# Date 2008-01-16 Time 00:51:58 PST -0800 (1200473518.22 s)
#phil __OFF__

Command line arguments: "../193.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10670
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 193

-------------------------------------------------------------------------------
  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: (68.845, 47.1647, 86.822, 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: (68.845, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7929 1.96078
Completeness in resolution range: 0.93907
Completeness with d_max=infinity: 0.936198

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7929
                             d_min =   1.9608

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: (68.845, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7929 1.96078
Completeness in resolution range: 0.93907
Completeness with d_max=infinity: 0.936198

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7934 -  4.1953 [2195/2223]  1972   223  10.2%
  bin  2:  4.1953 -  3.3425 [2087/2110]  1880   207   9.9%
  bin  3:  3.3425 -  2.9237 [2081/2103]  1875   206   9.9%
  bin  4:  2.9237 -  2.6581 [2070/2089]  1861   209  10.1%
  bin  5:  2.6581 -  2.4685 [2015/2044]  1811   204  10.1%
  bin  6:  2.4685 -  2.3236 [2041/2083]  1842   199   9.8%
  bin  7:  2.3236 -  2.2076 [2012/2048]  1811   201  10.0%
  bin  8:  2.2076 -  2.1118 [2022/2060]  1814   208  10.3%
  bin  9:  2.1118 -  2.0307 [2026/2057]  1831   195   9.6%
  bin 10:  2.0307 -  1.9608 [1040/2043]   933   107  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_193/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: 0.15 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:
        1.46 -     2.15: 15
        2.15 -     2.84: 999
        2.84 -     3.52: 4455
        3.52 -     4.21: 9354
        4.21 -     4.90: 13658
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.459 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.466 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.673 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.773 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.805 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28476 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_193/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_193/model_refine_001.geo

CPU time processing inputs: 9.17


============================ 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 = 68.845 47.16465 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4519   r_free= 0.4404   ksol= 0.00   Bsol= 0.00   scale= 0.815    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.252005                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6790 0.99   1425  158 0.3683 0.3618      6.5478      6.5685|
|  2:  4.6790 -  3.7335 0.99   1374  153 0.3452 0.3654      6.6694      6.7276|
|  3:  3.7335 -  3.2674 0.99   1333  150 0.4061 0.3840      6.6043      6.6093|
|  4:  3.2674 -  2.9713 0.99   1337  140 0.4364 0.4252      6.4642      6.4362|
|  5:  2.9713 -  2.7598 0.99   1314  149 0.4751 0.4470      6.3294      6.3536|
|  6:  2.7598 -  2.5980 0.98   1311  150 0.4805 0.5208      6.2634      6.1882|
|  7:  2.5980 -  2.4685 0.99   1305  149 0.4860 0.4905      6.2105      6.1551|
|  8:  2.4685 -  2.3615 0.99   1322  140 0.4996 0.4429      6.1628      6.1381|
|  9:  2.3615 -  2.2709 0.98   1308  145 0.5084 0.5065       6.098      6.1503|
| 10:  2.2709 -  2.1928 0.98   1299  141 0.5065 0.4663       6.101      6.0444|
| 11:  2.1928 -  2.1245 0.98   1305  149 0.5198 0.5000      6.0255      6.0239|
| 12:  2.1245 -  2.0639 0.99   1294  145 0.5204 0.4843      5.9616      5.9574|
| 13:  2.0639 -  2.0097 0.97   1273  135 0.5186 0.5140       5.878      5.8213|
| 14:  2.0097 -  1.9608 0.33    430   55 0.5309 0.4771      5.9081       5.718|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7934 -  4.6790  1425   158  0.70  34.03   0.82     0.71      68059.65|
|  2:  4.6790 -  3.7335  1374   153  0.74  32.12   0.91     0.78      88817.84|
|  3:  3.7335 -  3.2674  1333   150  0.66  38.50   0.86     0.76      90639.23|
|  4:  3.2674 -  2.9713  1337   140  0.59  44.23   0.82     0.68      77767.60|
|  5:  2.9713 -  2.7598  1314   149  0.50  52.23   0.75     0.58      69712.48|
|  6:  2.7598 -  2.5980  1311   150  0.45  55.69   0.74     0.52      64886.66|
|  7:  2.5980 -  2.4685  1305   149  0.42  57.98   0.77     0.49      61116.60|
|  8:  2.4685 -  2.3615  1322   140  0.44  56.54   0.75     0.51      51469.46|
|  9:  2.3615 -  2.2709  1308   145  0.46  55.16   0.74     0.56      45346.81|
| 10:  2.2709 -  2.1928  1299   141  0.49  53.02   0.76     0.56      39253.48|
| 11:  2.1928 -  2.1245  1305   149  0.45  56.40   0.74     0.56      39520.62|
| 12:  2.1245 -  2.0639  1294   145  0.41  58.96   0.78     0.53      37779.84|
| 13:  2.0639 -  2.0097  1273   135  0.40  60.12   0.74     0.51      33200.66|
| 14:  2.0097 -  1.9608   430    55  0.47  54.97   0.76     0.48      23572.09|
|alpha:            min =        0.48 max =            0.78 mean =         0.60|
|beta:             min =    23572.09 max =        90639.23 mean =     58505.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           90.00 mean =        50.27|
|phase err.(test): min =        0.00 max =           89.90 mean =        50.41|
|-----------------------------------------------------------------------------|

