " N   PHE A 130 " =    1.305
peak=    3.758 closest distance to " OG BSER A 164 " =    2.187
peak=    3.755 closest distance to " O   HOH Z  97 " =    2.018
peak=    3.754 closest distance to " CB BVAL A  41 " =    1.248
peak=    3.750 closest distance to " O   HOH Z  88 " =    3.249
peak=    3.747 closest distance to " CG1BVAL A  72 " =    1.591
peak=    3.744 closest distance to " CA  ASN A 215 " =    1.204
peak=    3.742 closest distance to " CB  ASN A  39 " =    0.940
peak=    3.742 closest distance to " O   HOH Z   2 " =    1.454
peak=    3.741 closest distance to " CB  GLU A 277 " =    3.550
peak=    3.725 closest distance to " CG  PRO A 243 " =    1.146
peak=    3.724 closest distance to " O   HOH Z  68 " =    2.165
peak=    3.718 closest distance to " CB  SER A 212 " =    1.164
peak=    3.704 closest distance to " O   HOH Z 248 " =    1.612
peak=    3.702 closest distance to " ND2 ASN A 249 " =    1.901
peak=    3.701 closest distance to " CG2 VAL A 257 " =    0.833
peak=    3.689 closest distance to " O   HOH Z 280 " =    2.936
peak=    3.689 closest distance to " O   HOH Z 371 " =    2.900
peak=    3.678 closest distance to " O   HOH Z 180 " =    2.138
peak=    3.671 closest distance to " O   HOH Z 437 " =    1.808
peak=    3.666 closest distance to " CA  ALA A 158 " =    1.252
peak=    3.661 closest distance to " CE  LYS A  76 " =    0.873
peak=    3.660 closest distance to " O   HOH Z 128 " =    2.077
peak=    3.651 closest distance to " O   HOH Z 214 " =    2.069
peak=    3.646 closest distance to " CA  ALA A  51 " =    0.989
peak=    3.646 closest distance to " CA  LYS A 117 " =    1.205
peak=    3.643 closest distance to " O   HOH Z 250 " =    1.389
peak=    3.642 closest distance to " O   HOH Z  10 " =    1.745
peak=    3.639 closest distance to " O   HOH Z 392 " =    3.217
peak=    3.635 closest distance to " O   HOH Z 423 " =    2.704
peak=    3.633 closest distance to " CB  THR A  82 " =    1.299
peak=    3.626 closest distance to " CD  ARG A 159 " =    0.709
peak=    3.625 closest distance to " O   HOH Z   1 " =    1.726
peak=    3.625 closest distance to " CZ  PHE A 218 " =    1.096
peak=    3.620 closest distance to " CG  GLN A  88 " =    1.087
peak=    3.612 closest distance to " O   HOH Z   1 " =    1.759
peak=    3.611 closest distance to " O   HOH Z 422 " =    2.650
peak=    3.608 closest distance to " CB  ARG A 190 " =    1.626
peak=    3.606 closest distance to " O   HOH Z 227 " =    1.720
peak=    3.605 closest distance to " O   HOH Z   7 " =    1.143
peak=    3.593 closest distance to " O   HOH Z 305 " =    3.518
peak=    3.592 closest distance to " O   HOH Z 368 " =    3.616
peak=    3.589 closest distance to " CB  ARG A 139 " =    0.977
peak=    3.586 closest distance to " NH1AARG A 145 " =    1.132
peak=    3.584 closest distance to " O   HOH Z 286 " =    2.390
peak=    3.583 closest distance to " O   HOH Z 419 " =    1.887
peak=    3.579 closest distance to " CB  LEU A 143 " =    1.172
peak=    3.579 closest distance to " O   HOH Z 147 " =    1.691
peak=    3.578 closest distance to " O   HOH Z 263 " =    1.637
peak=    3.575 closest distance to " CB  THR A 157 " =    1.150
peak=    3.574 closest distance to " CD1 ILE A  33 " =    1.660
peak=    3.574 closest distance to " CG2 ILE A  20 " =    1.557
peak=    3.571 closest distance to " CD1 LEU A 228 " =    1.936
peak=    3.562 closest distance to " O   HOH Z 273 " =    2.811
peak=    3.557 closest distance to " O   HOH Z 353 " =    2.591
peak=    3.539 closest distance to " O   HOH Z 409 " =    2.969
peak=    3.538 closest distance to " O   HOH Z 145 " =    3.596
peak=    3.537 closest distance to " O  BHOH Z 338 " =    2.456
peak=    3.536 closest distance to " OD2 ASP A 286 " =    2.795
peak=    3.533 closest distance to " OE2 GLU A  53 " =    1.961
peak=    3.530 closest distance to " CA  THR A 264 " =    0.725
peak=    3.530 closest distance to " CG2 THR A 221 " =    1.196
peak=    3.529 closest distance to " ND1 HIS A  86 " =    1.724
peak=    3.528 closest distance to " CA  GLY A 267 " =    0.801
peak=    3.523 closest distance to " CA  LYS A 290 " =    1.252
peak=    3.515 closest distance to " O   HOH Z 290 " =    0.977
peak=    3.512 closest distance to " O   HOH Z 366 " =    2.847
peak=    3.511 closest distance to " O   HOH Z 435 " =    1.962
peak=    3.503 closest distance to " CG1 ILE A  33 " =    1.261
peak=    3.501 closest distance to " CB  ASN A 187 " =    1.150
peak=    3.499 closest distance to " CB  HIS A 108 " =    0.846
peak=    3.479 closest distance to " CB  LEU A 228 " =    1.284
peak=    3.475 closest distance to " O   HOH Z 133 " =    1.599
peak=    3.475 closest distance to " CG  MET A 185 " =    1.267
peak=    3.473 closest distance to " CG BARG A 102 " =    1.849
peak=    3.468 closest distance to " O   HOH Z  58 " =    1.517
