# Date 2008-01-16 Time 01:39:59 PST -0800 (1200476399.30 s)
#phil __OFF__

Command line arguments: "../511.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 = 4615
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 511

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.2261, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.97229
Completeness in resolution range: 0.964358
Completeness with d_max=infinity: 0.961376

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9392
                             d_min =   1.9723

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.97229
Completeness in resolution range: 0.964358
Completeness with d_max=infinity: 0.961376

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9396 -  4.2202 [2132/2156]  1918   214  10.0%
  bin  2:  4.2202 -  3.3623 [2038/2058]  1836   202   9.9%
  bin  3:  3.3623 -  2.9410 [2031/2050]  1824   207  10.2%
  bin  4:  2.9410 -  2.6737 [1999/2029]  1802   197   9.9%
  bin  5:  2.6737 -  2.4830 [2008/2027]  1807   201  10.0%
  bin  6:  2.4830 -  2.3372 [1957/1982]  1762   195  10.0%
  bin  7:  2.3372 -  2.2206 [1979/2007]  1778   201  10.2%
  bin  8:  2.2206 -  2.1242 [1978/2014]  1784   194   9.8%
  bin  9:  2.1242 -  2.0426 [1928/1970]  1734   194  10.1%
  bin 10:  2.0426 -  1.9723 [1539/2020]  1385   154  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_511/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: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 32
        2.42 -     3.04: 2213
        3.04 -     3.66: 4755
        3.66 -     4.28: 9151
        4.28 -     4.90: 12400
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.968 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.156 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28546 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_511/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_511/model_refine_001.geo

CPU time processing inputs: 9.27


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.22605 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4532   r_free= 0.4446   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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.255496                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7070 0.99   1389  153 0.3815 0.3737      6.5552      6.5518|
|  2:  4.7070 -  3.7557 0.99   1328  152 0.3609 0.3351      6.7196       6.665|
|  3:  3.7557 -  3.2867 0.99   1304  140 0.3919 0.3654      6.6124      6.6211|
|  4:  3.2867 -  2.9888 0.99   1297  149 0.4361 0.4071      6.5023      6.4424|
|  5:  2.9888 -  2.7760 0.99   1293  145 0.4834 0.4772      6.3452      6.3583|
|  6:  2.7760 -  2.6133 0.99   1297  138 0.4740 0.5390      6.2649      6.2069|
|  7:  2.6133 -  2.4830 0.99   1279  144 0.4947 0.4548      6.2224      6.2021|
|  8:  2.4830 -  2.3754 0.98   1269  142 0.5110 0.4848      6.1858      6.1696|
|  9:  2.3754 -  2.2843 0.98   1257  140 0.4874 0.5325      6.0931      6.1544|
| 10:  2.2843 -  2.2057 1.00   1283  143 0.5136 0.4915      6.1197      6.0705|
| 11:  2.2057 -  2.1369 0.97   1254  137 0.5040 0.4596      6.0246      6.0305|
| 12:  2.1369 -  2.0760 0.98   1249  138 0.5027 0.4932       5.983      5.9889|
| 13:  2.0760 -  2.0215 0.99   1292  141 0.5113 0.5361      5.8818      5.8402|
| 14:  2.0215 -  1.9723 0.66    839   97 0.5366 0.5209      5.8687      5.7854|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7070  1389   153  0.70  34.13   0.81     0.75      70658.39|
|  2:  4.7070 -  3.7557  1328   152  0.75  30.83   0.90     0.82      85969.84|
|  3:  3.7557 -  3.2867  1304   140  0.67  37.82   0.88     0.78      89883.30|
|  4:  3.2867 -  2.9888  1297   149  0.60  44.21   0.82     0.68      81684.19|
|  5:  2.9888 -  2.7760  1293   145  0.48  53.62   0.77     0.57      72391.03|
|  6:  2.7760 -  2.6133  1297   138  0.45  55.99   0.74     0.50      65803.21|
|  7:  2.6133 -  2.4830  1279   144  0.40  59.97   0.75     0.46      63526.71|
|  8:  2.4830 -  2.3754  1269   142  0.38  61.21   0.74     0.45      58315.37|
|  9:  2.3754 -  2.2843  1257   140  0.42  58.61   0.75     0.48      50462.51|
| 10:  2.2843 -  2.2057  1283   143  0.44  56.87   0.77     0.51      42641.34|
| 11:  2.2057 -  2.1369  1254   137  0.44  56.74   0.78     0.53      39921.01|
| 12:  2.1369 -  2.0760  1249   138  0.39  60.63   0.80     0.48      39309.02|
| 13:  2.0760 -  2.0215  1292   141  0.35  64.13   0.73     0.42      35737.20|
| 14:  2.0215 -  1.9723   839    97  0.35  63.80   0.73     0.38      29273.87|
|alpha:            min =        0.38 max =            0.82 mean =         0.57|
|beta:             min =    29273.87 max =        89883.30 mean =     59994.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.99 mean =        52.25|
|phase err.(test): min =        0.00 max =           89.98 mean =        52.38|
|-----------------------------------------------------------------------------|