============================== 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 = 9.107750              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.079   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.750689              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.602   (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 |  1.180 -  1.552:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.552 -  1.924:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.924 -  2.296:      176 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.296 -  2.668:      686 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.668 -  3.040:     1486 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.040 -  3.412:     2632 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.412 -  3.784:     3973 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.784 -  4.156:     5110 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.156 -  4.528:     6659 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.528 -  4.900:     7769 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.471 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.180 |       2.392 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4590   r_free= 0.4448   ksol= 0.00   Bsol= 0.00   scale= 0.784    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.255103                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4432   r_free= 0.4308   ksol= 0.35   Bsol= 16.28   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.44,8.36,8.54,0.00,0.00,0.00); trace/3= 8.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.242146                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.852907              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.550   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.783102              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.165   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4432      final r-factor (work) = 0.3419          |
| start r-factor (free) = 0.4308      final r-factor (free) = 0.3602          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 81.1762 = 8.85 * 0.50 * 6.2590 + 1.00 * 53.4710                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2179 = 8.85 * 0.50 * 6.1199 + 1.00 * 0.1286                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3419      final r-factor (work) = 0.2846          |
| start r-factor (free) = 0.3602      final r-factor (free) = 0.3246          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8068 = 0.78 * 1.00 * 6.1199 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6875 = 0.78 * 1.00 * 5.9689 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.17   11.67    None  None   None       |
|    all(noH): 2823   0      0.00    65.17   11.67    None  None   None       |
|    Sol.    : 438    0      0.00    65.17   27.39    None  None   None       |
|    Mac.    : 2385   0      0.00    63.57   8.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.517: 1212   |   5:    32.585 -  39.102:   92        |
|      1:     6.517 -  13.034:  728   |   6:    39.102 -  45.619:   55        |
|      2:    13.034 -  19.551:  358   |   7:    45.619 -  52.136:   34        |
|      3:    19.551 -  26.068:  197   |   8:    52.136 -  58.653:   23        |
|      4:    26.068 -  32.585:  119   |   9:    58.653 -  65.170:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2846 r_free = 0.3246             target_work(ml) = 5.926         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2840 r_free = 0.3250             target_work(ml) = 5.925         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2840   r_free= 0.3250   ksol= 0.35   Bsol= 16.28   scale= 1.105   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.44,8.36,8.54,0.00,0.00,0.00); trace/3= 8.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.924550                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2792   r_free= 0.3189   ksol= 0.32   Bsol= 36.34   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.42,4.24,4.98,0.00,0.00,0.00); trace/3= 4.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.924012                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.972329              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.583   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.348182              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.381  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2792      final r-factor (work) = 0.1826          |
| start r-factor (free) = 0.3189      final r-factor (free) = 0.2245          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9720 = 5.97 * 0.50 * 5.9754 + 1.00 * 0.1286                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2410 = 5.97 * 0.50 * 5.7485 + 1.00 * 0.0750                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1826      final r-factor (work) = 0.1611          |
| start r-factor (free) = 0.2245      final r-factor (free) = 0.2038          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0208 = 0.35 * 1.00 * 5.7485 + 1.00 * 0.0193                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9571 = 0.35 * 1.00 * 5.4886 + 1.00 * 0.0460                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.94   11.88    None  None   None       |
|    all(noH): 2823   0      0.00    70.94   11.88    None  None   None       |
|    Sol.    : 438    0      1.28    63.60   32.37    None  None   None       |
|    Mac.    : 2385   0      0.00    70.94   8.12     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.094: 1426   |   5:    35.469 -  42.563:  109        |
|      1:     7.094 -  14.188:  708   |   6:    42.563 -  49.657:   77        |
|      2:    14.188 -  21.282:  217   |   7:    49.657 -  56.751:   34        |
|      3:    21.282 -  28.376:  119   |   8:    56.751 -  63.845:   17        |
|      4:    28.376 -  35.469:  113   |   9:    63.845 -  70.939:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1611 r_free = 0.2038             target_work(ml) = 5.440         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1609 r_free = 0.2040             target_work(ml) = 5.440         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1609   r_free= 0.2040   ksol= 0.32   Bsol= 36.34   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.42,4.24,4.98,0.00,0.00,0.00); trace/3= 4.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.439828                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1593   r_free= 0.2031   ksol= 0.31   Bsol= 36.34   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,3.18,4.02,0.00,0.00,0.00); trace/3= 3.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.436593                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.189143              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.930  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.767707              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.661   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1593      final r-factor (work) = 0.1273          |
| start r-factor (free) = 0.2031      final r-factor (free) = 0.1692          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8402 = 3.19 * 0.50 * 5.4970 + 1.00 * 0.0748                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5823 = 3.19 * 0.50 * 5.3411 + 1.00 * 0.0655                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1273      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1692      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1378 = 0.77 * 1.00 * 5.3411 + 1.00 * 0.0374                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0192 = 0.77 * 1.00 * 5.2187 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.30   12.48    None  None   None       |
|    all(noH): 2823   0      0.00    85.30   12.48    None  None   None       |
|    Sol.    : 438    0      0.43    75.08   36.12    None  None   None       |
|    Mac.    : 2385   0      0.00    85.30   8.14     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.530: 1708   |   5:    42.649 -  51.179:   93        |
|      1:     8.530 -  17.060:  536   |   6:    51.179 -  59.709:   56        |
|      2:    17.060 -  25.589:  171   |   7:    59.709 -  68.238:   30        |
|      3:    25.589 -  34.119:  102   |   8:    68.238 -  76.768:   13        |
|      4:    34.119 -  42.649:  110   |   9:    76.768 -  85.298:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1207 r_free = 0.1635             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1206 r_free = 0.1635             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1635   ksol= 0.31   Bsol= 36.34   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,3.18,4.02,0.00,0.00,0.00); trace/3= 3.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.202443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1639   ksol= 0.30   Bsol= 36.34   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.92,3.90,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.203205                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.053168              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.289  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.351707              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.539  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1639      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4242 = 2.05 * 0.50 * 5.2197 + 1.00 * 0.0657                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3823 = 2.05 * 0.50 * 5.1842 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8363 = 0.35 * 1.00 * 5.1842 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8358 = 0.35 * 1.00 * 5.1706 + 1.00 * 0.0173                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.31   12.48    None  None   None       |