peak=    3.459 closest distance to " O   HOH Z 132 " =    2.336
peak=    3.454 closest distance to " CD1AILE A 234 " =    0.875
peak=    3.453 closest distance to " CE1 TYR A 186 " =    1.339
peak=    3.449 closest distance to " O   HOH Z 193 " =    1.936
peak=    3.448 closest distance to " CA  PHE A 283 " =    1.311
peak=    3.447 closest distance to " O   HOH Z 380 " =    1.649
peak=    3.444 closest distance to " O   HOH Z   3 " =    1.875
peak=    3.435 closest distance to " O   HOH Z  61 " =    1.539
peak=    3.431 closest distance to " CD2 LEU A 255 " =    1.531
peak=    3.430 closest distance to " CB  LYS A 117 " =    1.218
peak=    3.429 closest distance to " O   HOH Z 345 " =    3.457
peak=    3.427 closest distance to " O   HOH Z 145 " =    1.862
peak=    3.422 closest distance to " CB  ASN A 224 " =    0.976
peak=    3.422 closest distance to " O   HOH Z  44 " =    1.601
peak=    3.421 closest distance to " CB  ALA A   9 " =    1.579
peak=    3.420 closest distance to " O   HOH Z 271 " =    2.069
peak=    3.416 closest distance to " O   HOH Z 371 " =    1.674
peak=    3.414 closest distance to " CA  ASN A  74 " =    1.241
peak=    3.414 closest distance to " O   HOH Z 425 " =    2.005
peak=    3.408 closest distance to " O   HOH Z  63 " =    1.346
peak=    3.407 closest distance to " CA  ALA A 291 " =    0.891
peak=    3.403 closest distance to " O   MET A 105 " =    1.824
peak=    3.402 closest distance to " CB  THR A  31 " =    1.689
peak=    3.401 closest distance to " O   HOH Z 303 " =    1.826
peak=    3.396 closest distance to " CA  LEU A 282 " =    1.096
peak=    3.395 closest distance to " O   HOH Z 148 " =    3.400
peak=    3.378 closest distance to " N   SER A 135 " =    1.351
peak=    3.368 closest distance to " CB  SER A 273 " =    0.856
peak=    3.362 closest distance to " O   HOH Z 417 " =    2.156
peak=    3.359 closest distance to " CA  SER A 146 " =    1.745
peak=    3.359 closest distance to " CA  TYR A  30 " =    1.047
peak=    3.354 closest distance to " CG1 VAL A 153 " =    0.954
peak=    3.353 closest distance to " O   HOH Z  21 " =    1.681
peak=    3.351 closest distance to " O   HOH Z 303 " =    3.050
peak=    3.350 closest distance to " CB  GLN A  88 " =    1.252
peak=    3.349 closest distance to " O   HOH Z 126 " =    1.483
peak=    3.348 closest distance to " CD  LYS A 166 " =    1.378
peak=    3.344 closest distance to " O   HOH Z 135 " =    2.014
peak=    3.343 closest distance to " NH2BARG A 145 " =    1.968
peak=    3.343 closest distance to " CG1 ILE A  49 " =    1.408
peak=    3.343 closest distance to " CB  ASN A 110 " =    1.170
peak=    3.341 closest distance to " CB  ALA A 291 " =    1.466
peak=    3.334 closest distance to " O   HOH Z 109 " =    2.495
peak=    3.332 closest distance to " O   ALA A 291 " =    1.584
peak=    3.331 closest distance to " O   HOH Z 175 " =    2.110
peak=    3.330 closest distance to " CG  GLN A 278 " =    1.314
peak=    3.326 closest distance to " CB  VAL A 250 " =    1.084
peak=    3.326 closest distance to " O   HOH Z 423 " =    1.446
peak=    3.323 closest distance to " OG  SER A  62 " =    2.953
peak=    3.314 closest distance to " O   HOH Z 128 " =    1.885
peak=    3.313 closest distance to " O   HOH Z 291 " =    1.559
peak=    3.311 closest distance to " O   HOH Z 189 " =    2.792
peak=    3.308 closest distance to " OD1BASN A 224 " =    2.340
peak=    3.307 closest distance to " NH2 ARG A 156 " =    1.109
peak=    3.306 closest distance to " O   HOH Z 392 " =    1.280
peak=    3.306 closest distance to " CA  ARG A 195 " =    1.177
peak=    3.305 closest distance to " O   HOH Z 172 " =    3.197
peak=    3.299 closest distance to " O   HOH Z 344 " =    2.970
peak=    3.298 closest distance to " CB  MET A  40 " =    0.852
peak=    3.290 closest distance to " O   HOH Z 285 " =    2.731
peak=    3.286 closest distance to " O   HOH Z 329 " =    3.888
peak=    3.285 closest distance to " O   GLN A 278 " =    1.285
peak=    3.282 closest distance to " C   ALA A 299 " =    0.974
peak=    3.281 closest distance to " O   HOH Z  85 " =    2.063
peak=    3.278 closest distance to " CA  SER A  87 " =    0.986
peak=    3.274 closest distance to " CA  TYR A 116 " =    1.403
peak=    3.273 closest distance to " CB  ILE A 120 " =    1.405
peak=    3.266 closest distance to " O   HOH Z 128 " =    2.164
peak=    3.266 closest distance to " CG1 ILE A 151 " =    1.116
peak=    3.261 closest distance to " OG  SER A  62 " =    2.883
peak=    3.260 closest distance to " O   HOH Z 368 " =    2.671
peak=    3.259 closest distance to " CD1 LEU A   5 " =    1.480
peak=    3.257 closest distance to " CB  ALA A  34 " =    1.009
peak=    3.255 closest distance to " CG  MET A 185 " =    1.041
peak=    3.255 closest distance to " O   HOH Z  97 " =    2.634
peak=    3.254 closest distance to " N   ALA A 256 " =    1.072
