# Date 2008-01-16 Time 02:37:59 PST -0800 (1200479879.74 s)
#phil __OFF__

Command line arguments: "../910.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31777
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 910

-------------------------------------------------------------------------------
  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: (70.9525, 46.93, 87.6859, 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: (70.9525, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.00232
Completeness in resolution range: 0.964643
Completeness with d_max=infinity: 0.961659

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1641
                             d_min =   2.0023

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: (70.9525, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.00232
Completeness in resolution range: 0.964643
Completeness with d_max=infinity: 0.961659

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1646 -  4.2845 [2132/2156]  1918   214  10.0%
  bin  2:  4.2845 -  3.4135 [2037/2057]  1835   202   9.9%
  bin  3:  3.4135 -  2.9857 [2032/2051]  1825   207  10.2%
  bin  4:  2.9857 -  2.7144 [1996/2026]  1799   197   9.9%
  bin  5:  2.7144 -  2.5208 [2010/2029]  1809   201  10.0%
  bin  6:  2.5208 -  2.3728 [1953/1978]  1758   195  10.0%
  bin  7:  2.3728 -  2.2544 [1977/2005]  1777   200  10.1%
  bin  8:  2.2544 -  2.1565 [1981/2017]  1786   195   9.8%
  bin  9:  2.1565 -  2.0737 [1926/1968]  1734   192  10.0%
  bin 10:  2.0737 -  2.0023 [1545/2020]  1389   156  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_910/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2167
        3.04 -     3.66: 4598
        3.66 -     4.28: 8895
        4.28 -     4.90: 12263
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.097 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.152 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.234 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27929 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_910/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_910/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 70.9525 46.93 87.68585 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: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4429   r_free= 0.4299   ksol= 0.00   Bsol= 0.00   scale= 0.808    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.238927                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.7787 0.99   1387  153 0.3693 0.3343      6.5561      6.4287|
|  2:  4.7787 -  3.8128 0.99   1329  152 0.3352 0.3530      6.6636      6.7459|
|  3:  3.8128 -  3.3367 0.99   1305  140 0.3916 0.3572      6.5892      6.5619|
|  4:  3.3367 -  3.0343 0.99   1293  149 0.4263 0.3837      6.4791       6.365|
|  5:  3.0343 -  2.8183 0.99   1290  144 0.4619 0.4502      6.3275      6.3363|
|  6:  2.8183 -  2.6531 0.99   1303  136 0.4655 0.5221      6.2422      6.1863|
|  7:  2.6531 -  2.5208 0.99   1279  147 0.4971 0.5058      6.2126      6.2264|
|  8:  2.5208 -  2.4115 0.98   1266  141 0.4953 0.4394      6.1635       6.101|
|  9:  2.4115 -  2.3190 0.98   1260  141 0.4793 0.5377      6.0836      6.1523|
| 10:  2.3190 -  2.2393 1.00   1283  142 0.5055 0.4538      6.1109      6.0419|
| 11:  2.2393 -  2.1695 0.97   1251  138 0.4926 0.4756      6.0068      6.0438|
| 12:  2.1695 -  2.1076 0.98   1248  138 0.5041 0.4548      5.9762      5.9626|
| 13:  2.1076 -  2.0523 0.99   1289  140 0.5100 0.4953       5.885      5.8286|
| 14:  2.0523 -  2.0023 0.67    847   98 0.5035 0.4536       5.853      5.7105|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.7787  1387   153  0.75  29.85   0.80     0.77      55161.45|
|  2:  4.7787 -  3.8128  1329   152  0.78  28.43   0.90     0.82      74801.11|
|  3:  3.8128 -  3.3367  1305   140  0.70  35.35   0.85     0.78      79128.36|
|  4:  3.3367 -  3.0343  1293   149  0.63  41.09   0.82     0.69      71884.53|
|  5:  3.0343 -  2.8183  1290   144  0.54  48.54   0.77     0.61      63576.34|
|  6:  2.8183 -  2.6531  1303   136  0.50  52.02   0.74     0.55      59384.15|
|  7:  2.6531 -  2.5208  1279   147  0.46  55.60   0.73     0.52      57005.74|
|  8:  2.5208 -  2.4115  1266   141  0.45  56.25   0.74     0.51      51957.90|
|  9:  2.4115 -  2.3190  1260   141  0.46  54.98   0.74     0.52      46658.37|
| 10:  2.3190 -  2.2393  1283   142  0.47  54.65   0.76     0.53      40637.00|
| 11:  2.2393 -  2.1695  1251   138  0.47  54.76   0.76     0.55      37708.75|
| 12:  2.1695 -  2.1076  1248   138  0.47  55.00   0.76     0.55      34714.01|
| 13:  2.1076 -  2.0523  1289   140  0.46  55.80   0.72     0.54      30107.80|
| 14:  2.0523 -  2.0023   847    98  0.51  51.72   0.73     0.52      23294.42|
|alpha:            min =        0.51 max =            0.82 mean =         0.61|
|beta:             min =    23294.42 max =        79128.36 mean =     52760.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           90.00 mean =        47.84|
|phase err.(test): min =        0.00 max =           89.92 mean =        47.90|
|-----------------------------------------------------------------------------|