|    all(noH): 2823   0      0.00    85.31   12.48    None  None   None       |
|    Sol.    : 438    0      0.68    75.07   36.11    None  None   None       |
|    Mac.    : 2385   0      0.00    85.31   8.15     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.531: 1715   |   5:    42.653 -  51.183:   93        |
|      1:     8.531 -  17.061:  529   |   6:    51.183 -  59.714:   56        |
|      2:    17.061 -  25.592:  171   |   7:    59.714 -  68.244:   30        |
|      3:    25.592 -  34.122:  103   |   8:    68.244 -  76.775:   13        |
|      4:    34.122 -  42.653:  109   |   9:    76.775 -  85.305:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1147 r_free = 0.1590             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1590             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1590   ksol= 0.30   Bsol= 36.34   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.92,3.90,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.169676                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1590   ksol= 0.31   Bsol= 36.34   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.92,3.90,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.169806                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.420226              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.309  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.311250              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.800   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7317 = 1.42 * 0.50 * 5.1703 + 1.00 * 0.0603                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7269 = 1.42 * 0.50 * 5.1736 + 1.00 * 0.0531                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1595      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6243 = 0.31 * 1.00 * 5.1736 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6215 = 0.31 * 1.00 * 5.1739 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.39   12.24    None  None   None       |
|    all(noH): 2823   0      0.00    85.39   12.24    None  None   None       |
|    Sol.    : 438    0      1.26    75.10   35.16    None  None   None       |
|    Mac.    : 2385   0      0.00    85.39   8.03     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.539: 1719   |   5:    42.694 -  51.233:   85        |
|      1:     8.539 -  17.078:  542   |   6:    51.233 -  59.772:   57        |
|      2:    17.078 -  25.617:  161   |   7:    59.772 -  68.311:   25        |
|      3:    25.617 -  34.155:  109   |   8:    68.311 -  76.849:   10        |
|      4:    34.155 -  42.694:  111   |   9:    76.849 -  85.388:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1584             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1584             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1584   ksol= 0.31   Bsol= 36.34   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.92,3.90,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.169726                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6790 0.99   1425  158 0.1003 0.1318      5.3998      5.5634|
|  2:  4.6790 -  3.7335 0.99   1374  153 0.0868 0.1114      5.4416      5.6422|
|  3:  3.7335 -  3.2674 0.99   1333  150 0.1078 0.1479      5.4775      5.8066|
|  4:  3.2674 -  2.9713 0.99   1337  140 0.1222 0.1598      5.4505      5.6249|
|  5:  2.9713 -  2.7598 0.99   1314  149 0.1377 0.1592      5.3446        5.49|
|  6:  2.7598 -  2.5980 0.98   1311  150 0.1283 0.2082      5.2312      5.5078|
|  7:  2.5980 -  2.4685 0.99   1305  149 0.1288 0.1625      5.1937       5.349|
|  8:  2.4685 -  2.3615 0.99   1322  140 0.1200 0.1717      5.1051      5.3307|
|  9:  2.3615 -  2.2709 0.98   1308  145 0.1238 0.2058      5.0553      5.3926|
| 10:  2.2709 -  2.1928 0.98   1299  141 0.1187 0.1576      4.9803      5.1359|
| 11:  2.1928 -  2.1245 0.98   1305  149 0.1188 0.1707       4.925      5.2358|
| 12:  2.1245 -  2.0639 0.99   1294  145 0.1160 0.1665      4.8719      5.1257|
| 13:  2.0639 -  2.0097 0.97   1273  135 0.1192 0.1749      4.8052      5.0117|
| 14:  2.0097 -  1.9608 0.33    430   55 0.1148 0.1774      4.7541      4.9765|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7934 -  4.6790  1425   158  0.94   9.23   0.98     0.95       7422.01|
|  2:  4.6790 -  3.7335  1374   153  0.95   8.05   1.02     1.01       8966.65|
|  3:  3.7335 -  3.2674  1333   150  0.93  11.42   1.03     1.02      10396.00|
|  4:  3.2674 -  2.9713  1337   140  0.92  13.52   1.01     1.00      10199.23|
|  5:  2.9713 -  2.7598  1314   149  0.90  16.31   1.00     0.97       8519.19|
|  6:  2.7598 -  2.5980  1311   150  0.89  16.69   0.98     0.95       7139.70|
|  7:  2.5980 -  2.4685  1305   149  0.90  15.87   0.99     0.95       6385.04|
|  8:  2.4685 -  2.3615  1322   140  0.90  15.97   1.00     0.97       5843.74|
|  9:  2.3615 -  2.2709  1308   145  0.90  16.32   1.01     0.98       5219.01|
| 10:  2.2709 -  2.1928  1299   141  0.90  16.41   1.00     0.97       4606.27|
| 11:  2.1928 -  2.1245  1305   149  0.90  15.96   1.00     0.97       4139.66|
| 12:  2.1245 -  2.0639  1294   145  0.91  15.54   1.01     1.01       3814.81|
| 13:  2.0639 -  2.0097  1273   135  0.90  16.13   1.00     0.99       3373.87|
| 14:  2.0097 -  1.9608   430    55  0.90  15.84   0.98     0.94       2926.41|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2926.41 max =        10396.00 mean =      6562.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.39|
|phase err.(test): min =        0.00 max =           89.57 mean =        13.91|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1583   ksol= 0.32   Bsol= 44.89   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.95,-0.01,0.96,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.169363                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1583   ksol= 0.32   Bsol= 44.89   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.95,-0.01,0.96,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.169363                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6790 0.99   1425  158 0.1005 0.1322      5.4023      5.5679|
|  2:  4.6790 -  3.7335 0.99   1374  153 0.0872 0.1117      5.4449      5.6448|
|  3:  3.7335 -  3.2674 0.99   1333  150 0.1078 0.1482      5.4788      5.8075|
|  4:  3.2674 -  2.9713 0.99   1337  140 0.1220 0.1593      5.4493      5.6229|
|  5:  2.9713 -  2.7598 0.99   1314  149 0.1374 0.1585      5.3423      5.4875|
|  6:  2.7598 -  2.5980 0.98   1311  150 0.1281 0.2078       5.229       5.505|
|  7:  2.5980 -  2.4685 0.99   1305  149 0.1286 0.1623      5.1918      5.3474|
|  8:  2.4685 -  2.3615 0.99   1322  140 0.1199 0.1714      5.1039      5.3294|
|  9:  2.3615 -  2.2709 0.98   1308  145 0.1238 0.2060      5.0547       5.393|
| 10:  2.2709 -  2.1928 0.98   1299  141 0.1186 0.1576      4.9799      5.1352|
| 11:  2.1928 -  2.1245 0.98   1305  149 0.1186 0.1702      4.9244      5.2348|
| 12:  2.1245 -  2.0639 0.99   1294  145 0.1159 0.1664      4.8712      5.1246|
| 13:  2.0639 -  2.0097 0.97   1273  135 0.1192 0.1747      4.8043      5.0106|
| 14:  2.0097 -  1.9608 0.33    430   55 0.1148 0.1772      4.7525      4.9741|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7934 -  4.6790  1425   158  0.94   9.28   0.98     0.95       7484.54|
|  2:  4.6790 -  3.7335  1374   153  0.95   8.10   1.02     1.00       9026.37|
|  3:  3.7335 -  3.2674  1333   150  0.93  11.46   1.03     1.02      10436.25|
|  4:  3.2674 -  2.9713  1337   140  0.92  13.50   1.01     1.00      10174.24|
|  5:  2.9713 -  2.7598  1314   149  0.90  16.27   1.00     0.97       8476.97|
|  6:  2.7598 -  2.5980  1311   150  0.89  16.64   0.98     0.95       7102.05|
|  7:  2.5980 -  2.4685  1305   149  0.90  15.84   0.99     0.95       6357.90|
|  8:  2.4685 -  2.3615  1322   140  0.90  15.95   1.00     0.97       5827.61|
|  9:  2.3615 -  2.2709  1308   145  0.90  16.30   1.01     0.98       5209.33|
| 10:  2.2709 -  2.1928  1299   141  0.90  16.40   1.00     0.97       4600.33|
| 11:  2.1928 -  2.1245  1305   149  0.90  15.93   1.00     0.97       4131.57|
| 12:  2.1245 -  2.0639  1294   145  0.91  15.53   1.01     1.01       3808.37|
| 13:  2.0639 -  2.0097  1273   135  0.90  16.11   1.00     0.99       3365.05|
| 14:  2.0097 -  1.9608   430    55  0.90  15.81   0.98     0.94       2911.29|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2911.29 max =        10436.25 mean =      6561.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.37|
|phase err.(test): min =        0.00 max =           89.27 mean =        13.89|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.94    88.32   15.18    None  None   None       |
|    all(noH): 2823   0      2.94    88.32   15.18    None  None   None       |
|    Sol.    : 438    0      4.20    78.03   38.09    None  None   None       |
|    Mac.    : 2385   0      2.94    88.32   10.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.937 -  11.475: 1719   |   5:    45.631 -  54.169:   85        |
|      1:    11.475 -  20.014:  542   |   6:    54.169 -  62.708:   57        |
|      2:    20.014 -  28.553:  161   |   7:    62.708 -  71.247:   25        |
|      3:    28.553 -  37.092:  109   |   8:    71.247 -  79.786:   10        |
|      4:    37.092 -  45.631:  111   |   9:    79.786 -  88.325:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 305         
Filter by distance & map next to the model:
   mapped sites are within: 0.316 - 4.718
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 305
   mapped sites are within: 0.704 - 4.718