peak=    3.254 closest distance to " O   HOH Z  20 " =    1.467
peak=    3.253 closest distance to " N   ASN A 127 " =    1.293
peak=    3.252 closest distance to " CA  ALA A  21 " =    1.156
peak=    3.249 closest distance to " CE  LYS A  48 " =    1.118
peak=    3.248 closest distance to " CG BARG A 275 " =    1.434
peak=    3.248 closest distance to " O   HOH Z 130 " =    2.115
peak=    3.247 closest distance to " CA  VAL A 126 " =    0.911
peak=    3.245 closest distance to " N   VAL A 126 " =    1.286
peak=    3.241 closest distance to " O   HOH Z 423 " =    1.667
peak=    3.236 closest distance to " O   ALA A 158 " =    1.451
peak=    3.233 closest distance to " O   HOH Z 133 " =    2.508
peak=    3.231 closest distance to " CA  MET A 105 " =    0.983
peak=    3.225 closest distance to " CA  ILE A 234 " =    0.977
peak=    3.221 closest distance to " CA  ASP A 162 " =    1.072
peak=    3.219 closest distance to " O   HOH Z 325 " =    2.293
peak=    3.216 closest distance to " O   HOH Z 124 " =    2.109
peak=    3.216 closest distance to " O   HOH Z  53 " =    2.502
peak=    3.214 closest distance to " OG  SER A  22 " =    2.861
peak=    3.212 closest distance to " CB  SER A  62 " =    1.264
peak=    3.211 closest distance to " CB  VAL A 268 " =    0.853
peak=    3.206 closest distance to " CB  GLU A  46 " =    1.064
peak=    3.203 closest distance to " NH1 ARG A 138 " =    1.209
peak=    3.202 closest distance to " O   HOH Z 116 " =    1.662
peak=    3.199 closest distance to " O   HOH Z 124 " =    1.325
peak=    3.199 closest distance to " O   HOH Z 313 " =    1.574
peak=    3.198 closest distance to " CA  ARG A 102 " =    1.128
peak=    3.194 closest distance to " CA  ARG A  36 " =    1.029
peak=    3.194 closest distance to " O   HOH Z 417 " =    3.195
peak=    3.193 closest distance to " CB  TRP A 150 " =    1.360
peak=    3.192 closest distance to " O   SER A 164 " =    1.238
peak=    3.189 closest distance to " O   HOH Z 227 " =    2.185
peak=    3.188 closest distance to " O   HOH Z 173 " =    2.122
peak=    3.187 closest distance to " O   HOH Z 154 " =    2.154
peak=    3.181 closest distance to " CD1 LEU A 300 " =    1.186
peak=    3.179 closest distance to " O   HOH Z 261 " =    1.311
peak=    3.177 closest distance to " OE2 GLU A   2 " =    1.742
peak=    3.175 closest distance to " CD1 ILE A 106 " =    1.020
peak=    3.172 closest distance to " O   HOH Z 279 " =    2.251
peak=    3.165 closest distance to " CB  ILE A  20 " =    1.457
peak=    3.164 closest distance to " O   HOH Z 260 " =    1.463
peak=    3.163 closest distance to " CG  GLN A  89 " =    1.427
peak=    3.157 closest distance to " CG  GLN A  77 " =    2.479
peak=    3.156 closest distance to " O   HOH Z  88 " =    2.685
peak=    3.155 closest distance to " N   GLN A 278 " =    1.228
peak=    3.149 closest distance to " O   HOH Z 112 " =    1.591
peak=    3.147 closest distance to " CB  ALA A   1 " =    4.761
peak=    3.146 closest distance to " N   ALA A   1 " =    1.952
peak=    3.142 closest distance to " O   PRO A  90 " =    1.434
peak=    3.140 closest distance to " NZ  LYS A  48 " =    1.360
peak=    3.139 closest distance to " CB  TYR A  30 " =    1.585
peak=    3.137 closest distance to " O   HOH Z 213 " =    2.373
peak=    3.128 closest distance to " ND1 HIS A  81 " =    1.709
peak=    3.126 closest distance to " O   HOH Z 359 " =    3.929
peak=    3.121 closest distance to " ND2 ASN A 249 " =    0.834
peak=    3.114 closest distance to " O   HOH Z 341 " =    2.291
peak=    3.112 closest distance to " CD2 TYR A 186 " =    1.042
peak=    3.108 closest distance to " O   LYS A 290 " =    2.430
peak=    3.104 closest distance to " CB  GLN A 205 " =    1.104
peak=    3.103 closest distance to " O   HOH Z 359 " =    1.208
peak=    3.103 closest distance to " CB  ALA A 104 " =    0.722
peak=    3.098 closest distance to " O   HOH Z 357 " =    1.943
peak=    3.095 closest distance to " CB  ARG A 138 " =    0.950
peak=    3.091 closest distance to " O   HOH Z 438 " =    3.142
peak=    3.088 closest distance to " O   HOH Z 407 " =    2.229
peak=    3.073 closest distance to " CA  VAL A  41 " =    0.904
peak=    3.072 closest distance to " O   HOH Z 148 " =    2.146
peak=    3.068 closest distance to " CB  SER A 245 " =    3.183
peak=    3.068 closest distance to " O   TRP A 274 " =    1.858
peak=    3.065 closest distance to " O   HOH Z   2 " =    1.463
peak=    3.058 closest distance to " CD  ARG A 195 " =    0.857
peak=    3.045 closest distance to " CB  ASN A 215 " =    1.110
peak=    3.045 closest distance to " O   HOH Z 273 " =    1.612
peak=    3.043 closest distance to " CB  ALA A 114 " =    1.466

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.747 - 5.457
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 212
   mapped sites are within: 0.747 - 5.457