============================== 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 = 8.433433              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.584   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.707679              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.054   (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:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      680 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1476 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2577 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3874 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5023 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6480 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7638 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.303 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.637 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    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: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4505   r_free= 0.4341   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| 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: 6.243504                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4346   r_free= 0.4168   ksol= 0.33   Bsol= 20.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.75,7.42,10.65,0.00,0.00,0.00); trace/3= 8.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.232361                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.870120              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.008   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.681207              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.872   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4346      final r-factor (work) = 0.3270          |
| start r-factor (free) = 0.4168      final r-factor (free) = 0.3468          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 78.8916 = 7.87 * 0.50 * 6.2486 + 1.00 * 54.3028                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.0729 = 7.87 * 0.50 * 6.0856 + 1.00 * 0.1255                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3270      final r-factor (work) = 0.2672          |
| start r-factor (free) = 0.3468      final r-factor (free) = 0.3043          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1604 = 0.68 * 1.00 * 6.0856 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0471 = 0.68 * 1.00 * 5.9225 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.88   11.05    None  None   None       |
|    all(noH): 2823   0      0.00    72.88   11.05    None  None   None       |
|    Sol.    : 438    0      0.00    72.88   28.02    None  None   None       |
|    Mac.    : 2385   0      0.00    60.50   7.93     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.289: 1421   |   5:    36.443 -  43.731:   67        |
|      1:     7.289 -  14.577:  730   |   6:    43.731 -  51.019:   46        |
|      2:    14.577 -  21.866:  245   |   7:    51.019 -  58.308:   15        |
|      3:    21.866 -  29.154:  176   |   8:    58.308 -  65.596:    7        |
|      4:    29.154 -  36.443:  113   |   9:    65.596 -  72.885:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2672 r_free = 0.3043             target_work(ml) = 5.870         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2666 r_free = 0.3049             target_work(ml) = 5.868         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2666   r_free= 0.3049   ksol= 0.33   Bsol= 20.00   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.75,7.42,10.65,0.00,0.00,0.00); trace/3= 8.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.868328                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2619   r_free= 0.2993   ksol= 0.33   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.40,3.99,6.94,0.00,0.00,0.00); trace/3= 5.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.866282                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.429061              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.693   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.332065              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.015  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2619      final r-factor (work) = 0.1817          |
| start r-factor (free) = 0.2993      final r-factor (free) = 0.2259          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2839 = 3.43 * 0.50 * 5.9250 + 1.00 * 0.1254                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8468 = 3.43 * 0.50 * 5.7038 + 1.00 * 0.0674                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1817      final r-factor (work) = 0.1639          |
| start r-factor (free) = 0.2259      final r-factor (free) = 0.2094          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9067 = 0.33 * 1.00 * 5.7038 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8524 = 0.33 * 1.00 * 5.4929 + 1.00 * 0.0284                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.47   11.36    None  None   None       |
|    all(noH): 2823   0      0.00    71.47   11.36    None  None   None       |
|    Sol.    : 438    0      0.00    71.47   32.21    None  None   None       |
|    Mac.    : 2385   0      0.00    61.15   7.54     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.147: 1526   |   5:    35.735 -  42.882:  109        |
|      1:     7.147 -  14.294:  645   |   6:    42.882 -  50.029:   81        |
|      2:    14.294 -  21.441:  189   |   7:    50.029 -  57.176:   28        |
|      3:    21.441 -  28.588:  118   |   8:    57.176 -  64.323:   10        |
|      4:    28.588 -  35.735:  114   |   9:    64.323 -  71.470:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1639 r_free = 0.2094             target_work(ml) = 5.459         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1638 r_free = 0.2095             target_work(ml) = 5.459         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1638   r_free= 0.2095   ksol= 0.33   Bsol= 50.00   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.40,3.99,6.94,0.00,0.00,0.00); trace/3= 5.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.459064                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1630   r_free= 0.2093   ksol= 0.33   Bsol= 58.64   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,3.24,4.99,0.00,0.00,0.00); trace/3= 3.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.459882                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.152147              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.216  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.862097              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.103   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1630      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.2093      final r-factor (free) = 0.1713          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4876 = 4.15 * 0.50 * 5.5009 + 1.00 * 0.0674                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1893 = 4.15 * 0.50 * 5.3516 + 1.00 * 0.0790                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1264      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1713      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6273 = 0.86 * 1.00 * 5.3516 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5120 = 0.86 * 1.00 * 5.2183 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.88   11.89    None  None   None       |
|    all(noH): 2823   0      0.00    73.88   11.89    None  None   None       |
|    Sol.    : 438    0      0.00    73.88   35.22    None  None   None       |
|    Mac.    : 2385   0      0.00    70.71   7.61     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.388: 1563   |   5:    36.942 -  44.330:   72        |
|      1:     7.388 -  14.777:  631   |   6:    44.330 -  51.718:   99        |
|      2:    14.777 -  22.165:  182   |   7:    51.718 -  59.106:   47        |
|      3:    22.165 -  29.553:   93   |   8:    59.106 -  66.495:   20        |
|      4:    29.553 -  36.942:  104   |   9:    66.495 -  73.883:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1198 r_free = 0.1666             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1197 r_free = 0.1666             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1666   ksol= 0.33   Bsol= 58.64   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,3.24,4.99,0.00,0.00,0.00); trace/3= 3.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.204583                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1665   ksol= 0.33   Bsol= 57.26   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,3.05,4.60,0.00,0.00,0.00); trace/3= 3.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.204091                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.451867              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.992  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.204687              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.788  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1665      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4759 = 2.45 * 0.50 * 5.2180 + 1.00 * 0.0790                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4391 = 2.45 * 0.50 * 5.1941 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0764 = 0.20 * 1.00 * 5.1941 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0731 = 0.20 * 1.00 * 5.1907 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.13   11.51    None  None   None       |