peak=   11.344 closest distance to " CB  VAL A 230 " =    1.464
peak=    6.328 closest distance to " CG  LEU A   5 " =    1.264
peak=    5.932 closest distance to " CG2 VAL A 296 " =    1.074
peak=    5.582 closest distance to " CG  PRO A  54 " =    1.330
peak=    5.581 closest distance to " CD2 LEU A   5 " =    1.219
peak=    5.571 closest distance to " CB  VAL A 296 " =    1.134
peak=    5.508 closest distance to " CG1 VAL A 296 " =    1.169
peak=    5.380 closest distance to " NH2 ARG A  56 " =    2.159
peak=    5.319 closest distance to " CB  ARG A 275 " =    0.968
peak=    5.198 closest distance to " NE2 GLN A  11 " =    1.085
peak=    5.134 closest distance to " CG  LEU A 228 " =    1.193
peak=    5.090 closest distance to " CB  GLN A 223 " =    1.491
peak=    4.994 closest distance to " CB  PRO A  54 " =    1.025
peak=    4.985 closest distance to " O   HOH Z 142 " =    1.753
peak=    4.982 closest distance to " O   HOH Z 209 " =    2.280
peak=    4.853 closest distance to " O   HOH Z 193 " =    1.764
peak=    4.805 closest distance to " O   HOH Z 402 " =    1.448
peak=    4.735 closest distance to " CG  PRO A 198 " =    1.239
peak=    4.719 closest distance to " O   HOH Z 126 " =    1.878
peak=    4.695 closest distance to " O   HOH Z  85 " =    1.546
peak=    4.672 closest distance to " CG  PRO A 243 " =    1.145
peak=    4.659 closest distance to " CB  VAL A 230 " =    1.163
peak=    4.656 closest distance to " O   HOH Z 272 " =    1.916
peak=    4.642 closest distance to " O   HOH Z 232 " =    2.314
peak=    4.572 closest distance to " CB  SER A  63 " =    1.200
peak=    4.567 closest distance to " O   HOH Z 346 " =    1.564
peak=    4.525 closest distance to " C   PRO A 198 " =    1.520
peak=    4.521 closest distance to " CG  PRO A 213 " =    1.284
peak=    4.500 closest distance to " CD2 LEU A 228 " =    1.326
peak=    4.467 closest distance to " O   HOH Z  63 " =    2.073
peak=    4.440 closest distance to " O   HOH Z 265 " =    2.239
peak=    4.399 closest distance to " O   SER A  87 " =    2.205
peak=    4.331 closest distance to " CB  ARG A  79 " =    1.442
peak=    4.321 closest distance to " O   HOH Z 124 " =    1.334
peak=    4.316 closest distance to " CZ  PHE A 218 " =    1.095
peak=    4.308 closest distance to " CB  GLN A 183 " =    1.303
peak=    4.276 closest distance to " CA  TYR A  30 " =    0.974
peak=    4.274 closest distance to " N   ASN A  39 " =    1.203
peak=    4.254 closest distance to " CD2 TRP A 179 " =    1.355
peak=    4.226 closest distance to " O   HOH Z 287 " =    1.847
peak=    4.223 closest distance to " CB  ASN A 148 " =    1.339
peak=    4.221 closest distance to " O   HOH Z 102 " =    1.324
peak=    4.214 closest distance to " O   HOH Z 248 " =    1.197
peak=    4.210 closest distance to " O   HOH Z 369 " =    2.281
peak=    4.183 closest distance to " CA  VAL A  41 " =    0.757
peak=    4.181 closest distance to " O   HOH Z 188 " =    2.851
peak=    4.130 closest distance to " O   HOH Z 130 " =    1.019
peak=    4.122 closest distance to " CB  GLU A 152 " =    1.135
peak=    4.122 closest distance to " O   HOH Z  80 " =    1.784
peak=    4.113 closest distance to " O   HOH Z 130 " =    2.568
peak=    4.099 closest distance to " O   HOH Z 316 " =    2.981
peak=    4.086 closest distance to " ND2 ASN A 187 " =    1.570
peak=    4.082 closest distance to " O   HOH Z 298 " =    1.740
peak=    4.074 closest distance to " O   HOH Z 423 " =    1.830
peak=    4.072 closest distance to " O   HOH Z 427 " =    2.817
peak=    4.072 closest distance to " O   HOH Z 234 " =    3.600
peak=    4.070 closest distance to " O   HOH Z  61 " =    1.653
peak=    4.068 closest distance to " O   HOH Z  43 " =    2.293
peak=    4.052 closest distance to " O   HOH Z  97 " =    1.965
peak=    4.036 closest distance to " O   HOH Z  59 " =    2.059
peak=    4.035 closest distance to " O   HOH Z 403 " =    1.820
peak=    4.021 closest distance to " O   HOH Z  78 " =    1.631
peak=    4.016 closest distance to " CA  ALA A  51 " =    1.017
peak=    4.007 closest distance to " O   HOH Z 368 " =    2.186
peak=    3.998 closest distance to " CB  VAL A 265 " =    1.238
peak=    3.981 closest distance to " CB  SER A   3 " =    1.223
peak=    3.967 closest distance to " O   HOH Z 246 " =    1.330
peak=    3.948 closest distance to " O   HOH Z 371 " =    3.047
peak=    3.944 closest distance to " O   HOH Z 128 " =    2.277
peak=    3.939 closest distance to " NZ  LYS A 117 " =    2.827
peak=    3.901 closest distance to " CB  ASN A  39 " =    0.842
peak=    3.897 closest distance to " CB  SER A  26 " =    1.803
peak=    3.881 closest distance to " O   HOH Z 406 " =    1.268
peak=    3.865 closest distance to " O   HOH Z 273 " =    2.869
peak=    3.852 closest distance to " CB  GLU A 277 " =    3.612
peak=    3.848 closest distance to " O   HOH Z  97 " =    2.315
peak=    3.844 closest distance to " CB  TRP A 266 " =    1.083
peak=    3.842 closest distance to " CB  ALA A   9 " =    1.633
peak=    3.835 closest distance to " O   HOH Z 411 " =    3.778
peak=    3.828 closest distance to " OE1 GLU A   2 " =    2.192
peak=    3.824 closest distance to " O   HOH Z 313 " =    1.799
peak=    3.816 closest distance to " CD  ARG A 269 " =    1.004
peak=    3.811 closest distance to " CB  VAL A 202 " =    1.492
peak=    3.809 closest distance to " O   HOH Z  54 " =    1.568
peak=    3.801 closest distance to " CG2AVAL A 121 " =    2.173
peak=    3.793 closest distance to " N   ALA A   1 " =    2.939
peak=    3.776 closest distance to " CB  GLU A 128 " =    1.013
peak=    3.772 closest distance to " CG2 ILE A  20 " =    1.460
peak=    3.757 closest distance to " CB  ALA A 248 " =    1.302
peak=    3.751 closest distance to " O   ASN A  74 " =    1.574
peak=    3.738 closest distance to " CA  ARG A  36 " =    1.028
peak=    3.738 closest distance to " O   HOH Z 261 " =    2.013
peak=    3.733 closest distance to " CB  ARG A 139 " =    0.934
peak=    3.728 closest distance to " CG AARG A 275 " =    1.188
peak=    3.724 closest distance to " CD  LYS A 166 " =    1.319
peak=    3.719 closest distance to " O   HOH Z  44 " =    1.931
peak=    3.717 closest distance to " OG  SER A 276 " =    1.406
peak=    3.715 closest distance to " O   HOH Z 389 " =    1.750
peak=    3.710 closest distance to " O   HOH Z 126 " =    1.517
peak=    3.709 closest distance to " O   HOH Z 154 " =    1.554
peak=    3.708 closest distance to " O   HOH Z 345 " =    2.986
peak=    3.697 closest distance to " CB  ARG A  79 " =    0.894
peak=    3.692 closest distance to " O   HOH Z 188 " =    1.219
peak=    3.688 closest distance to " CB  TRP A 179 " =    1.268
peak=    3.665 closest distance to " O   HOH Z 404 " =    2.195
peak=    3.658 closest distance to " CB  ALA A 295 " =    1.064
peak=    3.657 closest distance to " O   HOH Z 344 " =    2.811
peak=    3.656 closest distance to " O   HOH Z 250 " =    1.370
peak=    3.643 closest distance to " CD  ARG A 159 " =    0.746
peak=    3.642 closest distance to " CB  GLU A  46 " =    1.074
peak=    3.637 closest distance to " O   HOH Z  68 " =    2.038
peak=    3.628 closest distance to " O   HOH Z 214 " =    2.468
peak=    3.628 closest distance to " CA  ASN A 215 " =    1.018
peak=    3.619 closest distance to " CG  LEU A 167 " =    1.193
peak=    3.618 closest distance to " O   HOH Z 303 " =    2.137
peak=    3.616 closest distance to " O   HOH Z 172 " =    3.853
peak=    3.614 closest distance to " CB  ASN A 110 " =    1.053
peak=    3.612 closest distance to " CG  MET A 185 " =    1.207
peak=    3.610 closest distance to " CB  ASN A 142 " =    1.117
peak=    3.609 closest distance to " CD2 LEU A 297 " =    0.959
peak=    3.606 closest distance to " O   HOH Z 251 " =    1.448
peak=    3.592 closest distance to " CG2 VAL A 257 " =    0.877
peak=    3.591 closest distance to " CG BARG A 102 " =    1.781
peak=    3.590 closest distance to " CB BVAL A  41 " =    1.165
peak=    3.581 closest distance to " O   HOH Z 422 " =    2.524
peak=    3.581 closest distance to " O   HOH Z 322 " =    2.145
peak=    3.577 closest distance to " CG2 ILE A 120 " =    1.292
peak=    3.577 closest distance to " O   HOH Z 145 " =    2.278
peak=    3.572 closest distance to " O   HOH Z 245 " =    1.404
peak=    3.572 closest distance to " CB  PRO A 198 " =    1.014
peak=    3.571 closest distance to " CD1 LEU A  96 " =    0.704
peak=    3.567 closest distance to " O   HOH Z 158 " =    3.029
peak=    3.563 closest distance to " O   HOH Z 366 " =    2.788
peak=    3.552 closest distance to " O   TRP A 274 " =    1.823
peak=    3.551 closest distance to " CB  ARG A 190 " =    1.787
peak=    3.548 closest distance to " CG1 ILE A  33 " =    1.304
peak=    3.546 closest distance to " O   HOH Z  40 " =    1.655
peak=    3.544 closest distance to " ND2 ASN A 249 " =    0.896
peak=    3.544 closest distance to " CG2AVAL A  72 " =    1.665
peak=    3.541 closest distance to " CB  PHE A 204 " =    0.813
peak=    3.540 closest distance to " O   HOH Z  43 " =    0.994
peak=    3.539 closest distance to " CB  ARG A 219 " =    1.107
peak=    3.538 closest distance to " O   HOH Z 435 " =    1.895
peak=    3.521 closest distance to " CA  ARG A 195 " =    1.164
peak=    3.518 closest distance to " CA  ALA A  21 " =    1.151
peak=    3.516 closest distance to " O   HOH Z 383 " =    1.902
peak=    3.514 closest distance to " O   HOH Z 130 " =    2.323
peak=    3.511 closest distance to " O   HOH Z 421 " =    1.638
peak=    3.505 closest distance to " CB  THR A  31 " =    1.463
peak=    3.502 closest distance to " O   HOH Z 327 " =    1.469