peak=   -4.576 closest distance to " CG2 VAL A 230 " =    0.774
peak=   -4.525 closest distance to " CB  PRO A 243 " =    2.652
peak=   -4.460 closest distance to " O   HOH Z 266 " =    5.097
peak=   -4.458 closest distance to " CD  ARG A 156 " =    2.022
peak=   -4.436 closest distance to " SG  CYS A 254 " =    3.271
peak=   -4.272 closest distance to " OG BSER A 134 " =    1.260
peak=   -4.177 closest distance to " CG  GLN A 223 " =    2.057
peak=   -4.045 closest distance to " O   HOH Z 231 " =    1.926
peak=   -4.035 closest distance to " O   ILE A 109 " =    2.553
peak=   -4.020 closest distance to " O   HOH Z 435 " =    2.848
peak=   -4.018 closest distance to " CG2 VAL A 296 " =    1.310
peak=   -3.993 closest distance to " C   HIS A 108 " =    1.210
peak=   -3.923 closest distance to " O   HOH Z 290 " =    1.180
peak=   -3.853 closest distance to " O   HOH Z 350 " =    1.690
peak=   -3.853 closest distance to " O   HOH Z 377 " =    2.087
peak=   -3.851 closest distance to " O   VAL A  67 " =    2.625
peak=   -3.818 closest distance to " O   HOH Z 389 " =    1.996
peak=   -3.817 closest distance to " CB  ALA A  43 " =    2.538
peak=   -3.811 closest distance to " CB  ALA A 248 " =    2.040
peak=   -3.810 closest distance to " O   HOH Z 351 " =    1.527
peak=   -3.809 closest distance to " CZ3 TRP A 179 " =    1.205
peak=   -3.791 closest distance to " CD  GLN A  58 " =    1.080
peak=   -3.783 closest distance to " CB  PRO A 163 " =    2.501
peak=   -3.757 closest distance to " O   HOH Z 166 " =    2.212
peak=   -3.733 closest distance to " O   PRO A 163 " =    2.015
peak=   -3.733 closest distance to " OD1 ASN A 187 " =    1.644
peak=   -3.719 closest distance to " O   VAL A 189 " =    2.592
peak=   -3.718 closest distance to " NH2 ARG A  79 " =    1.977
peak=   -3.701 closest distance to " CD  LYS A 289 " =    2.479
peak=   -3.696 closest distance to " CB  PHE A 192 " =    1.909
peak=   -3.696 closest distance to " CE2 TYR A  30 " =    2.715
peak=   -3.692 closest distance to " CD1 LEU A 101 " =    2.355
peak=   -3.686 closest distance to " CA  GLY A 241 " =    2.228
peak=   -3.682 closest distance to " OXT GLY A 302 " =    3.018
peak=   -3.675 closest distance to " O   HOH Z  11 " =    1.893
peak=   -3.664 closest distance to " O   HOH Z 185 " =    2.242
peak=   -3.664 closest distance to " O   VAL A  67 " =    2.760
peak=   -3.659 closest distance to " CG1 VAL A 112 " =    2.796
peak=   -3.656 closest distance to " ND2 ASN A  45 " =    1.504
peak=   -3.647 closest distance to " CD1 LEU A 228 " =    2.197
peak=   -3.635 closest distance to " CE2 PHE A 218 " =    2.527
peak=   -3.634 closest distance to " OG  SER A  87 " =    1.411
peak=   -3.616 closest distance to " N   ALA A  43 " =    2.469
peak=   -3.615 closest distance to " CE  MET A 105 " =    2.295
peak=   -3.614 closest distance to " O   HOH Z 359 " =    3.277
peak=   -3.609 closest distance to " O   HOH Z  60 " =    2.179
peak=   -3.594 closest distance to " C   LEU A 222 " =    0.819
peak=   -3.589 closest distance to " O   HOH Z 211 " =    1.499
peak=   -3.588 closest distance to " CG2 THR A 178 " =    2.256
peak=   -3.579 closest distance to " CB  ALA A 291 " =    2.386
peak=   -3.571 closest distance to " C   ALA A 158 " =    1.325
peak=   -3.568 closest distance to " CG  TRP A 266 " =    1.867
peak=   -3.565 closest distance to " O   HOH Z 394 " =    1.535
peak=   -3.564 closest distance to " O   ALA A 161 " =    1.644
peak=   -3.562 closest distance to " ND2 ASN A 249 " =    2.482
peak=   -3.560 closest distance to " O   GLY A  80 " =    2.486
peak=   -3.556 closest distance to " O   PRO A 198 " =    1.377
peak=   -3.556 closest distance to " CG1 VAL A 296 " =    1.426
peak=   -3.551 closest distance to " O   ARG A 145 " =    1.609
peak=   -3.546 closest distance to " O   PRO A 198 " =    1.229
peak=   -3.545 closest distance to " O   HOH Z 313 " =    1.678
peak=   -3.544 closest distance to " O   HOH Z  52 " =    1.394
peak=   -3.539 closest distance to " CA  GLY A 203 " =    2.349
peak=   -3.537 closest distance to " CB  ALA A 291 " =    2.158
peak=   -3.533 closest distance to " O   HOH Z 140 " =    1.524
peak=   -3.528 closest distance to " CB  ALA A 248 " =    2.384
peak=   -3.526 closest distance to " N   ALA A 248 " =    1.574
peak=   -3.522 closest distance to " O   HOH Z  38 " =    1.767
peak=   -3.520 closest distance to " ND2 ASN A 187 " =    1.649
peak=   -3.517 closest distance to " CD1 LEU A 101 " =    2.596
peak=   -3.507 closest distance to " CD1 PHE A  59 " =    1.996
peak=   -3.504 closest distance to " O   HOH Z 339 " =    1.847
peak=   -3.500 closest distance to " O   HOH Z 114 " =    2.954
peak=   -3.496 closest distance to " N   GLN A  58 " =    1.626
peak=   -3.482 closest distance to " CG  PHE A 283 " =    2.633