|    all(noH): 2823   0      0.00    72.13   11.51    None  None   None       |
|    Sol.    : 438    0      0.91    72.13   33.64    None  None   None       |
|    Mac.    : 2385   0      0.00    70.82   7.44     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.213: 1601   |   5:    36.063 -  43.275:   73        |
|      1:     7.213 -  14.425:  595   |   6:    43.275 -  50.488:   90        |
|      2:    14.425 -  21.638:  184   |   7:    50.488 -  57.701:   47        |
|      3:    21.638 -  28.850:  100   |   8:    57.701 -  64.913:   16        |
|      4:    28.850 -  36.063:  104   |   9:    64.913 -  72.126:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1171 r_free = 0.1620             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1620             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1620   ksol= 0.33   Bsol= 57.26   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,3.05,4.60,0.00,0.00,0.00); trace/3= 3.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.183538                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1620   ksol= 0.33   Bsol= 57.26   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,3.05,4.60,0.00,0.00,0.00); trace/3= 3.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.183538                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.212069              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.365  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.466826              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.422  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1170      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4076 = 3.21 * 0.50 * 5.1904 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3820 = 3.21 * 0.50 * 5.1667 + 1.00 * 0.0841                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1605      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4224 = 0.47 * 1.00 * 5.1667 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4188 = 0.47 * 1.00 * 5.1563 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.69   11.51    None  None   None       |
|    all(noH): 2823   0      0.00    72.69   11.51    None  None   None       |
|    Sol.    : 438    0      0.84    72.08   33.77    None  None   None       |
|    Mac.    : 2385   0      0.00    72.69   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 -   7.270: 1602   |   5:    36.347 -  43.617:   79        |
|      1:     7.270 -  14.539:  591   |   6:    43.617 -  50.886:   91        |
|      2:    14.539 -  21.809:  179   |   7:    50.886 -  58.156:   39        |
|      3:    21.809 -  29.078:  105   |   8:    58.156 -  65.425:   18        |
|      4:    29.078 -  36.347:  107   |   9:    65.425 -  72.695:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1608             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1608             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1608   ksol= 0.33   Bsol= 57.26   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,3.05,4.60,0.00,0.00,0.00); trace/3= 3.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158757                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.7787 0.99   1387  153 0.1018 0.1388      5.4158      5.5743|
|  2:  4.7787 -  3.8128 0.99   1329  152 0.0860 0.1137      5.4542      5.6523|
|  3:  3.8128 -  3.3367 0.99   1305  140 0.1051 0.1490      5.4804      5.8365|
|  4:  3.3367 -  3.0343 0.99   1293  149 0.1174 0.1690      5.4424       5.632|
|  5:  3.0343 -  2.8183 0.99   1290  144 0.1335 0.1688      5.3387      5.5586|
|  6:  2.8183 -  2.6531 0.99   1303  136 0.1186 0.2035      5.2153      5.5096|
|  7:  2.6531 -  2.5208 0.99   1279  147 0.1300 0.1628      5.1898      5.3686|
|  8:  2.5208 -  2.4115 0.98   1266  141 0.1183 0.1724      5.1046      5.3615|
|  9:  2.4115 -  2.3190 0.98   1260  141 0.1177 0.1786      5.0657      5.3241|
| 10:  2.3190 -  2.2393 1.00   1283  142 0.1147 0.1682      4.9906      5.2202|
| 11:  2.2393 -  2.1695 0.97   1251  138 0.1145 0.1808      4.9607      5.2751|
| 12:  2.1695 -  2.1076 0.98   1248  138 0.1108 0.1806       4.886      5.2507|
| 13:  2.1076 -  2.0523 0.99   1289  140 0.1110 0.1732      4.7865      5.0438|
| 14:  2.0523 -  2.0023 0.67    847   98 0.1023 0.1667      4.6729       4.908|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.7787  1387   153  0.94   9.62   0.97     0.95       7899.62|
|  2:  4.7787 -  3.8128  1329   152  0.95   8.23   1.00     0.99       9552.67|
|  3:  3.8128 -  3.3367  1305   140  0.93  11.39   1.02     1.01      10627.41|
|  4:  3.3367 -  3.0343  1293   149  0.92  13.38   1.00     0.98      10221.49|
|  5:  3.0343 -  2.8183  1290   144  0.90  16.09   0.99     0.97       8617.78|
|  6:  2.8183 -  2.6531  1303   136  0.90  16.30   0.98     0.95       7363.87|
|  7:  2.6531 -  2.5208  1279   147  0.90  16.30   0.98     0.95       6541.72|
|  8:  2.5208 -  2.4115  1266   141  0.90  15.87   0.99     0.96       5785.44|
|  9:  2.4115 -  2.3190  1260   141  0.91  15.89   1.00     0.95       5406.14|
| 10:  2.3190 -  2.2393  1283   142  0.89  16.46   1.00     0.96       4765.64|
| 11:  2.2393 -  2.1695  1251   138  0.90  16.75   0.99     0.95       4636.30|
| 12:  2.1695 -  2.1076  1248   138  0.91  15.71   1.01     0.99       4109.99|
| 13:  2.1076 -  2.0523  1289   140  0.90  16.38   0.99     0.96       3391.92|
| 14:  2.0523 -  2.0023   847    98  0.92  14.13   0.97     0.94       2620.35|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2620.35 max =        10627.41 mean =      6669.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.42|
|phase err.(test): min =        0.00 max =           89.44 mean =        13.88|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1608   ksol= 0.32   Bsol= 56.52   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,-0.49,1.04,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158721                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1608   ksol= 0.32   Bsol= 56.52   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,-0.49,1.04,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158721                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.7787 0.99   1387  153 0.1014 0.1387      5.4119      5.5714|
|  2:  4.7787 -  3.8128 0.99   1329  152 0.0858 0.1134      5.4518      5.6495|
|  3:  3.8128 -  3.3367 0.99   1305  140 0.1049 0.1490      5.4794      5.8366|
|  4:  3.3367 -  3.0343 0.99   1293  149 0.1176 0.1691      5.4432      5.6328|
|  5:  3.0343 -  2.8183 0.99   1290  144 0.1336 0.1688      5.3401      5.5599|
|  6:  2.8183 -  2.6531 0.99   1303  136 0.1188 0.2038      5.2167      5.5112|
|  7:  2.6531 -  2.5208 0.99   1279  147 0.1301 0.1629      5.1909      5.3697|
|  8:  2.5208 -  2.4115 0.98   1266  141 0.1184 0.1725      5.1053      5.3619|
|  9:  2.4115 -  2.3190 0.98   1260  141 0.1177 0.1786       5.066      5.3243|
| 10:  2.3190 -  2.2393 1.00   1283  142 0.1148 0.1684       4.991      5.2206|
| 11:  2.2393 -  2.1695 0.97   1251  138 0.1146 0.1808       4.961      5.2752|
| 12:  2.1695 -  2.1076 0.98   1248  138 0.1108 0.1807      4.8861      5.2507|
| 13:  2.1076 -  2.0523 0.99   1289  140 0.1110 0.1733      4.7867      5.0442|
| 14:  2.0523 -  2.0023 0.67    847   98 0.1023 0.1669      4.6734      4.9085|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.7787  1387   153  0.94   9.59   0.97     0.95       7839.63|
|  2:  4.7787 -  3.8128  1329   152  0.95   8.19   1.00     0.99       9507.48|
|  3:  3.8128 -  3.3367  1305   140  0.93  11.38   1.02     1.01      10605.47|
|  4:  3.3367 -  3.0343  1293   149  0.92  13.40   1.00     0.98      10235.09|
|  5:  3.0343 -  2.8183  1290   144  0.90  16.11   0.99     0.97       8640.87|
|  6:  2.8183 -  2.6531  1303   136  0.90  16.33   0.98     0.95       7385.66|
|  7:  2.6531 -  2.5208  1279   147  0.90  16.32   0.98     0.95       6558.56|
|  8:  2.5208 -  2.4115  1266   141  0.90  15.88   0.99     0.96       5793.71|
|  9:  2.4115 -  2.3190  1260   141  0.91  15.90   1.00     0.95       5410.87|
| 10:  2.3190 -  2.2393  1283   142  0.89  16.46   1.00     0.96       4768.55|
| 11:  2.2393 -  2.1695  1251   138  0.90  16.76   0.99     0.95       4639.01|
| 12:  2.1695 -  2.1076  1248   138  0.91  15.72   1.01     0.99       4112.44|
| 13:  2.1076 -  2.0523  1289   140  0.90  16.38   0.99     0.96       3394.87|
| 14:  2.0523 -  2.0023   847    98  0.92  14.13   0.97     0.94       2623.65|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2623.65 max =        10605.47 mean =      6667.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.42|
|phase err.(test): min =        0.00 max =           89.55 mean =        13.88|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.57    76.26   15.07    None  None   None       |
|    all(noH): 2823   0      3.57    76.26   15.07    None  None   None       |
|    Sol.    : 438    0      4.40    75.65   37.34    None  None   None       |
|    Mac.    : 2385   0      3.57    76.26   10.99    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:     3.569 -  10.838: 1602   |   5:    39.916 -  47.185:   79        |
|      1:    10.838 -  18.108:  591   |   6:    47.185 -  54.455:   91        |
|      2:    18.108 -  25.377:  179   |   7:    54.455 -  61.724:   39        |
|      3:    25.377 -  32.646:  105   |   8:    61.724 -  68.994:   18        |
|      4:    32.646 -  39.916:  107   |   9:    68.994 -  76.263:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 318         
Filter by distance & map next to the model:
   mapped sites are within: 0.315 - 4.878
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 318
   mapped sites are within: 0.723 - 4.878