peak=    3.502 closest distance to " O   HOH Z 359 " =    1.383
peak=    3.500 closest distance to " O   HOH Z 407 " =    2.703
peak=    3.498 closest distance to " CA  SER A  32 " =    1.680
peak=    3.493 closest distance to " CE1 HIS A 108 " =    1.183
peak=    3.487 closest distance to " N   PHE A 130 " =    1.331
peak=    3.484 closest distance to " CE1 TYR A 186 " =    1.298
peak=    3.483 closest distance to " O   HOH Z  48 " =    1.638
peak=    3.480 closest distance to " O   HOH Z 380 " =    1.888
peak=    3.479 closest distance to " O   HOH Z 357 " =    1.892
peak=    3.477 closest distance to " CZ  PHE A  38 " =    1.136
peak=    3.473 closest distance to " O   HOH Z 203 " =    1.455
peak=    3.468 closest distance to " OG BSER A 212 " =    2.610
peak=    3.467 closest distance to " OG BSER A 164 " =    2.187
peak=    3.449 closest distance to " O   HOH Z  21 " =    1.773
peak=    3.441 closest distance to " CB  HIS A 108 " =    0.843
peak=    3.434 closest distance to " O   GLY A  91 " =    1.375
peak=    3.429 closest distance to " O   HOH Z 130 " =    2.422
peak=    3.422 closest distance to " O   ASP A 124 " =    1.273
peak=    3.422 closest distance to " CG  ARG A  66 " =    0.919
peak=    3.422 closest distance to " CB  THR A  52 " =    0.911
peak=    3.421 closest distance to " O   HOH Z 361 " =    3.105
peak=    3.420 closest distance to " N   ARG A 156 " =    1.383
peak=    3.418 closest distance to " O   HOH Z 222 " =    2.367
peak=    3.418 closest distance to " O   HOH Z 128 " =    1.876
peak=    3.416 closest distance to " O   HOH Z 426 " =    1.479
peak=    3.409 closest distance to " CA  ASN A 176 " =    1.041
peak=    3.404 closest distance to " CB  ALA A 114 " =    1.151
peak=    3.401 closest distance to " CA  PHE A 283 " =    1.027
peak=    3.399 closest distance to " O   HOH Z  88 " =    2.792
peak=    3.392 closest distance to " NH2BARG A 145 " =    2.205
peak=    3.391 closest distance to " O   HOH Z  15 " =    2.215
peak=    3.389 closest distance to " O   HOH Z 257 " =    2.295
peak=    3.388 closest distance to " NE2 GLN A  77 " =    3.213
peak=    3.388 closest distance to " NH1 ARG A  14 " =    1.089
peak=    3.379 closest distance to " O  BHOH Z  74 " =    1.244
peak=    3.377 closest distance to " O   HOH Z 353 " =    2.702
peak=    3.372 closest distance to " O   HOH Z 417 " =    3.338
peak=    3.368 closest distance to " CA  ALA A 160 " =    0.948
peak=    3.365 closest distance to " CB  GLN A 278 " =    0.898
peak=    3.362 closest distance to " CD  LYS A 119 " =    1.905
peak=    3.361 closest distance to " O   HOH Z 352 " =    1.301
peak=    3.359 closest distance to " CB  SER A 216 " =    0.985
peak=    3.359 closest distance to " CA  LYS A 117 " =    1.258
peak=    3.356 closest distance to " O   HOH Z 368 " =    3.566
peak=    3.355 closest distance to " CA  ASP A 162 " =    1.019
peak=    3.353 closest distance to " O   HOH Z 148 " =    3.263
peak=    3.348 closest distance to " CA  ILE A 234 " =    0.887
peak=    3.347 closest distance to " O   HOH Z 233 " =    1.634
peak=    3.345 closest distance to " OD1 ASN A  69 " =    2.506
peak=    3.342 closest distance to " CA  LYS A 290 " =    1.249
peak=    3.341 closest distance to " O   HOH Z   9 " =    2.101
peak=    3.341 closest distance to " CG2 THR A  29 " =    1.235
peak=    3.341 closest distance to " CA  ASN A 217 " =    1.286
peak=    3.340 closest distance to " O   HOH Z 173 " =    2.306
peak=    3.339 closest distance to " CB  SER A 273 " =    0.891
peak=    3.338 closest distance to " O   HOH Z 238 " =    0.832
peak=    3.321 closest distance to " OG1 THR A 221 " =    1.340
peak=    3.320 closest distance to " NH1AARG A 145 " =    1.231
peak=    3.319 closest distance to " CE  LYS A  76 " =    0.902
peak=    3.317 closest distance to " CZ2 TRP A 150 " =    1.111
peak=    3.317 closest distance to " OH  TYR A 116 " =    1.153
peak=    3.315 closest distance to " O   SER A 164 " =    1.237
peak=    3.313 closest distance to " N   SER A 135 " =    1.398
peak=    3.310 closest distance to " O   HOH Z 438 " =    2.457
peak=    3.305 closest distance to " O   HOH Z 301 " =    1.825
peak=    3.301 closest distance to " CB  ASP A 140 " =    1.081
peak=    3.301 closest distance to " O   HOH Z  63 " =    2.077
peak=    3.301 closest distance to " CB  PRO A  90 " =    1.079
peak=    3.295 closest distance to " CG  LYS A 119 " =    1.141
peak=    3.285 closest distance to " O   GLN A 194 " =    1.607
peak=    3.284 closest distance to " NH2 ARG A 156 " =    1.099
peak=    3.282 closest distance to " O   HOH Z 293 " =    1.881
peak=    3.282 closest distance to " O   HOH Z 367 " =    3.505
peak=    3.281 closest distance to " CG1 ILE A 120 " =    1.094
peak=    3.280 closest distance to " CB  PRO A 243 " =    1.222
peak=    3.278 closest distance to " O   HOH Z 227 " =    1.501
peak=    3.278 closest distance to " CG2 THR A 294 " =    1.705
peak=    3.275 closest distance to " CA  GLY A 133 " =    3.597
peak=    3.275 closest distance to " CB  GLN A  89 " =    1.282
peak=    3.274 closest distance to " CA  PHE A  59 " =    0.919
peak=    3.274 closest distance to " CE  LYS A 119 " =    0.958
peak=    3.271 closest distance to " O   HOH Z 109 " =    2.109
peak=    3.270 closest distance to " O   HOH Z 193 " =    1.891
peak=    3.270 closest distance to " CB  ASN A  45 " =    1.059
peak=    3.269 closest distance to " CB  SER A  62 " =    1.244
peak=    3.269 closest distance to " CB  GLN A  88 " =    1.183
peak=    3.268 closest distance to " O   HOH Z  19 " =    1.684
peak=    3.268 closest distance to " O   HOH Z 425 " =    1.373
peak=    3.266 closest distance to " CB  SER A 141 " =    1.125
peak=    3.264 closest distance to " O   HOH Z 414 " =    1.333
peak=    3.263 closest distance to " C   ALA A 299 " =    0.865
peak=    3.260 closest distance to " OG  SER A  62 " =    2.734
peak=    3.258 closest distance to " O   HOH Z 337 " =    3.493
peak=    3.253 closest distance to " O   HOH Z 236 " =    1.438
peak=    3.249 closest distance to " CA  SER A 146 " =    1.944
peak=    3.246 closest distance to " O   THR A 182 " =    1.428
peak=    3.244 closest distance to " O   HOH Z 116 " =    2.591
peak=    3.242 closest distance to " O   HOH Z 162 " =    2.180
peak=    3.240 closest distance to " O   HOH Z 406 " =    1.602
peak=    3.240 closest distance to " O   HOH Z  94 " =    2.127
peak=    3.236 closest distance to " O   HOH Z 298 " =    2.370
peak=    3.224 closest distance to " CA  ALA A 291 " =    0.809
peak=    3.220 closest distance to " O   HOH Z 419 " =    1.664
peak=    3.220 closest distance to " CB  SER A  62 " =    0.926
peak=    3.217 closest distance to " N   ARG A 190 " =    0.988
peak=    3.217 closest distance to " CG2 THR A 221 " =    1.189
peak=    3.217 closest distance to " ND2 ASN A 110 " =    1.512
peak=    3.216 closest distance to " CG  GLU A 277 " =    2.128
peak=    3.215 closest distance to " O   HOH Z 180 " =    2.167
peak=    3.214 closest distance to " CA  ASP A 191 " =    1.143
peak=    3.212 closest distance to " CB  ALA A 104 " =    0.717
peak=    3.209 closest distance to " O   HOH Z 392 " =    2.714
peak=    3.205 closest distance to " O   HOH Z 132 " =    2.547
peak=    3.201 closest distance to " N   ASP A 162 " =    1.249
peak=    3.199 closest distance to " CG  ARG A 269 " =    1.286
peak=    3.192 closest distance to " O   HOH Z   3 " =    1.685
peak=    3.191 closest distance to " CB  ALA A 291 " =    1.212
peak=    3.181 closest distance to " CG1 ILE A  49 " =    1.485
peak=    3.177 closest distance to " N   ALA A 256 " =    1.032
peak=    3.173 closest distance to " CG  GLN A  77 " =    2.395
peak=    3.157 closest distance to " O   HOH Z 227 " =    2.096
peak=    3.156 closest distance to " O   HOH Z 342 " =    0.860
peak=    3.156 closest distance to " C   SER A  32 " =    1.835
peak=    3.156 closest distance to " O   HOH Z 134 " =    1.289
peak=    3.155 closest distance to " O   HOH Z 294 " =    1.562
peak=    3.149 closest distance to " O   LEU A 228 " =    1.730
peak=    3.148 closest distance to " CD2 TYR A 186 " =    1.058
peak=    3.147 closest distance to " CB  THR A 235 " =    1.219
peak=    3.147 closest distance to " O   HOH Z   4 " =    1.526
peak=    3.132 closest distance to " O   HOH Z 345 " =    1.611
peak=    3.131 closest distance to " O   HOH Z  35 " =    2.328
peak=    3.126 closest distance to " O   HOH Z 250 " =    1.471
peak=    3.125 closest distance to " O   HOH Z 423 " =    3.271
peak=    3.123 closest distance to " CB  ILE A 120 " =    1.300
peak=    3.119 closest distance to " CA  SER A  87 " =    1.012
peak=    3.119 closest distance to " O   HOH Z 368 " =    4.718
peak=    3.110 closest distance to " O   HOH Z 263 " =    1.660
peak=    3.102 closest distance to " CA  LEU A 282 " =    1.232
peak=    3.101 closest distance to " CG2 ILE A 106 " =    0.812
peak=    3.095 closest distance to " O   HOH Z 299 " =    4.206
peak=    3.090 closest distance to " O   HOH Z  47 " =    1.815
peak=    3.086 closest distance to " CA  TRP A  85 " =    1.127
peak=    3.083 closest distance to " OE2 GLU A  53 " =    2.006
peak=    3.076 closest distance to " CG2 VAL A 197 " =    1.021
peak=    3.070 closest distance to " NZ  LYS A  76 " =    1.428
peak=    3.066 closest distance to " CG  GLN A 205 " =    0.936
peak=    3.059 closest distance to " O   HOH Z 329 " =    3.942
peak=    3.020 closest distance to " CB  ASN A 215 " =    1.107
peak=    3.018 closest distance to " CA  MET A 105 " =    1.023