============================== 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 = 10.435243             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.009   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.987805              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.478   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       31 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      694 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1521 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2675 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3976 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5109 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6616 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7794 |
|-----------------------------------------------------------------------------|
|-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 |       53.335 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.901 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    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 = 11.658)------------------------------------------|
|    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: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4616   r_free= 0.4491   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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.259637                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4452   r_free= 0.4310   ksol= 0.36   Bsol= 5.16   scale= 1.022    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.27,10.37,8.06,0.00,0.00,0.00); trace/3= 8.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.249284                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.829550              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.786   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.888335              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.590   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4452      final r-factor (work) = 0.3542          |
| start r-factor (free) = 0.4310      final r-factor (free) = 0.3737          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.9698 = 8.83 * 0.50 * 6.2596 + 1.00 * 53.3352                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2258 = 8.83 * 0.50 * 6.1385 + 1.00 * 0.1257                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3542      final r-factor (work) = 0.3008          |
| start r-factor (free) = 0.3737      final r-factor (free) = 0.3436          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4678 = 0.89 * 1.00 * 6.1385 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3583 = 0.89 * 1.00 * 6.0159 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.13   12.02    None  None   None       |
|    all(noH): 2823   0      0.00    73.13   12.02    None  None   None       |
|    Sol.    : 438    0      0.00    73.13   25.93    None  None   None       |
|    Mac.    : 2385   0      0.00    68.83   9.47     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 -   7.313: 1213   |   5:    36.563 -  43.875:   66        |
|      1:     7.313 -  14.625:  781   |   6:    43.875 -  51.188:   37        |
|      2:    14.625 -  21.938:  383   |   7:    51.188 -  58.500:   13        |
|      3:    21.938 -  29.250:  201   |   8:    58.500 -  65.813:    1        |
|      4:    29.250 -  36.563:  125   |   9:    65.813 -  73.126:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3008 r_free = 0.3436             target_work(ml) = 5.983         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3002 r_free = 0.3427             target_work(ml) = 5.982         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3002   r_free= 0.3427   ksol= 0.36   Bsol= 5.16   scale= 1.113    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.27,10.37,8.06,0.00,0.00,0.00); trace/3= 8.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.981779                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2950   r_free= 0.3362   ksol= 0.34   Bsol= 29.14   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.66,5.70,4.69,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.979379                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.997996              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.172   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.423750              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.168  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2950      final r-factor (work) = 0.2099          |
| start r-factor (free) = 0.3362      final r-factor (free) = 0.2608          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1592 = 5.00 * 0.50 * 6.0161 + 1.00 * 0.1250                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6254 = 5.00 * 0.50 * 5.8202 + 1.00 * 0.0807                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2099      final r-factor (work) = 0.1860          |
| start r-factor (free) = 0.2608      final r-factor (free) = 0.2393          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4803 = 0.42 * 1.00 * 5.8202 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3919 = 0.42 * 1.00 * 5.6187 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.84   11.96    None  None   None       |