peak=   -3.480 closest distance to " CB  ALA A 244 " =    2.098
peak=   -3.477 closest distance to " CD2 LEU A   5 " =    1.114
peak=   -3.476 closest distance to " O   GLY A 203 " =    2.382
peak=   -3.476 closest distance to " NE2 GLN A  88 " =    1.977
peak=   -3.469 closest distance to " CZ  PHE A  59 " =    1.503
peak=   -3.469 closest distance to " O   SER A  22 " =    2.229
peak=   -3.469 closest distance to " C   MET A 188 " =    1.474
peak=   -3.464 closest distance to " C   ASN A 187 " =    1.781
peak=   -3.462 closest distance to " O   HOH Z 198 " =    2.187
peak=   -3.447 closest distance to " N   THR A 157 " =    1.438
peak=   -3.427 closest distance to " O   HOH Z  73 " =    2.188
peak=   -3.426 closest distance to " O   HOH Z 103 " =    1.743
peak=   -3.426 closest distance to " CG1 VAL A 112 " =    2.626
peak=   -3.419 closest distance to " O   HOH Z  90 " =    2.833
peak=   -3.417 closest distance to " CA  ASP A  27 " =    2.421
peak=   -3.414 closest distance to " OG  SER A  97 " =    2.214
peak=   -3.408 closest distance to " CG  ASP A 231 " =    0.747
peak=   -3.408 closest distance to " O   MET A  40 " =    2.765
peak=   -3.404 closest distance to " O   HOH Z 131 " =    4.103
peak=   -3.401 closest distance to " O   HOH Z 292 " =    1.814
peak=   -3.398 closest distance to " NZ  LYS A 119 " =    3.391
peak=   -3.396 closest distance to " O   HOH Z 166 " =    1.451
peak=   -3.395 closest distance to " CD2 TYR A 247 " =    2.479
peak=   -3.392 closest distance to " O   HOH Z 102 " =    1.577
peak=   -3.389 closest distance to " NH2BARG A 275 " =    1.601
peak=   -3.379 closest distance to " O   HOH Z 111 " =    2.261
peak=   -3.376 closest distance to " CG1 VAL A 197 " =    2.252
peak=   -3.372 closest distance to " OXT GLY A 302 " =    3.472
peak=   -3.371 closest distance to " CB  ASP A 171 " =    2.235
peak=   -3.371 closest distance to " O   HOH Z 407 " =    3.106
peak=   -3.366 closest distance to " CD2 LEU A 237 " =    2.773
peak=   -3.362 closest distance to " OG BSER A 134 " =    1.671
peak=   -3.359 closest distance to " O   HOH Z 243 " =    1.966
peak=   -3.358 closest distance to " O   HOH Z 191 " =    5.457
peak=   -3.354 closest distance to " CG1 VAL A 250 " =    2.722
peak=   -3.351 closest distance to " O   HOH Z  43 " =    1.787
peak=   -3.345 closest distance to " O   HOH Z 281 " =    2.713
peak=   -3.344 closest distance to " N   THR A 235 " =    1.299
peak=   -3.344 closest distance to " N   ALA A 226 " =    2.103
peak=   -3.340 closest distance to " NH2AARG A 275 " =    5.230
peak=   -3.339 closest distance to " OH  TYR A 214 " =    1.219
peak=   -3.337 closest distance to " CG  GLN A 278 " =    2.149
peak=   -3.330 closest distance to " CB  TYR A  15 " =    2.129
peak=   -3.328 closest distance to " CB  ASP A 132 " =    2.269
peak=   -3.321 closest distance to " O   HOH Z 372 " =    2.409
peak=   -3.317 closest distance to " CZ  PHE A 192 " =    2.675
peak=   -3.317 closest distance to " O   HOH Z 426 " =    1.685
peak=   -3.311 closest distance to " CG2 VAL A 296 " =    1.816
peak=   -3.307 closest distance to " O   HOH Z  56 " =    2.590
peak=   -3.307 closest distance to " CD  ARG A 139 " =    1.583
peak=   -3.307 closest distance to " CG  GLU A 152 " =    1.512
peak=   -3.306 closest distance to " O   HOH Z 389 " =    1.485
peak=   -3.303 closest distance to " CZ  TYR A 169 " =    1.521
peak=   -3.300 closest distance to " CD2 HIS A 207 " =    2.404
peak=   -3.299 closest distance to " O   SER A 135 " =    1.456
peak=   -3.295 closest distance to " O   HOH Z 359 " =    1.654
peak=   -3.291 closest distance to " O   SER A 271 " =    2.132
peak=   -3.290 closest distance to " CD  PRO A 213 " =    2.126
peak=   -3.290 closest distance to " CB  VAL A 230 " =    1.065
peak=   -3.289 closest distance to " OG  SER A  26 " =    1.201
peak=   -3.284 closest distance to " OG ASER A 134 " =    1.156
peak=   -3.276 closest distance to " OD2 ASP A 191 " =    1.419
peak=   -3.274 closest distance to " O   HOH Z 139 " =    2.980
peak=   -3.272 closest distance to " NE2 GLN A 278 " =    1.971
peak=   -3.269 closest distance to " CB  ASP A 132 " =    2.331
peak=   -3.267 closest distance to " CE1 TYR A 169 " =    2.569
peak=   -3.267 closest distance to " C   GLY A  17 " =    1.232
peak=   -3.261 closest distance to " N   SER A 276 " =    1.339
peak=   -3.260 closest distance to " CD2 LEU A 300 " =    2.632
peak=   -3.251 closest distance to " CD1 ILE A 199 " =    2.475
peak=   -3.251 closest distance to " O   HOH Z  51 " =    1.217
peak=   -3.250 closest distance to " N   ALA A 248 " =    1.872
peak=   -3.249 closest distance to " CG2 VAL A 202 " =    2.696
peak=   -3.248 closest distance to " O   HOH Z 346 " =    1.771
peak=   -3.248 closest distance to " O   HOH Z 357 " =    1.979
peak=   -3.246 closest distance to " C   LYS A  76 " =    1.647