peak=   10.865 closest distance to " CG2 VAL A 230 " =    1.500
peak=    6.428 closest distance to " NH2 ARG A  56 " =    2.238
peak=    6.249 closest distance to " CG  LEU A   5 " =    1.200
peak=    6.168 closest distance to " CG2 VAL A 296 " =    1.071
peak=    5.939 closest distance to " CG  LEU A 228 " =    1.155
peak=    5.353 closest distance to " NE2 GLN A  11 " =    1.192
peak=    5.351 closest distance to " CB  GLN A 223 " =    1.452
peak=    5.250 closest distance to " CD2 LEU A   5 " =    1.169
peak=    5.149 closest distance to " CB  GLN A 183 " =    1.271
peak=    5.036 closest distance to " O   HOH Z 142 " =    1.770
peak=    4.962 closest distance to " CB  VAL A 296 " =    1.090
peak=    4.751 closest distance to " O   HOH Z 232 " =    2.335
peak=    4.655 closest distance to " O   HOH Z 265 " =    2.300
peak=    4.626 closest distance to " O   HOH Z 369 " =    2.128
peak=    4.601 closest distance to " O   HOH Z 126 " =    1.950
peak=    4.569 closest distance to " CB  SER A  63 " =    1.251
peak=    4.559 closest distance to " O   HOH Z 303 " =    2.075
peak=    4.486 closest distance to " O   HOH Z 427 " =    3.117
peak=    4.440 closest distance to " CB  VAL A 230 " =    1.158
peak=    4.401 closest distance to " O   HOH Z  61 " =    1.740
peak=    4.376 closest distance to " CZ  PHE A 218 " =    1.134
peak=    4.360 closest distance to " CB  ARG A  79 " =    1.502
peak=    4.350 closest distance to " C   PRO A 198 " =    1.547
peak=    4.310 closest distance to " CB  ARG A 275 " =    0.924
peak=    4.307 closest distance to " CB  TRP A 266 " =    1.003
peak=    4.269 closest distance to " CB  GLU A 152 " =    1.185
peak=    4.240 closest distance to " CB  ASN A 148 " =    1.469
peak=    4.215 closest distance to " O   SER A  87 " =    2.317
peak=    4.213 closest distance to " O   HOH Z 298 " =    1.855
peak=    4.201 closest distance to " CG  PRO A 213 " =    1.194
peak=    4.179 closest distance to " ND2 ASN A 187 " =    1.480
peak=    4.166 closest distance to " CB  ASP A 140 " =    0.972
peak=    4.163 closest distance to " CB  ARG A 190 " =    1.479
peak=    4.162 closest distance to " O   HOH Z 368 " =    2.193
peak=    4.156 closest distance to " O   HOH Z 158 " =    3.221
peak=    4.141 closest distance to " O   HOH Z 236 " =    2.077
peak=    4.125 closest distance to " CA  TYR A  30 " =    1.019
peak=    4.084 closest distance to " O   HOH Z 346 " =    1.634
peak=    4.066 closest distance to " O   HOH Z 214 " =    2.215
peak=    4.064 closest distance to " CB  GLU A 277 " =    3.675
peak=    4.010 closest distance to " CG  PRO A 243 " =    1.122
peak=    4.004 closest distance to " O   HOH Z 425 " =    1.406
peak=    4.002 closest distance to " O   HOH Z 261 " =    2.023
peak=    3.996 closest distance to " O   HOH Z 248 " =    1.610
peak=    3.996 closest distance to " O   HOH Z 423 " =    1.795
peak=    3.987 closest distance to " CG  MET A 185 " =    1.189
peak=    3.977 closest distance to " CB  VAL A 265 " =    1.312
peak=    3.970 closest distance to " O   HOH Z  78 " =    1.639
peak=    3.966 closest distance to " O   HOH Z 411 " =    3.802
peak=    3.939 closest distance to " O   HOH Z 403 " =    1.605
peak=    3.910 closest distance to " O   HOH Z 272 " =    1.854
peak=    3.909 closest distance to " CG  PRO A 198 " =    1.294
peak=    3.904 closest distance to " N   PHE A 130 " =    1.251
peak=    3.901 closest distance to " CD2 LEU A 228 " =    1.160
peak=    3.900 closest distance to " NH1AARG A 145 " =    1.186
peak=    3.892 closest distance to " CB  ALA A   9 " =    1.627
peak=    3.879 closest distance to " CD  ARG A 159 " =    0.738
peak=    3.879 closest distance to " CB  GLU A 128 " =    0.989
peak=    3.878 closest distance to " OG  SER A  97 " =    3.023
peak=    3.877 closest distance to " O   HOH Z 234 " =    3.699
peak=    3.877 closest distance to " CB  ASN A 142 " =    1.102
peak=    3.875 closest distance to " O   HOH Z  92 " =    2.459
peak=    3.866 closest distance to " CG1 ILE A  49 " =    1.453
peak=    3.824 closest distance to " CB  VAL A 202 " =    1.588
peak=    3.787 closest distance to " CA  ALA A  51 " =    0.948
peak=    3.777 closest distance to " O   HOH Z 313 " =    1.825
peak=    3.775 closest distance to " O   HOH Z 171 " =    3.900
peak=    3.765 closest distance to " CB  GLU A  46 " =    0.967
peak=    3.760 closest distance to " O   HOH Z  43 " =    2.016
peak=    3.758 closest distance to " O   HOH Z   9 " =    1.310
peak=    3.754 closest distance to " O  BHOH Z 338 " =    2.360
peak=    3.742 closest distance to " CB  ALA A 104 " =    0.743
peak=    3.734 closest distance to " O   HOH Z  21 " =    1.718
peak=    3.729 closest distance to " OD1 ASN A  69 " =    2.671
peak=    3.724 closest distance to " OG ASER A 258 " =    3.147
peak=    3.723 closest distance to " CD  LYS A 166 " =    1.297
peak=    3.721 closest distance to " ND2 ASN A 249 " =    1.881
peak=    3.713 closest distance to " O   HOH Z 126 " =    1.588
peak=    3.703 closest distance to " O   HOH Z 209 " =    2.312
peak=    3.701 closest distance to " CB  SER A 212 " =    1.256
peak=    3.700 closest distance to " CA  ARG A 195 " =    1.211
peak=    3.693 closest distance to " O   HOH Z  10 " =    1.779
peak=    3.680 closest distance to " O   HOH Z 193 " =    1.912
peak=    3.668 closest distance to " O   HOH Z 280 " =    2.991
peak=    3.661 closest distance to " CA  ALA A 291 " =    0.910
peak=    3.650 closest distance to " CB AVAL A  41 " =    1.215
peak=    3.649 closest distance to " CA  TYR A 116 " =    1.444
peak=    3.639 closest distance to " O   HOH Z 180 " =    2.181
peak=    3.638 closest distance to " CB  ASN A  39 " =    0.900
peak=    3.637 closest distance to " CA  THR A 264 " =    0.784
peak=    3.635 closest distance to " O   HOH Z 213 " =    1.868
peak=    3.631 closest distance to " CB  THR A  82 " =    1.345
peak=    3.629 closest distance to " O   HOH Z 422 " =    2.722
peak=    3.622 closest distance to " CD  ARG A  66 " =    2.487
peak=    3.619 closest distance to " CG2AVAL A  72 " =    1.711
peak=    3.611 closest distance to " CA  ARG A  36 " =    1.161
peak=    3.604 closest distance to " N   ASN A  39 " =    1.220
peak=    3.601 closest distance to " O   HOH Z 193 " =    2.052
peak=    3.599 closest distance to " CB  SER A 245 " =    3.289
peak=    3.594 closest distance to " OG BSER A 164 " =    2.236
peak=    3.593 closest distance to " CB  LEU A 228 " =    1.199
peak=    3.593 closest distance to " O   MET A 105 " =    1.845
peak=    3.589 closest distance to " CG  LEU A 167 " =    1.241
peak=    3.584 closest distance to " O   HOH Z 371 " =    2.979
peak=    3.577 closest distance to " O   HOH Z   9 " =    1.974
peak=    3.571 closest distance to " CB  PRO A  54 " =    0.808
peak=    3.564 closest distance to " O   HOH Z 285 " =    2.454
peak=    3.545 closest distance to " CB  ASN A 187 " =    1.158
peak=    3.540 closest distance to " CG2 VAL A 257 " =    0.893
peak=    3.540 closest distance to " CB  ALA A 291 " =    1.329
peak=    3.536 closest distance to " CB  SER A   3 " =    1.327
peak=    3.536 closest distance to " CA  LYS A 117 " =    1.238
peak=    3.533 closest distance to " CA  ALA A 295 " =    1.060
peak=    3.525 closest distance to " O   HOH Z 197 " =    3.082
peak=    3.523 closest distance to " CB  TRP A 150 " =    1.401
peak=    3.517 closest distance to " O   HOH Z 166 " =    3.829
peak=    3.506 closest distance to " O   HOH Z 251 " =    1.515
peak=    3.506 closest distance to " O   HOH Z 147 " =    1.799
peak=    3.505 closest distance to " CG  MET A 185 " =    1.038
peak=    3.503 closest distance to " O   HOH Z 406 " =    1.534
peak=    3.502 closest distance to " CD1 LEU A  96 " =    0.725
peak=    3.502 closest distance to " O   HOH Z  59 " =    2.170
peak=    3.495 closest distance to " CA  MET A 105 " =    0.987
peak=    3.493 closest distance to " CG BARG A 275 " =    1.453
peak=    3.491 closest distance to " CB  MET A  40 " =    0.808
peak=    3.489 closest distance to " CA  SER A  87 " =    0.992
peak=    3.488 closest distance to " CG2 THR A 221 " =    1.056
peak=    3.485 closest distance to " O   HOH Z 299 " =    4.236
peak=    3.477 closest distance to " O   HOH Z 291 " =    1.610
peak=    3.474 closest distance to " O   HOH Z 359 " =    1.458
peak=    3.472 closest distance to " CG  GLN A  88 " =    1.052
peak=    3.470 closest distance to " O   HOH Z 203 " =    1.703
peak=    3.463 closest distance to " CB  TRP A 179 " =    1.444
peak=    3.461 closest distance to " CA  GLY A 267 " =    0.734
peak=    3.461 closest distance to " CB  LEU A 143 " =    1.198
peak=    3.450 closest distance to " O   HOH Z   3 " =    1.877
peak=    3.449 closest distance to " O   HOH Z  78 " =    2.235
peak=    3.443 closest distance to " N   SER A 135 " =    1.396
peak=    3.443 closest distance to " O   HOH Z 141 " =    1.710
peak=    3.442 closest distance to " O   HOH Z  40 " =    1.824
peak=    3.436 closest distance to " CB  LYS A 117 " =    1.224
peak=    3.431 closest distance to " CA  ALA A 233 " =    1.351
peak=    3.431 closest distance to " OG  SER A  22 " =    2.823
peak=    3.428 closest distance to " CB  ASN A 110 " =    1.105
peak=    3.426 closest distance to " O   HOH Z 128 " =    2.231
peak=    3.425 closest distance to " CG  ARG A 269 " =    1.858
peak=    3.425 closest distance to " O   HOH Z 148 " =    3.315
peak=    3.422 closest distance to " O   HOH Z 353 " =    2.608
peak=    3.420 closest distance to " NE2 HIS A 207 " =    1.327
peak=    3.420 closest distance to " CA  LEU A 282 " =    1.078
peak=    3.420 closest distance to " CG1 VAL A 153 " =    0.944
peak=    3.419 closest distance to " CB  LEU A  83 " =    0.775
peak=    3.417 closest distance to " CD  ARG A 269 " =    0.965
peak=    3.415 closest distance to " CB  ALA A  34 " =    1.019
peak=    3.413 closest distance to " O   HOH Z 273 " =    2.838
peak=    3.407 closest distance to " CA  ALA A 158 " =    1.241
peak=    3.407 closest distance to " O   HOH Z 294 " =    1.533