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.719 - 5.598
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 189 from: 190
   mapped sites are within: 0.719 - 5.598

peak=   -5.371 closest distance to " CG2 VAL A 230 " =    0.719
peak=   -4.681 closest distance to " CG  GLN A  58 " =    1.177
peak=   -4.539 closest distance to " SG  CYS A 254 " =    3.293
peak=   -4.401 closest distance to " C   HIS A 108 " =    1.178
peak=   -4.274 closest distance to " OG BSER A 134 " =    1.299
peak=   -4.266 closest distance to " O   VAL A  67 " =    2.549
peak=   -4.261 closest distance to " CD  ARG A 156 " =    2.022
peak=   -4.233 closest distance to " OXT GLY A 302 " =    2.786
peak=   -4.201 closest distance to " O   HOH Z 351 " =    1.445
peak=   -4.182 closest distance to " O   HOH Z 266 " =    5.208
peak=   -4.083 closest distance to " O   HOH Z 166 " =    1.889
peak=   -4.028 closest distance to " ND2 ASN A 187 " =    1.487
peak=   -4.013 closest distance to " CG  GLN A 223 " =    2.188
peak=   -4.009 closest distance to " CG1 VAL A 296 " =    1.042
peak=   -4.006 closest distance to " CD2 PHE A 192 " =    2.088
peak=   -3.994 closest distance to " CD1 LEU A 101 " =    2.376
peak=   -3.985 closest distance to " NE2 GLN A  88 " =    1.088
peak=   -3.959 closest distance to " CE2 TYR A  30 " =    2.747
peak=   -3.955 closest distance to " O   PRO A 163 " =    2.134
peak=   -3.953 closest distance to " CB  ALA A 248 " =    2.285
peak=   -3.951 closest distance to " O   PRO A 198 " =    1.176
peak=   -3.877 closest distance to " ND2 ASN A  45 " =    1.036
peak=   -3.852 closest distance to " O   HOH Z 423 " =    2.248
peak=   -3.812 closest distance to " O   HOH Z 290 " =    1.076
peak=   -3.804 closest distance to " CE  MET A 105 " =    2.292
peak=   -3.802 closest distance to " CG  ASP A 231 " =    0.826
peak=   -3.784 closest distance to " O   HOH Z 231 " =    2.245
peak=   -3.774 closest distance to " O   ASN A  45 " =    1.877
peak=   -3.765 closest distance to " CB  ALA A 161 " =    2.446
peak=   -3.740 closest distance to " O   HOH Z 114 " =    3.183
peak=   -3.736 closest distance to " CB  ALA A 248 " =    2.073
peak=   -3.733 closest distance to " N   ALA A 226 " =    1.913
peak=   -3.731 closest distance to " O   HOH Z 103 " =    1.705
peak=   -3.725 closest distance to " N   ALA A 248 " =    1.916
peak=   -3.711 closest distance to " CG2 THR A 178 " =    2.276
peak=   -3.706 closest distance to " CD2 TYR A 293 " =    1.924
peak=   -3.701 closest distance to " CG2 VAL A 296 " =    1.357
peak=   -3.696 closest distance to " O   HOH Z 394 " =    1.654
peak=   -3.685 closest distance to " CB  PRO A 243 " =    2.666
peak=   -3.684 closest distance to " O   HOH Z 193 " =    1.599
peak=   -3.674 closest distance to " CG1 VAL A 112 " =    2.787
peak=   -3.649 closest distance to " O   HOH Z 407 " =    2.787
peak=   -3.643 closest distance to " O   GLY A  80 " =    2.393
peak=   -3.642 closest distance to " N   THR A  52 " =    1.710
peak=   -3.633 closest distance to " C   THR A 279 " =    1.204
peak=   -3.626 closest distance to " CA  VAL A  67 " =    2.969
peak=   -3.620 closest distance to " CD2 LEU A 237 " =    2.525
peak=   -3.610 closest distance to " O   HOH Z 166 " =    1.727
peak=   -3.589 closest distance to " CZ3 TRP A 179 " =    1.353
peak=   -3.579 closest distance to " CD1 LEU A 255 " =    2.759
peak=   -3.579 closest distance to " O   SER A 210 " =    1.924
peak=   -3.574 closest distance to " CB  PRO A 163 " =    2.577
peak=   -3.560 closest distance to " N   GLN A  58 " =    2.053
peak=   -3.548 closest distance to " CA  ASP A 298 " =    1.073
peak=   -3.542 closest distance to " OG  SER A  97 " =    2.320
peak=   -3.530 closest distance to " O   HOH Z 102 " =    1.758
peak=   -3.526 closest distance to " CB  VAL A 296 " =    1.034
peak=   -3.525 closest distance to " OD1 ASN A  39 " =    2.241
peak=   -3.523 closest distance to " ND2 ASN A  39 " =    1.117
peak=   -3.518 closest distance to " O   VAL A 174 " =    2.110
peak=   -3.517 closest distance to " O   HOH Z 196 " =    2.142
peak=   -3.507 closest distance to " NH2AARG A 275 " =    4.772
peak=   -3.505 closest distance to " O   PHE A 218 " =    1.632
peak=   -3.502 closest distance to " O   HOH Z 389 " =    1.964
peak=   -3.501 closest distance to " OD2 ASP A 171 " =    2.240
peak=   -3.500 closest distance to " OG  SER A   3 " =    1.493
peak=   -3.497 closest distance to " CB  SER A 210 " =    1.172
peak=   -3.496 closest distance to " O   HOH Z 185 " =    2.373
peak=   -3.483 closest distance to " O   HOH Z 131 " =    4.119
peak=   -3.459 closest distance to " CZ  ARG A  66 " =    1.145
peak=   -3.458 closest distance to " O   ALA A   8 " =    1.974
peak=   -3.456 closest distance to " O   GLY A 196 " =    1.090
peak=   -3.449 closest distance to " CA  GLY A 241 " =    2.377
peak=   -3.448 closest distance to " C   MET A 188 " =    1.400
peak=   -3.442 closest distance to " O   HOH Z 165 " =    1.897
peak=   -3.433 closest distance to " CG  TRP A 266 " =    1.930
peak=   -3.432 closest distance to " NE2 GLN A  88 " =    1.851
peak=   -3.431 closest distance to " CG  GLU A  53 " =    1.513
peak=   -3.429 closest distance to " ND2 ASN A  69 " =    1.800
peak=   -3.418 closest distance to " O   HOH Z 426 " =    1.750
peak=   -3.417 closest distance to " O   HOH Z  52 " =    1.786
peak=   -3.417 closest distance to " C   ASP A 231 " =    2.432
peak=   -3.416 closest distance to " C   ASN A 285 " =    2.184
peak=   -3.414 closest distance to " O   GLU A 277 " =    1.047
peak=   -3.409 closest distance to " OD2 ASP A 191 " =    1.498
peak=   -3.408 closest distance to " N   SER A 206 " =    1.817
peak=   -3.394 closest distance to " N   ALA A  43 " =    2.668
peak=   -3.389 closest distance to " CE3 TRP A 150 " =    2.067
peak=   -3.380 closest distance to " CD  ARG A 139 " =    1.664
peak=   -3.379 closest distance to " O   ALA A 227 " =    1.388
peak=   -3.377 closest distance to " O   SER A 271 " =    2.187
peak=   -3.373 closest distance to " CB  ASP A 132 " =    2.287
peak=   -3.370 closest distance to " CB  ASP A 132 " =    2.354