peak=   -3.242 closest distance to " O   HOH Z 134 " =    3.607
peak=   -3.241 closest distance to " ND2 ASN A 252 " =    1.913
peak=   -3.241 closest distance to " O   HOH Z   9 " =    1.535
peak=   -3.234 closest distance to " N   PHE A  59 " =    2.093
peak=   -3.233 closest distance to " CA  GLY A  98 " =    1.924
peak=   -3.233 closest distance to " O   SER A 210 " =    1.884
peak=   -3.219 closest distance to " CE BMET A  47 " =    1.607
peak=   -3.218 closest distance to " O   HOH Z 148 " =    1.859
peak=   -3.217 closest distance to " O   HOH Z 198 " =    1.565
peak=   -3.216 closest distance to " CA  ASP A 298 " =    1.042
peak=   -3.214 closest distance to " ND2 ASN A  60 " =    1.791
peak=   -3.211 closest distance to " O   ALA A  51 " =    1.337
peak=   -3.209 closest distance to " CG  MET A 105 " =    0.945
peak=   -3.207 closest distance to " O   HOH Z 165 " =    2.125
peak=   -3.207 closest distance to " CA  ASN A 127 " =    1.151
peak=   -3.204 closest distance to " C   LEU A 143 " =    1.091
peak=   -3.196 closest distance to " O   HOH Z 295 " =    1.563
peak=   -3.183 closest distance to " CD2 LEU A 300 " =    3.367
peak=   -3.180 closest distance to " N   ALA A 248 " =    2.502
peak=   -3.179 closest distance to " O   GLY A  80 " =    2.606
peak=   -3.173 closest distance to " OG  SER A  62 " =    1.616
peak=   -3.172 closest distance to " O   GLY A  75 " =    2.057
peak=   -3.172 closest distance to " O   HOH Z 423 " =    1.179
peak=   -3.172 closest distance to " O   ASN A 301 " =    1.549
peak=   -3.172 closest distance to " O   HOH Z 417 " =    2.802
peak=   -3.172 closest distance to " O   HOH Z 281 " =    3.113
peak=   -3.171 closest distance to " CA  GLY A 241 " =    3.118
peak=   -3.171 closest distance to " CG  PRO A 163 " =    2.513
peak=   -3.169 closest distance to " O   HOH Z  13 " =    1.807
peak=   -3.168 closest distance to " O   PHE A 218 " =    1.552
peak=   -3.165 closest distance to " CG1 VAL A 230 " =    1.923
peak=   -3.163 closest distance to " O   HOH Z 149 " =    2.300
peak=   -3.159 closest distance to " NE2 GLN A 223 " =    1.736
peak=   -3.155 closest distance to " ND2 ASN A  69 " =    1.782
peak=   -3.154 closest distance to " CE3 TRP A 150 " =    2.164
peak=   -3.148 closest distance to " CD2 TYR A 293 " =    2.029
peak=   -3.147 closest distance to " O   HOH Z 412 " =    4.264
peak=   -3.146 closest distance to " O   HOH Z 234 " =    4.084
peak=   -3.135 closest distance to " C   VAL A 174 " =    1.827
peak=   -3.133 closest distance to " OE2 GLU A 152 " =    1.202
peak=   -3.131 closest distance to " CA  GLY A 133 " =    2.281
peak=   -3.130 closest distance to " O   HOH Z  89 " =    3.022
peak=   -3.130 closest distance to " O   TYR A  30 " =    2.830
peak=   -3.128 closest distance to " OG1 THR A 178 " =    1.271
peak=   -3.123 closest distance to " O   HOH Z 371 " =    2.306
peak=   -3.117 closest distance to " O   HOH Z 168 " =    1.792
peak=   -3.109 closest distance to " CB  ALA A 114 " =    2.463
peak=   -3.090 closest distance to " OD2 ASP A  50 " =    2.243
peak=   -3.083 closest distance to " O   HOH Z 189 " =    1.952
peak=   -3.079 closest distance to " O   HOH Z 111 " =    4.388
peak=   -3.078 closest distance to " O   HOH Z 410 " =    2.187
peak=   -3.076 closest distance to " O   HOH Z 231 " =    1.382
peak=   -3.069 closest distance to " OD1 ASP A 171 " =    1.648
peak=   -3.062 closest distance to " ND2BASN A 224 " =    1.630
peak=   -3.057 closest distance to " O   HOH Z 111 " =    1.212
peak=   -3.054 closest distance to " OD1 ASN A 301 " =    2.017
peak=   -3.051 closest distance to " OD1 ASP A 200 " =    1.490
peak=   -3.050 closest distance to " O   HOH Z 210 " =    1.155
peak=   -3.046 closest distance to " O   HOH Z 336 " =    5.424
peak=   -3.038 closest distance to " C   ARG A 269 " =    1.455

================= 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    :  0.4327 0.4181   6.225660e+00   6.200512e+00
   1_bss:  0.4243 0.4040   6.221186e+00   6.187291e+00
   1_xyz:  0.3170 0.3369   6.014568e+00   6.054573e+00
   1_adp:  0.2526 0.2911   5.828000e+00   5.934355e+00
   1_occ:  0.2521 0.2912   5.826692e+00   5.935618e+00
   2_bss:  0.2465 0.2842   5.823087e+00   5.929092e+00
   2_xyz:  0.1647 0.2077   5.463123e+00   5.642371e+00
   2_adp:  0.1471 0.1922   5.367519e+00   5.567269e+00
   2_occ:  0.1470 0.1921   5.367028e+00   5.566778e+00
   3_bss:  0.1468 0.1911   5.365789e+00   5.564665e+00
   3_xyz:  0.1266 0.1694   5.237691e+00   5.453219e+00
   3_adp:  0.1218 0.1659   5.208721e+00   5.432592e+00
   3_occ:  0.1217 0.1659   5.208141e+00   5.431795e+00
   4_bss:  0.1217 0.1658   5.207902e+00   5.431546e+00
   4_xyz:  0.1158 0.1609   5.174194e+00   5.410528e+00
   4_adp:  0.1160 0.1585   5.166872e+00   5.395045e+00
   4_occ:  0.1159 0.1584   5.166153e+00   5.394066e+00