peak=    3.402 closest distance to " CB  HIS A 108 " =    0.801
peak=    3.400 closest distance to " CG1 ILE A 151 " =    1.098
peak=    3.395 closest distance to " CD ALYS A 290 " =    1.047
peak=    3.393 closest distance to " CE  LYS A  76 " =    0.912
peak=    3.391 closest distance to " CA  ASN A 215 " =    1.154
peak=    3.390 closest distance to " CA  ALA A  21 " =    1.140
peak=    3.388 closest distance to " CZ  PHE A  38 " =    1.116
peak=    3.382 closest distance to " O   HOH Z 145 " =    1.922
peak=    3.375 closest distance to " O   HOH Z 187 " =    2.305
peak=    3.369 closest distance to " CA  ASN A 217 " =    1.262
peak=    3.369 closest distance to " CA  ALA A 154 " =    1.030
peak=    3.369 closest distance to " CE1 TYR A 186 " =    1.287
peak=    3.366 closest distance to " NE2 GLN A  77 " =    3.341
peak=    3.364 closest distance to " O   HOH Z 250 " =    1.315
peak=    3.363 closest distance to " O   HOH Z 193 " =    1.746
peak=    3.362 closest distance to " NH2AARG A 275 " =    3.510
peak=    3.362 closest distance to " CB  ALA A 248 " =    1.062
peak=    3.362 closest distance to " O   HOH Z 133 " =    2.396
peak=    3.360 closest distance to " O   HOH Z 313 " =    1.600
peak=    3.359 closest distance to " O   TRP A 274 " =    1.842
peak=    3.358 closest distance to " OG1 THR A 294 " =    2.449
peak=    3.358 closest distance to " CA  VAL A 125 " =    1.171
peak=    3.356 closest distance to " O   ASP A 124 " =    1.162
peak=    3.355 closest distance to " O   HOH Z 409 " =    3.120
peak=    3.353 closest distance to " NZ  LYS A 117 " =    3.261
peak=    3.351 closest distance to " CG1 VAL A 296 " =    1.211
peak=    3.351 closest distance to " O   HOH Z 172 " =    3.563
peak=    3.350 closest distance to " CB  GLN A  88 " =    1.227
peak=    3.350 closest distance to " CG2 ILE A  20 " =    1.502
peak=    3.345 closest distance to " CB  THR A  31 " =    1.582
peak=    3.340 closest distance to " O   HOH Z  97 " =    2.512
peak=    3.340 closest distance to " CA  ASP A 162 " =    0.978
peak=    3.340 closest distance to " CB  ASP A 298 " =    1.191
peak=    3.339 closest distance to " CZ  PHE A 192 " =    0.957
peak=    3.337 closest distance to " CD1 LEU A 228 " =    2.104
peak=    3.336 closest distance to " NZ  LYS A  48 " =    1.314
peak=    3.335 closest distance to " O   HOH Z 156 " =    3.008
peak=    3.334 closest distance to " O   HOH Z  63 " =    1.769
peak=    3.332 closest distance to " O   HOH Z  80 " =    1.634
peak=    3.330 closest distance to " CD2 TRP A 179 " =    1.287
peak=    3.330 closest distance to " O   HOH Z 290 " =    1.093
peak=    3.328 closest distance to " O   HOH Z 245 " =    1.358
peak=    3.326 closest distance to " O   ALA A 158 " =    1.429
peak=    3.326 closest distance to " O   HOH Z 260 " =    1.581
peak=    3.323 closest distance to " CD1 LEU A   5 " =    1.333
peak=    3.323 closest distance to " O   HOH Z 128 " =    2.180
peak=    3.318 closest distance to " CB  ALA A 227 " =    0.977
peak=    3.318 closest distance to " OG  SER A 245 " =    1.654
peak=    3.317 closest distance to " CB  PRO A  90 " =    1.242
peak=    3.310 closest distance to " CB  SER A 216 " =    0.834
peak=    3.307 closest distance to " NE  ARG A  79 " =    1.186
peak=    3.306 closest distance to " OE2 GLU A  53 " =    1.928
peak=    3.294 closest distance to " N   ASP A 162 " =    1.241
peak=    3.293 closest distance to " O   HOH Z 329 " =    4.116
peak=    3.292 closest distance to " CG BARG A 102 " =    1.810
peak=    3.288 closest distance to " O   HOH Z 261 " =    1.533
peak=    3.286 closest distance to " CB  GLN A  89 " =    1.215
peak=    3.282 closest distance to " OG BSER A 134 " =    3.000
peak=    3.280 closest distance to " CB  VAL A 268 " =    0.859
peak=    3.280 closest distance to " CB  ALA A 295 " =    1.361
peak=    3.279 closest distance to " CG2 ILE A 234 " =    0.906
peak=    3.279 closest distance to " CA  TYR A  30 " =    1.059
peak=    3.278 closest distance to " O   HOH Z 263 " =    1.723
peak=    3.275 closest distance to " CB  SER A 273 " =    0.872
peak=    3.274 closest distance to " CD1 ILE A  33 " =    1.745
peak=    3.273 closest distance to " O   HOH Z  48 " =    1.553
peak=    3.273 closest distance to " CB  GLN A 103 " =    1.049
peak=    3.272 closest distance to " CB  ASN A 224 " =    1.015
peak=    3.270 closest distance to " O   HOH Z 402 " =    1.429
peak=    3.265 closest distance to " O   HOH Z   1 " =    1.954
peak=    3.262 closest distance to " O   HOH Z 302 " =    1.975
peak=    3.260 closest distance to " C   ALA A 299 " =    0.952
peak=    3.259 closest distance to " O   HOH Z 417 " =    3.350
peak=    3.259 closest distance to " CZ3 TRP A 274 " =    4.624
peak=    3.259 closest distance to " CB  THR A 157 " =    1.122
peak=    3.258 closest distance to " CB  ASN A 215 " =    1.210
peak=    3.258 closest distance to " CB  ARG A 139 " =    0.953
peak=    3.257 closest distance to " CB  ALA A 114 " =    1.315
peak=    3.256 closest distance to " CD1 LEU A 300 " =    1.161
peak=    3.255 closest distance to " O   HOH Z 130 " =    2.205
peak=    3.253 closest distance to " O   HOH Z 305 " =    3.522
peak=    3.248 closest distance to " CA  ARG A 159 " =    1.240
peak=    3.247 closest distance to " O   HOH Z  68 " =    2.156
peak=    3.246 closest distance to " CB  TYR A 116 " =    0.870
peak=    3.242 closest distance to " O   HOH Z  88 " =    3.452
peak=    3.241 closest distance to " OG BSER A 210 " =    1.251
peak=    3.237 closest distance to " CZ3 TRP A 266 " =    1.112
peak=    3.237 closest distance to " CB  ILE A 120 " =    1.347
peak=    3.235 closest distance to " NH2 ARG A 156 " =    1.083
peak=    3.234 closest distance to " O   PHE A  61 " =    1.389
peak=    3.232 closest distance to " CB  GLN A 205 " =    1.074
peak=    3.232 closest distance to " O   HOH Z 368 " =    3.592
peak=    3.228 closest distance to " OE2 GLU A   2 " =    1.867
peak=    3.228 closest distance to " ND1 HIS A  81 " =    1.746
peak=    3.223 closest distance to " O   GLY A  75 " =    1.473
peak=    3.221 closest distance to " O   HOH Z  97 " =    2.032
peak=    3.218 closest distance to " CA  THR A 221 " =    0.957
peak=    3.204 closest distance to " CB  GLN A 278 " =    0.892
peak=    3.204 closest distance to " O   HOH Z 171 " =    2.151
peak=    3.198 closest distance to " O   HOH Z  88 " =    3.194
peak=    3.197 closest distance to " OG  SER A  62 " =    2.905
peak=    3.195 closest distance to " O   HOH Z 286 " =    2.451
peak=    3.194 closest distance to " O   HOH Z 173 " =    2.219
peak=    3.192 closest distance to " CB  ALA A 100 " =    1.186
peak=    3.189 closest distance to " O   HOH Z 329 " =    2.914
peak=    3.188 closest distance to " CD1 ILE A 106 " =    0.953
peak=    3.187 closest distance to " ND2 ASN A 249 " =    0.862
peak=    3.182 closest distance to " O   HOH Z 184 " =    1.333
peak=    3.174 closest distance to " CG1 ILE A  33 " =    1.279
peak=    3.165 closest distance to " CG  LYS A  76 " =    0.898
peak=    3.164 closest distance to " O   HOH Z 215 " =    2.986
peak=    3.161 closest distance to " CB  ARG A 138 " =    0.980
peak=    3.160 closest distance to " O   PHE A 192 " =    1.442
peak=    3.160 closest distance to " CD1 ILE A 263 " =    1.166
peak=    3.159 closest distance to " CB  LEU A 261 " =    0.723
peak=    3.159 closest distance to " CE2 TYR A  30 " =    0.907
peak=    3.158 closest distance to " O   HOH Z  30 " =    1.346
peak=    3.158 closest distance to " CB  SER A  26 " =    1.798
peak=    3.150 closest distance to " O   HOH Z 425 " =    1.981
peak=    3.147 closest distance to " CA  GLY A 211 " =    1.348
peak=    3.141 closest distance to " OH  TYR A 214 " =    1.245
peak=    3.136 closest distance to " CD  LYS A 119 " =    2.029
peak=    3.134 closest distance to " N   ASN A 127 " =    1.245
peak=    3.134 closest distance to " CB  ALA A   1 " =    4.878
peak=    3.131 closest distance to " O   HOH Z 359 " =    4.156
peak=    3.130 closest distance to " CA  ASN A 127 " =    1.034
peak=    3.129 closest distance to " ND1 HIS A  86 " =    1.619
peak=    3.127 closest distance to " O   HOH Z 435 " =    2.017
peak=    3.123 closest distance to " O   HOH Z  89 " =    1.773
peak=    3.122 closest distance to " O   HOH Z 325 " =    2.278
peak=    3.122 closest distance to " CA  ARG A 139 " =    1.023
peak=    3.122 closest distance to " CB  ALA A  43 " =    0.817
peak=    3.118 closest distance to " CE3 TRP A 150 " =    1.001
peak=    3.117 closest distance to " O   HOH Z 128 " =    1.895
peak=    3.117 closest distance to " CA  ALA A 129 " =    1.429
peak=    3.113 closest distance to " O   HOH Z 426 " =    1.583
peak=    3.111 closest distance to " OG BSER A  99 " =    2.190
peak=    3.110 closest distance to " O   HOH Z 156 " =    3.507
peak=    3.107 closest distance to " O   GLN A  88 " =    1.671
peak=    3.104 closest distance to " O   HOH Z 116 " =    1.783
peak=    3.093 closest distance to " O   HOH Z 132 " =    3.216
peak=    3.090 closest distance to " CB  ARG A 145 " =    0.770
peak=    3.087 closest distance to " O   HOH Z  85 " =    2.244
peak=    3.085 closest distance to " CA  ASP A 191 " =    0.921
peak=    3.077 closest distance to " O   HOH Z 171 " =    3.598
peak=    3.077 closest distance to " CA  ILE A 106 " =    0.758
peak=    3.071 closest distance to " CA  LYS A 290 " =    1.296
peak=    3.066 closest distance to " O   HOH Z 162 " =    4.033
peak=    3.060 closest distance to " CB  PRO A  54 " =    1.262
peak=    3.059 closest distance to " O   HOH Z 350 " =    1.657
peak=    3.054 closest distance to " CB  LEU A 300 " =    0.833
peak=    3.050 closest distance to " O   SER A 164 " =    1.223
peak=    3.042 closest distance to " CZ3 TRP A  85 " =    0.992
peak=    3.031 closest distance to " CB  PRO A 243 " =    1.469
peak=    3.012 closest distance to " O   GLN A 278 " =    1.530
peak=    3.003 closest distance to " O   GLU A   2 " =    1.508