peak=   -3.367 closest distance to " O   HOH Z  11 " =    1.964
peak=   -3.357 closest distance to " O   GLY A  75 " =    1.662
peak=   -3.354 closest distance to " CG2 ILE A 263 " =    2.272
peak=   -3.353 closest distance to " O   HOH Z  13 " =    1.725
peak=   -3.346 closest distance to " O   HOH Z 301 " =    2.417
peak=   -3.340 closest distance to " O   HOH Z  11 " =    1.891
peak=   -3.337 closest distance to " O   HOH Z 174 " =    4.013
peak=   -3.332 closest distance to " NE  ARG A  66 " =    4.157
peak=   -3.329 closest distance to " O   HOH Z 275 " =    1.824
peak=   -3.329 closest distance to " CZ  TYR A 169 " =    1.868
peak=   -3.327 closest distance to " O   HOH Z  63 " =    1.236
peak=   -3.324 closest distance to " O   HOH Z 353 " =    2.182
peak=   -3.321 closest distance to " O   HOH Z 191 " =    5.598
peak=   -3.319 closest distance to " O   HOH Z 427 " =    1.464
peak=   -3.319 closest distance to " CB  PRO A 280 " =    2.091
peak=   -3.317 closest distance to " O   HOH Z 374 " =    1.871
peak=   -3.314 closest distance to " CG  MET A 105 " =    0.853
peak=   -3.314 closest distance to " N   THR A 157 " =    1.498
peak=   -3.308 closest distance to " O   HOH Z 154 " =    1.638
peak=   -3.305 closest distance to " CB  ALA A  43 " =    2.396
peak=   -3.305 closest distance to " O   ASN A 187 " =    1.562
peak=   -3.304 closest distance to " N   SER A 276 " =    1.313
peak=   -3.300 closest distance to " CA  GLY A 133 " =    1.867
peak=   -3.298 closest distance to " N   VAL A 230 " =    1.116
peak=   -3.298 closest distance to " CB  ALA A 291 " =    2.250
peak=   -3.296 closest distance to " OG  SER A 206 " =    1.522
peak=   -3.296 closest distance to " O   HOH Z 211 " =    1.527
peak=   -3.294 closest distance to " N   THR A 235 " =    1.262
peak=   -3.293 closest distance to " O   ALA A 161 " =    1.703
peak=   -3.288 closest distance to " O   SER A 146 " =    1.153
peak=   -3.285 closest distance to " C   ALA A 158 " =    1.335
peak=   -3.283 closest distance to " O   HOH Z 136 " =    2.368
peak=   -3.277 closest distance to " CA  GLY A  23 " =    1.844
peak=   -3.274 closest distance to " CD1 PHE A  59 " =    1.962
peak=   -3.270 closest distance to " O   ALA A  51 " =    1.301
peak=   -3.267 closest distance to " CA  ASN A 127 " =    1.255
peak=   -3.264 closest distance to " O   HOH Z 421 " =    3.430
peak=   -3.263 closest distance to " CE1 TYR A 247 " =    2.539
peak=   -3.262 closest distance to " CG  LEU A   5 " =    0.901
peak=   -3.261 closest distance to " O   SER A  95 " =    1.581
peak=   -3.259 closest distance to " CA  GLY A 133 " =    2.292
peak=   -3.259 closest distance to " CD  GLN A  88 " =    0.919
peak=   -3.259 closest distance to " C   LYS A  76 " =    1.430
peak=   -3.258 closest distance to " O   HOH Z 243 " =    1.934
peak=   -3.258 closest distance to " O   HOH Z 252 " =    3.958
peak=   -3.245 closest distance to " O   ILE A 120 " =    1.302
peak=   -3.245 closest distance to " OE1 GLN A 183 " =    1.615
peak=   -3.243 closest distance to " CZ  PHE A  38 " =    2.127
peak=   -3.241 closest distance to " O   HOH Z 193 " =    1.879
peak=   -3.234 closest distance to " O   HOH Z 139 " =    5.014
peak=   -3.233 closest distance to " CE BMET A  47 " =    1.345
peak=   -3.230 closest distance to " O   HOH Z 369 " =    2.239
peak=   -3.227 closest distance to " NH2 ARG A  79 " =    2.100
peak=   -3.224 closest distance to " CB  ASN A  39 " =    2.260
peak=   -3.221 closest distance to " CE  LYS A 166 " =    2.997
peak=   -3.219 closest distance to " OXT GLY A 302 " =    3.529
peak=   -3.218 closest distance to " O   LEU A 282 " =    2.053
peak=   -3.214 closest distance to " CD  LYS A 289 " =    2.523
peak=   -3.213 closest distance to " CE1 TYR A 169 " =    2.481
peak=   -3.198 closest distance to " O   MET A  40 " =    2.760
peak=   -3.197 closest distance to " CD2 LEU A   5 " =    1.258
peak=   -3.194 closest distance to " OG ASER A 134 " =    1.391
peak=   -3.190 closest distance to " CA  VAL A 296 " =    0.916
peak=   -3.189 closest distance to " OG BSER A 134 " =    1.750
peak=   -3.188 closest distance to " O   HOH Z 377 " =    1.396
peak=   -3.183 closest distance to " CB  TYR A 172 " =    2.460
peak=   -3.178 closest distance to " CD2 PHE A  61 " =    2.118
peak=   -3.174 closest distance to " O   HOH Z  19 " =    2.369
peak=   -3.172 closest distance to " CD1 ILE A 199 " =    2.389
peak=   -3.171 closest distance to " CH2 TRP A 150 " =    1.047
peak=   -3.163 closest distance to " O   HOH Z 313 " =    1.817
peak=   -3.161 closest distance to " O   HOH Z 111 " =    4.687
peak=   -3.161 closest distance to " CG1 VAL A  78 " =    2.513
peak=   -3.154 closest distance to " CB  PHE A 208 " =    2.313
peak=   -3.151 closest distance to " O   LEU A 167 " =    1.543
peak=   -3.150 closest distance to " O   HOH Z 422 " =    1.609
peak=   -3.143 closest distance to " O   HOH Z 339 " =    1.757
peak=   -3.139 closest distance to " NH2 ARG A  66 " =    5.134
peak=   -3.132 closest distance to " O   TRP A  92 " =    1.937
peak=   -3.117 closest distance to " O   HOH Z 256 " =    1.318
peak=   -3.115 closest distance to " CD2 LEU A 237 " =    2.828
peak=   -3.112 closest distance to " OD1 ASN A 301 " =    1.989
peak=   -3.111 closest distance to " C   SER A 206 " =    1.605
peak=   -3.110 closest distance to " OG1 THR A  82 " =    1.288
peak=   -3.108 closest distance to " CD2 TYR A 247 " =    2.299
peak=   -3.100 closest distance to " CG  PHE A 283 " =    2.727
peak=   -3.097 closest distance to " O   SER A   3 " =    1.019
peak=   -3.094 closest distance to " O   HOH Z 174 " =    2.208
peak=   -3.092 closest distance to " CB  TRP A  85 " =    2.626
peak=   -3.090 closest distance to " CG  ARG A 269 " =    2.168
peak=   -3.086 closest distance to " CD  GLN A 223 " =    0.741
peak=   -3.082 closest distance to " O   PRO A 198 " =    1.182
peak=   -3.081 closest distance to " OH  TYR A 169 " =    0.827
peak=   -3.049 closest distance to " O   HOH Z 134 " =    2.857
peak=   -3.037 closest distance to " O   HOH Z 234 " =    3.927
peak=   -3.024 closest distance to " O   HOH Z 110 " =    1.504