   5_bss:  0.1159 0.1587   5.166450e+00   5.393821e+00
   5_xyz:  0.1100 0.1554   5.130528e+00   5.374995e+00
   5_adp:  0.1087 0.1568   5.131247e+00   5.384464e+00
   5_occ:  0.1087 0.1568   5.131018e+00   5.384151e+00
   5_bss:  0.1087 0.1568   5.130981e+00   5.384099e+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:  0.352  16.551   7.508   9.358   8.035   0.000   0.000   0.000
   1_xyz:  0.352  16.551   7.508   9.358   8.035   0.000   0.000   0.000
   1_adp:  0.352  16.551   7.508   9.358   8.035   0.000   0.000   0.000
   1_occ:  0.352  16.551   7.508   9.358   8.035   0.000   0.000   0.000
   2_bss:  0.343  39.261   3.989   4.865   4.849   0.000   0.000   0.000
   2_xyz:  0.343  39.261   3.989   4.865   4.849   0.000   0.000   0.000
   2_adp:  0.343  39.261   3.989   4.865   4.849   0.000   0.000   0.000
   2_occ:  0.343  39.261   3.989   4.865   4.849   0.000   0.000   0.000
   3_bss:  0.330  45.652   3.292   3.437   4.428   0.000   0.000   0.000
   3_xyz:  0.330  45.652   3.292   3.437   4.428   0.000   0.000   0.000
   3_adp:  0.330  45.652   3.292   3.437   4.428   0.000   0.000   0.000
   3_occ:  0.330  45.652   3.292   3.437   4.428   0.000   0.000   0.000
   4_bss:  0.330  45.652   3.152   3.173   4.353   0.000   0.000   0.000
   4_xyz:  0.330  45.652   3.152   3.173   4.353   0.000   0.000   0.000
   4_adp:  0.330  45.652   3.152   3.173   4.353   0.000   0.000   0.000
   4_occ:  0.330  45.652   3.152   3.173   4.353   0.000   0.000   0.000
   5_bss:  0.325  45.652   3.152   3.173   4.353   0.000   0.000   0.000
   5_xyz:  0.325  45.652   3.152   3.173   4.353   0.000   0.000   0.000
   5_adp:  0.325  45.652   3.152   3.173   4.353   0.000   0.000   0.000
   5_occ:  0.325  45.652   3.152   3.173   4.353   0.000   0.000   0.000
   5_bss:  0.325  49.268  -0.384  -0.447   0.830   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.046 0.5585  0.6273    50969.618
   1_bss:  47.073 0.5557  0.7970    48490.089
   1_xyz:  36.296 0.6856  0.9559    31254.064
   1_adp:  28.790 0.7722  1.0575    21981.747
   1_occ:  28.839 0.7715  1.0555    21974.377
   2_bss:  28.446 0.7757  0.9267    21468.198
   2_xyz:  19.852 0.8630  0.9935    10788.808
   2_adp:  17.881 0.8819  1.0031     9240.065
   2_occ:  17.866 0.8820  1.0031     9221.859
   3_bss:  17.775 0.8828  0.9729     9162.250
   3_xyz:  15.395 0.9034  0.9848     7267.712
   3_adp:  14.925 0.9076  0.9848     7001.487
   3_occ:  14.907 0.9077  0.9848     6989.555
   4_bss:  14.901 0.9078  0.9792     6985.330
   4_xyz:  14.459 0.9114  0.9799     6644.806
   4_adp:  14.085 0.9146  0.9810     6454.872
   4_occ:  14.065 0.9148  0.9810     6441.258
   5_bss:  14.082 0.9146  0.9807     6455.929
   5_xyz:  13.740 0.9171  0.9825     6200.393
   5_adp:  13.924 0.9157  0.9780     6300.877
   5_occ:  13.921 0.9158  0.9780     6297.170
   5_bss:  13.920 0.9158  0.9800     6297.214
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3721e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3721e+01
   1_xyz:   1.493  0.011  0.099 18.056  0.005  4.120   1.1540e-01
   1_adp:   1.493  0.011  0.099 18.056  0.005  4.120   1.1540e-01
   1_occ:   1.493  0.011  0.099 18.056  0.005  4.120   1.1540e-01
   2_bss:   1.493  0.011  0.099 18.056  0.005  4.120   1.1540e-01
   2_xyz:   1.010  0.007  0.076 16.162  0.004  4.120   6.4631e-02
   2_adp:   1.010  0.007  0.076 16.162  0.004  4.120   6.4631e-02
   2_occ:   1.010  0.007  0.076 16.162  0.004  4.120   6.4631e-02
   3_bss:   1.010  0.007  0.076 16.162  0.004  4.120   6.4631e-02
   3_xyz:   0.924  0.006  0.074 15.730  0.003  4.123   5.4903e-02
   3_adp:   0.924  0.006  0.074 15.730  0.003  4.123   5.4903e-02
   3_occ:   0.924  0.006  0.074 15.730  0.003  4.123   5.4903e-02
   4_bss:   0.924  0.006  0.074 15.730  0.003  4.123   5.4903e-02
   4_xyz:   0.946  0.006  0.076 15.700  0.003  4.126   5.6752e-02
   4_adp:   0.946  0.006  0.076 15.700  0.003  4.126   5.6752e-02
   4_occ:   0.946  0.006  0.076 15.700  0.003  4.126   5.6752e-02
   5_bss:   0.946  0.006  0.076 15.700  0.003  4.126   5.6752e-02
   5_xyz:   1.070  0.009  0.087 15.690  0.004  4.111   7.0092e-02
   5_adp:   1.070  0.009  0.087 15.690  0.004  4.111   7.0092e-02
   5_occ:   1.070  0.009  0.087 15.690  0.004  4.111   7.0092e-02
   5_bss:   1.070  0.009  0.087 15.690  0.004  4.111   7.0092e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9652e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9652e+00
   1_xyz:  11.629  0.144  0.422 89.384  0.030  2.255   8.4848e-02
   1_adp:  11.629  0.144  0.422 89.384  0.030  2.255   8.4848e-02
   1_occ:  11.629  0.144  0.422 89.384  0.030  2.255   8.4848e-02
   2_bss:  11.629  0.144  0.422 89.384  0.030  2.255   8.4848e-02
   2_xyz:   6.680  0.056  0.354 81.954  0.043  2.300   5.3323e-02
   2_adp:   6.680  0.056  0.354 81.954  0.043  2.300   5.3323e-02