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.603 - 5.619
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.724 - 5.619

peak=   -5.288 closest distance to " CG2 VAL A 230 " =    0.742
peak=   -4.530 closest distance to " CG1 VAL A 112 " =    2.654
peak=   -4.461 closest distance to " CD  GLN A  58 " =    0.965
peak=   -4.416 closest distance to " CD  ARG A  14 " =    3.285
peak=   -4.269 closest distance to " CD  ARG A 156 " =    2.055
peak=   -4.257 closest distance to " O   HOH Z 266 " =    5.422
peak=   -4.254 closest distance to " O   HOH Z 162 " =    2.647
peak=   -4.164 closest distance to " O   VAL A  67 " =    2.720
peak=   -4.117 closest distance to " CZ3 TRP A 179 " =    1.165
peak=   -4.060 closest distance to " O   HOH Z  73 " =    2.244
peak=   -4.015 closest distance to " CB  PHE A 192 " =    1.930
peak=   -4.005 closest distance to " O   HOH Z 211 " =    1.342
peak=   -4.001 closest distance to " CG  GLN A 223 " =    2.132
peak=   -3.955 closest distance to " O   HOH Z 196 " =    2.209
peak=   -3.933 closest distance to " OG BSER A 134 " =    1.325
peak=   -3.915 closest distance to " O   VAL A  67 " =    2.781
peak=   -3.910 closest distance to " CG2 ILE A  49 " =    2.795
peak=   -3.889 closest distance to " O   HOH Z 290 " =    1.333
peak=   -3.866 closest distance to " OG  SER A  97 " =    2.337
peak=   -3.858 closest distance to " O   HOH Z 231 " =    2.095
peak=   -3.854 closest distance to " O   HOH Z 351 " =    1.573
peak=   -3.840 closest distance to " CG1 VAL A 112 " =    2.819
peak=   -3.804 closest distance to " CG2 VAL A 296 " =    1.127
peak=   -3.798 closest distance to " C   HIS A 108 " =    1.208
peak=   -3.788 closest distance to " CE BMET A  47 " =    1.669
peak=   -3.786 closest distance to " CA  GLY A 241 " =    3.179
peak=   -3.767 closest distance to " CD1 LEU A 255 " =    2.825
peak=   -3.764 closest distance to " O   VAL A 189 " =    2.624
peak=   -3.752 closest distance to " CB  ALA A 248 " =    2.387
peak=   -3.747 closest distance to " N   ALA A  43 " =    2.509
peak=   -3.741 closest distance to " CA  ASP A 298 " =    1.063
peak=   -3.740 closest distance to " CG1 VAL A 250 " =    2.779
peak=   -3.736 closest distance to " CB  ALA A  43 " =    2.482
peak=   -3.728 closest distance to " NH2AARG A 275 " =    5.342
peak=   -3.696 closest distance to " CA  GLY A 241 " =    2.376
peak=   -3.695 closest distance to " O   HOH Z 394 " =    1.584
peak=   -3.671 closest distance to " OD1 ASN A 148 " =    1.456
peak=   -3.657 closest distance to " CE2 TYR A  30 " =    2.700
peak=   -3.643 closest distance to " C   MET A 188 " =    1.369
peak=   -3.636 closest distance to " O   HOH Z 216 " =    1.335
peak=   -3.636 closest distance to " O   ILE A 109 " =    2.669
peak=   -3.625 closest distance to " O   HOH Z 429 " =    2.054
peak=   -3.625 closest distance to " O   HOH Z 185 " =    2.374
peak=   -3.615 closest distance to " O   HOH Z 166 " =    2.037
peak=   -3.609 closest distance to " O   HOH Z  52 " =    1.536
peak=   -3.584 closest distance to " O   PRO A 163 " =    2.169
peak=   -3.577 closest distance to " CG  ASP A 231 " =    0.763
peak=   -3.573 closest distance to " CE3 TRP A 150 " =    2.187
peak=   -3.560 closest distance to " OG  SER A  87 " =    1.455
peak=   -3.556 closest distance to " ND2 ASN A  45 " =    2.011
peak=   -3.549 closest distance to " O   HOH Z 407 " =    3.181
peak=   -3.546 closest distance to " CG  HIS A  86 " =    1.139
peak=   -3.542 closest distance to " CD2 TYR A 293 " =    2.080
peak=   -3.534 closest distance to " O   HOH Z  38 " =    1.643
peak=   -3.528 closest distance to " OXT GLY A 302 " =    3.002
peak=   -3.520 closest distance to " CB  PRO A 163 " =    2.512
peak=   -3.513 closest distance to " C   ALA A 158 " =    1.366
peak=   -3.509 closest distance to " O   HOH Z  37 " =    1.852
peak=   -3.507 closest distance to " O   HOH Z  11 " =    1.885
peak=   -3.501 closest distance to " CG  ARG A 269 " =    2.432
peak=   -3.500 closest distance to " O   HOH Z  10 " =    1.490
peak=   -3.499 closest distance to " O   PRO A 198 " =    1.236
peak=   -3.494 closest distance to " CD2 LEU A 237 " =    2.808
peak=   -3.490 closest distance to " CD1 LEU A 228 " =    2.332
peak=   -3.483 closest distance to " N   THR A 157 " =    1.543
peak=   -3.482 closest distance to " O   HOH Z 426 " =    1.625
peak=   -3.481 closest distance to " CG1 VAL A 265 " =    2.426
peak=   -3.477 closest distance to " NE2 GLN A 194 " =    1.826
peak=   -3.469 closest distance to " CG  LEU A 101 " =    2.482
peak=   -3.468 closest distance to " O   HOH Z 174 " =    2.490
peak=   -3.467 closest distance to " ND2 ASN A 249 " =    2.418
peak=   -3.466 closest distance to " C   ILE A 239 " =    2.140
peak=   -3.461 closest distance to " O   HOH Z 114 " =    3.022
peak=   -3.457 closest distance to " O   HOH Z  44 " =    2.271
peak=   -3.455 closest distance to " CE  MET A 105 " =    2.287
peak=   -3.448 closest distance to " O   HOH Z 389 " =    2.090
peak=   -3.443 closest distance to " CD  PRO A 213 " =    2.177
peak=   -3.438 closest distance to " O   SER A 271 " =    2.174
peak=   -3.438 closest distance to " CG  TRP A 266 " =    1.828
peak=   -3.435 closest distance to " O   HOH Z 359 " =    3.028
peak=   -3.422 closest distance to " O   HOH Z 166 " =    1.616
peak=   -3.421 closest distance to " CD1 TRP A 274 " =    1.005
peak=   -3.413 closest distance to " N   ALA A 226 " =    2.189
peak=   -3.412 closest distance to " CD  ARG A 139 " =    1.618
peak=   -3.410 closest distance to " O   HOH Z 176 " =    0.779
peak=   -3.407 closest distance to " CA  GLY A 203 " =    2.496
peak=   -3.401 closest distance to " O   GLY A 203 " =    2.345
peak=   -3.384 closest distance to " CD2 PHE A  61 " =    2.588
peak=   -3.383 closest distance to " CG1 VAL A 197 " =    2.270
peak=   -3.380 closest distance to " O   HOH Z 241 " =    1.227
peak=   -3.377 closest distance to " O   HOH Z 262 " =    2.844
peak=   -3.375 closest distance to " CB  VAL A 230 " =    1.059
peak=   -3.367 closest distance to " CG1 VAL A 296 " =    1.390
peak=   -3.366 closest distance to " CG1 VAL A 125 " =    2.044
peak=   -3.358 closest distance to " O   GLY A 196 " =    1.300
peak=   -3.356 closest distance to " CB  ALA A 291 " =    2.231
peak=   -3.353 closest distance to " CD1 LEU A   5 " =    2.592
peak=   -3.349 closest distance to " O   MET A  40 " =    2.819
peak=   -3.342 closest distance to " O   HOH Z  60 " =    1.985
peak=   -3.342 closest distance to " O   HOH Z  47 " =    1.675
peak=   -3.333 closest distance to " O   HOH Z 134 " =    2.979