================= 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    :  0.4519 0.4404   6.252005e+00   6.236244e+00
   1_bss:  0.4432 0.4308   6.242146e+00   6.227723e+00
   1_xyz:  0.3419 0.3602   6.068774e+00   6.112682e+00
   1_adp:  0.2846 0.3246   5.925509e+00   6.027852e+00
   1_occ:  0.2840 0.3250   5.924550e+00   6.028541e+00
   2_bss:  0.2792 0.3189   5.924012e+00   6.027366e+00
   2_xyz:  0.1826 0.2245   5.550552e+00   5.729880e+00
   2_adp:  0.1611 0.2038   5.440192e+00   5.633806e+00
   2_occ:  0.1609 0.2040   5.439828e+00   5.634205e+00
   3_bss:  0.1593 0.2031   5.436593e+00   5.628599e+00
   3_xyz:  0.1273 0.1692   5.242973e+00   5.458035e+00
   3_adp:  0.1207 0.1635   5.202884e+00   5.426313e+00
   3_occ:  0.1206 0.1635   5.202443e+00   5.425831e+00
   4_bss:  0.1209 0.1639   5.203205e+00   5.424587e+00
   4_xyz:  0.1148 0.1592   5.171070e+00   5.401149e+00
   4_adp:  0.1147 0.1590   5.169955e+00   5.400020e+00
   4_occ:  0.1146 0.1590   5.169676e+00   5.400229e+00
   5_bss:  0.1146 0.1590   5.169806e+00   5.400352e+00
   5_xyz:  0.1158 0.1595   5.174471e+00   5.401898e+00
   5_adp:  0.1155 0.1584   5.169976e+00   5.394803e+00
   5_occ:  0.1155 0.1584   5.169726e+00   5.394565e+00
   5_bss:  0.1154 0.1583   5.169363e+00   5.394126e+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:  0.345  16.284   8.436   8.362   8.545   0.000   0.000   0.000
   1_xyz:  0.345  16.284   8.436   8.362   8.545   0.000   0.000   0.000
   1_adp:  0.345  16.284   8.436   8.362   8.545   0.000   0.000   0.000
   1_occ:  0.345  16.284   8.436   8.362   8.545   0.000   0.000   0.000
   2_bss:  0.325  36.344   4.415   4.239   4.978   0.000   0.000   0.000
   2_xyz:  0.325  36.344   4.415   4.239   4.978   0.000   0.000   0.000
   2_adp:  0.325  36.344   4.415   4.239   4.978   0.000   0.000   0.000
   2_occ:  0.325  36.344   4.415   4.239   4.978   0.000   0.000   0.000
   3_bss:  0.312  36.344   2.332   3.184   4.015   0.000   0.000   0.000
   3_xyz:  0.312  36.344   2.332   3.184   4.015   0.000   0.000   0.000
   3_adp:  0.312  36.344   2.332   3.184   4.015   0.000   0.000   0.000
   3_occ:  0.312  36.344   2.332   3.184   4.015   0.000   0.000   0.000
   4_bss:  0.303  36.344   1.987   2.924   3.899   0.000   0.000   0.000
   4_xyz:  0.303  36.344   1.987   2.924   3.899   0.000   0.000   0.000
   4_adp:  0.303  36.344   1.987   2.924   3.899   0.000   0.000   0.000
   4_occ:  0.303  36.344   1.987   2.924   3.899   0.000   0.000   0.000
   5_bss:  0.311  36.344   1.987   2.924   3.899   0.000   0.000   0.000
   5_xyz:  0.311  36.344   1.987   2.924   3.899   0.000   0.000   0.000
   5_adp:  0.311  36.344   1.987   2.924   3.899   0.000   0.000   0.000
   5_occ:  0.311  36.344   1.987   2.924   3.899   0.000   0.000   0.000
   5_bss:  0.319  44.889  -0.950  -0.012   0.962   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.281 0.5188  0.5963    58500.472
   1_bss:  50.337 0.5162  0.7681    56464.540
   1_xyz:  39.748 0.6449  0.9263    36732.653
   1_adp:  33.846 0.7148  1.0328    28678.445
   1_occ:  33.876 0.7144  1.0314    28697.364
   2_bss:  33.636 0.7172  0.9011    28491.531
   2_xyz:  22.478 0.8363  1.0021    13127.334
   2_adp:  19.653 0.8649  1.0228    10740.705
   2_occ:  19.659 0.8649  1.0225    10744.996
   3_bss:  19.555 0.8657  0.9717    10606.340
   3_xyz:  15.766 0.8999  0.9873     7424.870
   3_adp:  15.067 0.9061  0.9872     6987.984
   3_occ:  15.055 0.9062  0.9873     6979.838
   4_bss:  15.048 0.9062  0.9787     6970.846
   4_xyz:  14.465 0.9114  0.9800     6638.988
   4_adp:  14.439 0.9117  0.9802     6625.703
   4_occ:  14.439 0.9117  0.9800     6628.789
   5_bss:  14.442 0.9117  0.9801     6632.823
   5_xyz:  14.513 0.9109  0.9797     6648.571
   5_adp:  14.343 0.9124  0.9786     6565.062
   5_occ:  14.338 0.9124  0.9786     6561.810
   5_bss:  14.327 0.9125  0.9789     6560.263
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3471e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3471e+01
   1_xyz:   1.609  0.012  0.105 17.845  0.006  4.109   1.2856e-01
   1_adp:   1.609  0.012  0.105 17.845  0.006  4.109   1.2856e-01
   1_occ:   1.609  0.012  0.105 17.845  0.006  4.109   1.2856e-01
   2_bss:   1.609  0.012  0.105 17.845  0.006  4.109   1.2856e-01
   2_xyz:   1.116  0.008  0.079 16.013  0.005  4.123   7.5040e-02
   2_adp:   1.116  0.008  0.079 16.013  0.005  4.123   7.5040e-02
   2_occ:   1.116  0.008  0.079 16.013  0.005  4.123   7.5040e-02
   3_bss:   1.116  0.008  0.079 16.013  0.005  4.123   7.5040e-02
   3_xyz:   1.057  0.007  0.081 15.699  0.004  4.124   6.5520e-02
   3_adp:   1.057  0.007  0.081 15.699  0.004  4.124   6.5520e-02
   3_occ:   1.057  0.007  0.081 15.699  0.004  4.124   6.5520e-02
   4_bss:   1.057  0.007  0.081 15.699  0.004  4.124   6.5520e-02
   4_xyz:   1.001  0.007  0.078 15.446  0.004  4.117   6.0261e-02
   4_adp:   1.001  0.007  0.078 15.446  0.004  4.117   6.0261e-02
   4_occ:   1.001  0.007  0.078 15.446  0.004  4.117   6.0261e-02
   5_bss:   1.001  0.007  0.078 15.446  0.004  4.117   6.0261e-02
   5_xyz:   0.927  0.005  0.073 15.158  0.003  4.117   5.3096e-02
   5_adp:   0.927  0.005  0.073 15.158  0.003  4.117   5.3096e-02
   5_occ:   0.927  0.005  0.073 15.158  0.003  4.117   5.3096e-02
   5_bss:   0.927  0.005  0.073 15.158  0.003  4.117   5.3096e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.180   6.9274e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.180   6.9274e+00
   1_xyz:  14.388  0.153  0.473 84.921  0.035  2.258   9.4626e-02
   1_adp:  14.388  0.153  0.473 84.921  0.035  2.258   9.4626e-02
   1_occ:  14.388  0.153  0.473 84.921  0.035  2.258   9.4626e-02
   2_bss:  14.388  0.153  0.473 84.921  0.035  2.258   9.4626e-02
   2_xyz:   6.705  0.123  0.312 83.224  0.041  2.262   6.9940e-02
   2_adp:   6.705  0.123  0.312 83.224  0.041  2.262   6.9940e-02
   2_occ:   6.705  0.123  0.312 83.224  0.041  2.262   6.9940e-02
   3_bss:   6.705  0.123  0.312 83.224  0.041  2.262   6.9940e-02
   3_xyz:   7.029  0.048  0.481 82.321  0.039  2.297   4.9837e-02
   3_adp:   7.029  0.048  0.481 82.321  0.039  2.297   4.9837e-02
   3_occ:   7.029  0.048  0.481 82.321  0.039  2.297   4.9837e-02
   4_bss:   7.029  0.048  0.481 82.321  0.039  2.297   4.9837e-02
   4_xyz:   6.874  0.044  0.406 81.103  0.035  2.336   3.7489e-02
   4_adp:   6.874  0.044  0.406 81.103  0.035  2.336   3.7489e-02
   4_occ:   6.874  0.044  0.406 81.103  0.035  2.336   3.7489e-02
   5_bss:   6.874  0.044  0.406 81.103  0.035  2.336   3.7489e-02
   5_xyz:   6.337  0.042  0.355 81.976  0.033  2.355   2.8666e-02
   5_adp:   6.337  0.042  0.355 81.976  0.033  2.355   2.8666e-02
   5_occ:   6.337  0.042  0.355 81.976  0.033  2.355   2.8666e-02
   5_bss:   6.337  0.042  0.355 81.976  0.033  2.355   2.8666e-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:  65.17   0.00  11.67  63.57   0.00   8.79  65.17   0.00  27.39
   1_occ:  65.17   0.00  11.67  63.57   0.00   8.79  65.17   0.00  27.39
   2_bss:  65.17   0.00  11.67  63.57   0.00   8.79  65.17   0.00  27.39
   2_xyz:  65.17   0.00  11.67  63.57   0.00   8.79  65.17   0.00  27.39
   2_adp:  70.94   0.00  11.88  70.94   0.00   8.12  63.60   1.28  32.37
   2_occ:  70.94   0.00  11.88  70.94   0.00   8.12  63.60   1.28  32.37
   3_bss:  70.94   0.00  11.88  70.94   0.00   8.12  63.60   1.28  32.37
   3_xyz:  70.94   0.00  11.88  70.94   0.00   8.12  63.60   1.28  32.37
   3_adp:  85.30   0.00  12.48  85.30   0.00   8.14  75.08   0.43  36.12
   3_occ:  85.30   0.00  12.48  85.30   0.00   8.14  75.08   0.43  36.12
   4_bss:  85.30   0.00  12.48  85.30   0.00   8.14  75.08   0.43  36.12
   4_xyz:  85.30   0.00  12.48  85.30   0.00   8.14  75.08   0.43  36.12
   4_adp:  85.31   0.00  12.48  85.31   0.00   8.15  75.07   0.68  36.11
   4_occ:  85.31   0.00  12.48  85.31   0.00   8.15  75.07   0.68  36.11
   5_bss:  85.31   0.00  12.48  85.31   0.00   8.15  75.07   0.68  36.11
   5_xyz:  85.31   0.00  12.48  85.31   0.00   8.15  75.07   0.68  36.11
   5_adp:  85.39   0.00  12.24  85.39   0.00   8.03  75.10   1.26  35.16
   5_occ:  85.39   0.00  12.24  85.39   0.00   8.03  75.10   1.26  35.16
   5_bss:  88.32   2.94  15.18  88.32   2.94  10.97  78.03   4.20  38.09
------------------------------------------------------------------------
 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:    1.244    0.022    0.409
   1_adp:    1.244    0.022    0.409
   1_occ:    1.244    0.022    0.409
   2_bss:    1.244    0.022    0.409
   2_xyz:    1.548    0.016    0.547
   2_adp:    1.548    0.016    0.547
   2_occ:    1.548    0.016    0.547
   3_bss:    1.548    0.016    0.547
   3_xyz:    1.565    0.041    0.587
   3_adp:    1.565    0.041    0.587
   3_occ:    1.565    0.041    0.587
   4_bss:    1.565    0.041    0.587
   4_xyz:    1.759    0.014    0.607
   4_adp:    1.759    0.014    0.607
   4_occ:    1.759    0.014    0.607
   5_bss:    1.759    0.014    0.607
   5_xyz:    1.775    0.040    0.610
   5_adp:    1.775    0.040    0.610
   5_occ:    1.775    0.040    0.610
   5_bss:    1.775    0.040    0.610
------------------------------------------------------------------------

CPU time actual refinement: 323.79


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_193/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_193/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_193/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_193/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_193/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.64 
  Macro-tasks:
    bulk solvent and scale       = 40.65  
    individual site refinement   = 124.78 
    weights calculation          = 33.01  
    collect and process          = 6.67   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 205.24 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 99.38  
    alpha_beta                      = 8.57   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 107.41 
    fmodel                         = 7.15   
    r_factors                      = 0.21   
    phase_errors                   = 11.02  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 237.04 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.677 micro seconds
Total CPU time: 5.62 minutes
from_scatterers_fft:    622 calls, 99.09 s
gradients_fft:          566 calls, 95.16 s

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

# Date 2008-01-16 Time 00:57:35 PST -0800 (1200473855.73 s)
Start R-work = 0.4519, R-free = 0.4404 (no bulk solvent and anisotropic scale)
Final R-work = 0.1331, R-free = 0.1734 (no bulk solvent and anisotropic scale)

Start R-work = 0.4432, R-free = 0.4308
Final R-work = 0.1154, R-free = 0.1583