   2_occ:   6.680  0.056  0.354 81.954  0.043  2.300   5.3323e-02
   3_bss:   6.680  0.056  0.354 81.954  0.043  2.300   5.3323e-02
   3_xyz:   7.189  0.048  0.397 83.532  0.028  2.334   3.8627e-02
   3_adp:   7.189  0.048  0.397 83.532  0.028  2.334   3.8627e-02
   3_occ:   7.189  0.048  0.397 83.532  0.028  2.334   3.8627e-02
   4_bss:   7.189  0.048  0.397 83.532  0.028  2.334   3.8627e-02
   4_xyz:   7.895  0.051  0.436 83.112  0.036  2.360   4.0125e-02
   4_adp:   7.895  0.051  0.436 83.112  0.036  2.360   4.0125e-02
   4_occ:   7.895  0.051  0.436 83.112  0.036  2.360   4.0125e-02
   5_bss:   7.895  0.051  0.436 83.112  0.036  2.360   4.0125e-02
   5_xyz:   6.846  0.043  0.601 84.117  0.039  2.275   5.4280e-02
   5_adp:   6.846  0.043  0.601 84.117  0.039  2.275   5.4280e-02
   5_occ:   6.846  0.043  0.601 84.117  0.039  2.275   5.4280e-02
   5_bss:   6.846  0.043  0.601 84.117  0.039  2.275   5.4280e-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:  66.59   0.00  10.93  65.30   0.00   7.83  66.59   0.00  27.78
   1_occ:  66.59   0.00  10.93  65.30   0.00   7.83  66.59   0.00  27.78
   2_bss:  66.59   0.00  10.93  65.30   0.00   7.83  66.59   0.00  27.78
   2_xyz:  66.59   0.00  10.93  65.30   0.00   7.83  66.59   0.00  27.78
   2_adp:  69.11   0.00  11.22  68.45   0.00   7.36  69.11   0.66  32.24
   2_occ:  69.11   0.00  11.22  68.45   0.00   7.36  69.11   0.66  32.24
   3_bss:  69.11   0.00  11.22  68.45   0.00   7.36  69.11   0.66  32.24
   3_xyz:  69.11   0.00  11.22  68.45   0.00   7.36  69.11   0.66  32.24
   3_adp:  80.86   0.00  11.97  80.86   0.00   7.58  76.94   0.75  35.90
   3_occ:  80.86   0.00  11.97  80.86   0.00   7.58  76.94   0.75  35.90
   4_bss:  80.86   0.00  11.97  80.86   0.00   7.58  76.94   0.75  35.90
   4_xyz:  80.86   0.00  11.97  80.86   0.00   7.58  76.94   0.75  35.90
   4_adp:  80.79   0.00  11.68  80.79   0.00   7.43  75.76   1.20  34.80
   4_occ:  80.79   0.00  11.68  80.79   0.00   7.43  75.76   1.20  34.80
   5_bss:  80.79   0.00  11.68  80.79   0.00   7.43  75.76   1.20  34.80
   5_xyz:  80.79   0.00  11.68  80.79   0.00   7.43  75.76   1.20  34.80
   5_adp:  83.45   0.00  11.72  83.45   0.00   7.42  76.81   0.86  35.16
   5_occ:  83.45   0.00  11.72  83.45   0.00   7.42  76.81   0.86  35.16
   5_bss:  87.07   3.62  15.34  87.07   3.62  11.04  80.43   4.47  38.78
------------------------------------------------------------------------
 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:    1.174    0.017    0.399
   1_adp:    1.174    0.017    0.399
   1_occ:    1.174    0.017    0.399
   2_bss:    1.174    0.017    0.399
   2_xyz:    1.310    0.025    0.509
   2_adp:    1.310    0.025    0.509
   2_occ:    1.310    0.025    0.509
   3_bss:    1.310    0.025    0.509
   3_xyz:    1.497    0.037    0.532
   3_adp:    1.497    0.037    0.532
   3_occ:    1.497    0.037    0.532
   4_bss:    1.497    0.037    0.532
   4_xyz:    1.620    0.031    0.552
   4_adp:    1.620    0.031    0.552
   4_occ:    1.620    0.031    0.552
   5_bss:    1.620    0.031    0.552
   5_xyz:    1.644    0.046    0.560
   5_adp:    1.644    0.046    0.560
   5_occ:    1.644    0.046    0.560
   5_bss:    1.644    0.046    0.560
------------------------------------------------------------------------

CPU time actual refinement: 329.39


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_764/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_764/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_764/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_764/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_764/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.24 
  Macro-tasks:
    bulk solvent and scale       = 41.18  
    individual site refinement   = 132.78 
    weights calculation          = 32.52  
    collect and process          = 6.66   
    model show statistics        = 0.16   
    TOTAL for macro-tasks        = 213.30 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 100.43 
    alpha_beta                      = 8.34   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 110.73 
    fmodel                         = 7.39   
    r_factors                      = 0.22   
    phase_errors                   = 10.61  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 240.89 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.653 micro seconds
Total CPU time: 5.72 minutes
from_scatterers_fft:    645 calls, 100.11 s
gradients_fft:          590 calls,  97.24 s

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

# Date 2008-01-16 Time 02:22:07 PST -0800 (1200478927.24 s)
Start R-work = 0.4327, R-free = 0.4181 (no bulk solvent and anisotropic scale)
Final R-work = 0.1263, R-free = 0.1732 (no bulk solvent and anisotropic scale)

Start R-work = 0.4243, R-free = 0.4040
Final R-work = 0.1087, R-free = 0.1568