peak=   -3.332 closest distance to " O   HOH Z 177 " =    1.817
peak=   -3.330 closest distance to " OG  SER A  62 " =    4.569
peak=   -3.329 closest distance to " CB  ARG A  79 " =    2.640
peak=   -3.329 closest distance to " CD1 LEU A 101 " =    2.423
peak=   -3.328 closest distance to " N   SER A   3 " =    2.078
peak=   -3.320 closest distance to " OH  TYR A 247 " =    2.054
peak=   -3.316 closest distance to " CD2 LEU A 300 " =    2.874
peak=   -3.315 closest distance to " CD2 LEU A 167 " =    1.856
peak=   -3.314 closest distance to " ND2 ASN A  45 " =    1.377
peak=   -3.310 closest distance to " O   HOH Z 140 " =    1.880
peak=   -3.309 closest distance to " CB  ALA A 291 " =    2.334
peak=   -3.302 closest distance to " O   PRO A 198 " =    1.397
peak=   -3.300 closest distance to " CG1 VAL A  67 " =    2.873
peak=   -3.299 closest distance to " CG  GLU A 277 " =    1.255
peak=   -3.296 closest distance to " CD1 PHE A  59 " =    1.962
peak=   -3.288 closest distance to " O   GLY A  17 " =    1.231
peak=   -3.284 closest distance to " CG  ASP A 132 " =    2.310
peak=   -3.283 closest distance to " CG2 THR A 178 " =    2.243
peak=   -3.281 closest distance to " N   ALA A 248 " =    2.413
peak=   -3.280 closest distance to " O   HOH Z 417 " =    2.919
peak=   -3.278 closest distance to " O   ASP A  27 " =    2.074
peak=   -3.273 closest distance to " O   HOH Z 326 " =    5.146
peak=   -3.271 closest distance to " NE2 GLN A  88 " =    2.072
peak=   -3.269 closest distance to " OE1 GLN A  88 " =    0.932
peak=   -3.267 closest distance to " CG1 VAL A 112 " =    2.874
peak=   -3.266 closest distance to " O   HOH Z 275 " =    1.491
peak=   -3.264 closest distance to " C   LEU A 143 " =    1.048
peak=   -3.262 closest distance to " NH2 ARG A  79 " =    1.593
peak=   -3.253 closest distance to " N   ALA A 248 " =    1.857
peak=   -3.251 closest distance to " CB  ASN A 252 " =    1.645
peak=   -3.247 closest distance to " CG  PRO A 163 " =    2.549
peak=   -3.247 closest distance to " CA  GLY A  98 " =    1.939
peak=   -3.242 closest distance to " OD2 ASP A  50 " =    2.238
peak=   -3.242 closest distance to " OD1 ASP A 171 " =    1.704
peak=   -3.238 closest distance to " O   HOH Z  13 " =    1.641
peak=   -3.238 closest distance to " CD2 PHE A  61 " =    1.960
peak=   -3.233 closest distance to " NH2 ARG A  79 " =    2.046
peak=   -3.225 closest distance to " C   LEU A 222 " =    0.865
peak=   -3.222 closest distance to " O   HOH Z 350 " =    2.002
peak=   -3.220 closest distance to " O   HOH Z 285 " =    1.890
peak=   -3.218 closest distance to " OG BSER A 134 " =    1.819
peak=   -3.217 closest distance to " O   HOH Z 232 " =    1.752
peak=   -3.213 closest distance to " ND2 ASN A  60 " =    1.358
peak=   -3.211 closest distance to " CA  SER A 135 " =    1.349
peak=   -3.209 closest distance to " N   THR A  52 " =    1.690
peak=   -3.206 closest distance to " O   HOH Z 380 " =    1.453
peak=   -3.202 closest distance to " O   LYS A 117 " =    1.823
peak=   -3.202 closest distance to " O   PHE A 218 " =    1.751
peak=   -3.201 closest distance to " O   HOH Z 353 " =    2.078
peak=   -3.199 closest distance to " NE2 GLN A 278 " =    1.885
peak=   -3.194 closest distance to " C   LYS A  76 " =    1.600
peak=   -3.194 closest distance to " O   LEU A 101 " =    2.766
peak=   -3.193 closest distance to " OH  TYR A 214 " =    1.209
peak=   -3.190 closest distance to " OG  SER A 206 " =    1.793
peak=   -3.186 closest distance to " O   HOH Z 396 " =    2.177
peak=   -3.184 closest distance to " O   HOH Z 252 " =    3.929
peak=   -3.179 closest distance to " N   MET A 188 " =    1.877
peak=   -3.179 closest distance to " CG2 VAL A 189 " =    2.011
peak=   -3.174 closest distance to " CB  ASN A  69 " =    1.248
peak=   -3.173 closest distance to " O   HOH Z 123 " =    2.466
peak=   -3.173 closest distance to " CA  GLY A 133 " =    2.335
peak=   -3.168 closest distance to " O   HOH Z 191 " =    5.619
peak=   -3.166 closest distance to " OD1 ASN A 187 " =    1.608
peak=   -3.165 closest distance to " CD1 ILE A  33 " =    2.486
peak=   -3.157 closest distance to " O   HOH Z 136 " =    2.352
peak=   -3.156 closest distance to " O   HOH Z  89 " =    3.049
peak=   -3.153 closest distance to " CD  GLN A  88 " =    0.854
peak=   -3.152 closest distance to " CB  ASP A 171 " =    2.267
peak=   -3.152 closest distance to " O   HOH Z 111 " =    1.377
peak=   -3.152 closest distance to " O   SER A  22 " =    2.292
peak=   -3.150 closest distance to " O   HOH Z  51 " =    1.311
peak=   -3.145 closest distance to " CA  GLY A 241 " =    2.858
peak=   -3.144 closest distance to " CD2 PHE A 225 " =    1.115
peak=   -3.142 closest distance to " O   SER A 276 " =    1.657
peak=   -3.141 closest distance to " CZ  TYR A 169 " =    1.732
peak=   -3.141 closest distance to " N   ASN A  60 " =    1.338
peak=   -3.134 closest distance to " CG  LEU A 228 " =    0.976
peak=   -3.132 closest distance to " O   HOH Z 369 " =    2.264
peak=   -3.128 closest distance to " CD2 TYR A 247 " =    2.327
peak=   -3.126 closest distance to " CG  ARG A 269 " =    2.061
peak=   -3.114 closest distance to " CG2 VAL A 202 " =    2.728
peak=   -3.113 closest distance to " CG  PHE A 283 " =    2.740
peak=   -3.112 closest distance to " CD1 ILE A 151 " =    2.460
peak=   -3.108 closest distance to " C   ASP A 270 " =    1.341
peak=   -3.103 closest distance to " O   HOH Z 234 " =    4.340
peak=   -3.103 closest distance to " O   THR A  18 " =    1.513
peak=   -3.099 closest distance to " CD  GLN A 223 " =    0.724
peak=   -3.098 closest distance to " O   HOH Z 106 " =    1.851
peak=   -3.097 closest distance to " SD BMET A  47 " =    1.118
peak=   -3.095 closest distance to " OG BSER A 210 " =    1.561
peak=   -3.090 closest distance to " N   SER A 276 " =    1.411
peak=   -3.087 closest distance to " O   HOH Z 128 " =    2.646
peak=   -3.083 closest distance to " O   HOH Z 313 " =    1.164
peak=   -3.082 closest distance to " CE  LYS A  76 " =    2.607
peak=   -3.082 closest distance to " CD1 TYR A 247 " =    2.309
peak=   -3.076 closest distance to " CG2 VAL A 112 " =    2.500
peak=   -3.065 closest distance to " O   HOH Z 313 " =    1.637
peak=   -3.064 closest distance to " CB  GLN A  11 " =    1.795
peak=   -3.050 closest distance to " OG  SER A  63 " =    1.223
peak=   -3.028 closest distance to " O   HOH Z 193 " =    1.816
peak=   -3.022 closest distance to " OH  TYR A 247 " =    1.918
peak=   -3.020 closest distance to " CG2AVAL A  72 " =    2.998
peak=   -3.019 closest distance to " O   HOH Z 193 " =    2.115
peak=   -3.017 closest distance to " O   HOH Z 139 " =    3.026

================= 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    :  0.4429 0.4299   6.238927e+00   6.208912e+00
   1_bss:  0.4346 0.4168   6.232361e+00   6.197633e+00
   1_xyz:  0.3270 0.3468   6.035184e+00   6.074079e+00
   1_adp:  0.2672 0.3043   5.869605e+00   5.978625e+00
   1_occ:  0.2666 0.3049   5.868328e+00   5.980393e+00
   2_bss:  0.2619 0.2993   5.866282e+00   5.975377e+00
   2_xyz:  0.1817 0.2259   5.543338e+00   5.712312e+00
   2_adp:  0.1639 0.2094   5.459497e+00   5.643913e+00
   2_occ:  0.1638 0.2095   5.459064e+00   5.643789e+00
   3_bss:  0.1630 0.2093   5.459882e+00   5.644495e+00
   3_xyz:  0.1264 0.1713   5.243175e+00   5.467733e+00
   3_adp:  0.1198 0.1666   5.204902e+00   5.442312e+00
   3_occ:  0.1197 0.1666   5.204583e+00   5.442138e+00
   4_bss:  0.1198 0.1665   5.204091e+00   5.440903e+00
   4_xyz:  0.1162 0.1637   5.185878e+00   5.425941e+00
   4_adp:  0.1171 0.1620   5.183519e+00   5.414555e+00
   4_occ:  0.1170 0.1620   5.183538e+00   5.414955e+00
   5_bss:  0.1170 0.1620   5.183538e+00   5.414955e+00
   5_xyz:  0.1128 0.1605   5.161196e+00   5.406066e+00
   5_adp:  0.1118 0.1608   5.158950e+00   5.408433e+00
   5_occ:  0.1118 0.1608   5.158757e+00   5.408281e+00
   5_bss:  0.1118 0.1608   5.158721e+00   5.408340e+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:  0.327  20.001   7.750   7.420  10.647   0.000   0.000   0.000
   1_xyz:  0.327  20.001   7.750   7.420  10.647   0.000   0.000   0.000
   1_adp:  0.327  20.001   7.750   7.420  10.647   0.000   0.000   0.000
   1_occ:  0.327  20.001   7.750   7.420  10.647   0.000   0.000   0.000
   2_bss:  0.332  50.001   4.395   3.993   6.939   0.000   0.000   0.000
   2_xyz:  0.332  50.001   4.395   3.993   6.939   0.000   0.000   0.000
   2_adp:  0.332  50.001   4.395   3.993   6.939   0.000   0.000   0.000
   2_occ:  0.332  50.001   4.395   3.993   6.939   0.000   0.000   0.000
   3_bss:  0.331  58.636   3.204   3.242   4.987   0.000   0.000   0.000
   3_xyz:  0.331  58.636   3.204   3.242   4.987   0.000   0.000   0.000
   3_adp:  0.331  58.636   3.204   3.242   4.987   0.000   0.000   0.000
   3_occ:  0.331  58.636   3.204   3.242   4.987   0.000   0.000   0.000
   4_bss:  0.329  57.258   2.994   3.047   4.599   0.000   0.000   0.000
   4_xyz:  0.329  57.258   2.994   3.047   4.599   0.000   0.000   0.000
   4_adp:  0.329  57.258   2.994   3.047   4.599   0.000   0.000   0.000
   4_occ:  0.329  57.258   2.994   3.047   4.599   0.000   0.000   0.000
   5_bss:  0.329  57.258   2.994   3.047   4.599   0.000   0.000   0.000
   5_xyz:  0.329  57.258   2.994   3.047   4.599   0.000   0.000   0.000
   5_adp:  0.329  57.258   2.994   3.047   4.599   0.000   0.000   0.000
   5_occ:  0.329  57.258   2.994   3.047   4.599   0.000   0.000   0.000
   5_bss:  0.321  56.522  -0.549  -0.494   1.043  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.847 0.5485  0.6097    52761.690
   1_bss:  47.465 0.5521  0.7964    50843.475
   1_xyz:  37.746 0.6687  0.9284    33017.430
   1_adp:  31.431 0.7424  1.0146    24784.754
   1_occ:  31.491 0.7417  1.0132    24865.953
   2_bss:  31.200 0.7448  0.8986    24467.212
   2_xyz:  21.834 0.8435  0.9902    12714.027
   2_adp:  19.768 0.8644  1.0037    10988.436
   2_occ:  19.767 0.8644  1.0036    10982.187
   3_bss:  19.767 0.8645  0.9574    11034.271
   3_xyz:  15.722 0.9005  0.9782     7516.585
   3_adp:  15.146 0.9056  0.9783     7141.924
   3_occ:  15.143 0.9056  0.9784     7140.896
   4_bss:  15.139 0.9056  0.9685     7118.411
   4_xyz:  14.700 0.9097  0.9687     6874.304
   4_adp:  14.434 0.9120  0.9679     6753.404
   4_occ:  14.443 0.9119  0.9678     6754.494
   5_bss:  14.443 0.9119  0.9678     6754.494
   5_xyz:  14.301 0.9130  0.9692     6659.086
   5_adp:  14.365 0.9124  0.9655     6672.578
   5_occ:  14.362 0.9125  0.9655     6669.897
   5_bss:  14.366 0.9124  0.9661     6667.547
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4303e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4303e+01
   1_xyz:   1.573  0.012  0.104 18.076  0.006  4.126   1.2552e-01
   1_adp:   1.573  0.012  0.104 18.076  0.006  4.126   1.2552e-01
   1_occ:   1.573  0.012  0.104 18.076  0.006  4.126   1.2552e-01
   2_bss:   1.573  0.012  0.104 18.076  0.006  4.126   1.2552e-01
   2_xyz:   1.036  0.008  0.074 16.540  0.004  4.129   6.7438e-02
   2_adp:   1.036  0.008  0.074 16.540  0.004  4.129   6.7438e-02
   2_occ:   1.036  0.008  0.074 16.540  0.004  4.129   6.7438e-02
   3_bss:   1.036  0.008  0.074 16.540  0.004  4.129   6.7438e-02
   3_xyz:   1.138  0.010  0.090 16.165  0.004  4.144   7.9005e-02
   3_adp:   1.138  0.010  0.090 16.165  0.004  4.144   7.9005e-02
   3_occ:   1.138  0.010  0.090 16.165  0.004  4.144   7.9005e-02
   4_bss:   1.138  0.010  0.090 16.165  0.004  4.144   7.9005e-02
   4_xyz:   1.059  0.009  0.086 15.876  0.004  4.113   7.1570e-02
   4_adp:   1.059  0.009  0.086 15.876  0.004  4.113   7.1570e-02
   4_occ:   1.059  0.009  0.086 15.876  0.004  4.113   7.1570e-02
   5_bss:   1.059  0.009  0.086 15.876  0.004  4.113   7.1570e-02
   5_xyz:   1.159  0.011  0.095 15.906  0.004  4.117   8.4136e-02
   5_adp:   1.159  0.011  0.095 15.906  0.004  4.117   8.4136e-02
   5_occ:   1.159  0.011  0.095 15.906  0.004  4.117   8.4136e-02
   5_bss:   1.159  0.011  0.095 15.906  0.004  4.117   8.4136e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0412e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0412e+00
   1_xyz:  13.502  0.145  0.407 85.348  0.036  2.232   9.4768e-02
   1_adp:  13.502  0.145  0.407 85.348  0.036  2.232   9.4768e-02
   1_occ:  13.502  0.145  0.407 85.348  0.036  2.232   9.4768e-02
   2_bss:  13.502  0.145  0.407 85.348  0.036  2.232   9.4768e-02
   2_xyz:   6.377  0.083  0.266 86.294  0.039  2.416   5.7876e-02
   2_adp:   6.377  0.083  0.266 86.294  0.039  2.416   5.7876e-02
   2_occ:   6.377  0.083  0.266 86.294  0.039  2.416   5.7876e-02
   3_bss:   6.377  0.083  0.266 86.294  0.039  2.416   5.7876e-02
   3_xyz:   7.074  0.055  0.566 83.450  0.040  2.324   5.5735e-02
   3_adp:   7.074  0.055  0.566 83.450  0.040  2.324   5.5735e-02
   3_occ:   7.074  0.055  0.566 83.450  0.040  2.324   5.5735e-02
   4_bss:   7.074  0.055  0.566 83.450  0.040  2.324   5.5735e-02
   4_xyz:   7.257  0.049  0.563 83.006  0.039  2.366   4.7379e-02
   4_adp:   7.257  0.049  0.563 83.006  0.039  2.366   4.7379e-02
   4_occ:   7.257  0.049  0.563 83.006  0.039  2.366   4.7379e-02
   5_bss:   7.257  0.049  0.563 83.006  0.039  2.366   4.7379e-02
   5_xyz:   7.378  0.054  0.663 82.845  0.039  2.260   5.8714e-02
   5_adp:   7.378  0.054  0.663 82.845  0.039  2.260   5.8714e-02
   5_occ:   7.378  0.054  0.663 82.845  0.039  2.260   5.8714e-02
   5_bss:   7.378  0.054  0.663 82.845  0.039  2.260   5.8714e-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:  72.88   0.00  11.05  60.50   0.00   7.93  72.88   0.00  28.02
   1_occ:  72.88   0.00  11.05  60.50   0.00   7.93  72.88   0.00  28.02
   2_bss:  72.88   0.00  11.05  60.50   0.00   7.93  72.88   0.00  28.02
   2_xyz:  72.88   0.00  11.05  60.50   0.00   7.93  72.88   0.00  28.02
   2_adp:  71.47   0.00  11.36  61.15   0.00   7.54  71.47   0.00  32.21
   2_occ:  71.47   0.00  11.36  61.15   0.00   7.54  71.47   0.00  32.21
   3_bss:  71.47   0.00  11.36  61.15   0.00   7.54  71.47   0.00  32.21
   3_xyz:  71.47   0.00  11.36  61.15   0.00   7.54  71.47   0.00  32.21
   3_adp:  73.88   0.00  11.89  70.71   0.00   7.61  73.88   0.00  35.22
   3_occ:  73.88   0.00  11.89  70.71   0.00   7.61  73.88   0.00  35.22
   4_bss:  73.88   0.00  11.89  70.71   0.00   7.61  73.88   0.00  35.22
   4_xyz:  73.88   0.00  11.89  70.71   0.00   7.61  73.88   0.00  35.22
   4_adp:  72.13   0.00  11.51  70.82   0.00   7.44  72.13   0.91  33.64
   4_occ:  72.13   0.00  11.51  70.82   0.00   7.44  72.13   0.91  33.64
   5_bss:  72.13   0.00  11.51  70.82   0.00   7.44  72.13   0.91  33.64
   5_xyz:  72.13   0.00  11.51  70.82   0.00   7.44  72.13   0.91  33.64
   5_adp:  72.69   0.00  11.51  72.69   0.00   7.42  72.08   0.84  33.77
   5_occ:  72.69   0.00  11.51  72.69   0.00   7.42  72.08   0.84  33.77
   5_bss:  76.26   3.57  15.07  76.26   3.57  10.99  75.65   4.40  37.34
------------------------------------------------------------------------
 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:    1.235    0.015    0.406
   1_adp:    1.235    0.015    0.406
   1_occ:    1.235    0.015    0.406
   2_bss:    1.235    0.015    0.406
   2_xyz:    1.633    0.044    0.518
   2_adp:    1.633    0.044    0.518
   2_occ:    1.633    0.044    0.518
   3_bss:    1.633    0.044    0.518
   3_xyz:    1.602    0.067    0.562
   3_adp:    1.602    0.067    0.562
   3_occ:    1.602    0.067    0.562
   4_bss:    1.602    0.067    0.562
   4_xyz:    1.685    0.056    0.572
   4_adp:    1.685    0.056    0.572
   4_occ:    1.685    0.056    0.572
   5_bss:    1.685    0.056    0.572
   5_xyz:    1.646    0.084    0.585
   5_adp:    1.646    0.084    0.585
   5_occ:    1.646    0.084    0.585
   5_bss:    1.646    0.084    0.585
------------------------------------------------------------------------

CPU time actual refinement: 311.91


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_910/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_910/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_910/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_910/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_910/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 311.75 
  Macro-tasks:
    bulk solvent and scale       = 41.93  
    individual site refinement   = 122.21 
    weights calculation          = 31.19  
    collect and process          = 6.51   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 201.94 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 93.04  
    alpha_beta                      = 8.00   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 102.86 
    fmodel                         = 7.00   
    r_factors                      = 0.24   
    phase_errors                   = 10.91  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 225.18 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.458 micro seconds
Total CPU time: 5.42 minutes
from_scatterers_fft:    628 calls, 92.75 s
gradients_fft:          573 calls, 90.07 s

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

# Date 2008-01-16 Time 02:43:23 PST -0800 (1200480203.83 s)
Start R-work = 0.4429, R-free = 0.4299 (no bulk solvent and anisotropic scale)
Final R-work = 0.1292, R-free = 0.1768 (no bulk solvent and anisotropic scale)

Start R-work = 0.4346, R-free = 0.4168
Final R-work = 0.1118, R-free = 0.1608