|    all(noH): 2823   0      0.00    78.84   11.96    None  None   None       |
|    Sol.    : 438    0      1.18    78.84   31.79    None  None   None       |
|    Mac.    : 2385   0      0.00    72.27   8.32     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 -   7.884: 1510   |   5:    39.421 -  47.305:   95        |
|      1:     7.884 -  15.768:  660   |   6:    47.305 -  55.189:   44        |
|      2:    15.768 -  23.652:  211   |   7:    55.189 -  63.073:    8        |
|      3:    23.652 -  31.537:  148   |   8:    63.073 -  70.957:    1        |
|      4:    31.537 -  39.421:  144   |   9:    70.957 -  78.841:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1860 r_free = 0.2393             target_work(ml) = 5.579         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1858 r_free = 0.2387             target_work(ml) = 5.578         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1858   r_free= 0.2387   ksol= 0.34   Bsol= 29.14   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.66,5.70,4.69,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.577965                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1842   r_free= 0.2360   ksol= 0.33   Bsol= 39.84   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.62,3.28,3.93,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.573924                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.432392              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.395   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.732899              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.523  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1842      final r-factor (work) = 0.1377          |
| start r-factor (free) = 0.2360      final r-factor (free) = 0.1871          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7307 = 3.43 * 0.50 * 5.6230 + 1.00 * 0.0805                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4185 = 3.43 * 0.50 * 5.4500 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1377      final r-factor (work) = 0.1271          |
| start r-factor (free) = 0.1871      final r-factor (free) = 0.1761          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0051 = 0.73 * 1.00 * 5.4500 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8842 = 0.73 * 1.00 * 5.2831 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.80   12.42    None  None   None       |
|    all(noH): 2823   0      0.00    82.80   12.42    None  None   None       |
|    Sol.    : 438    0      1.39    80.90   35.82    None  None   None       |
|    Mac.    : 2385   0      0.00    82.80   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 -   8.280: 1649   |   5:    41.399 -  49.679:   96        |
|      1:     8.280 -  16.560:  574   |   6:    49.679 -  57.959:   68        |
|      2:    16.560 -  24.840:  174   |   7:    57.959 -  66.239:   34        |
|      3:    24.840 -  33.119:  108   |   8:    66.239 -  74.519:    6        |
|      4:    33.119 -  41.399:  112   |   9:    74.519 -  82.798:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1271 r_free = 0.1761             target_work(ml) = 5.252         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1270 r_free = 0.1759             target_work(ml) = 5.252         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1759   ksol= 0.33   Bsol= 39.84   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.62,3.28,3.93,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.251528                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1272   r_free= 0.1753   ksol= 0.32   Bsol= 43.09   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,2.63,3.78,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.250164                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.034577              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.387  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.268291              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.305  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1272      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1753      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0830 = 3.03 * 0.50 * 5.2842 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9703 = 3.03 * 0.50 * 5.2116 + 1.00 * 0.0629                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1635      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4103 = 0.27 * 1.00 * 5.2116 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4011 = 0.27 * 1.00 * 5.1718 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.56   12.01    None  None   None       |
|    all(noH): 2823   0      0.00    83.56   12.01    None  None   None       |
|    Sol.    : 438    0      1.80    78.57   34.39    None  None   None       |
|    Mac.    : 2385   0      0.00    83.56   7.90     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 -   8.356: 1689   |   5:    41.781 -  50.137:   85        |
|      1:     8.356 -  16.712:  582   |   6:    50.137 -  58.493:   61        |
|      2:    16.712 -  25.069:  145   |   7:    58.493 -  66.850:   22        |
|      3:    25.069 -  33.425:  126   |   8:    66.850 -  75.206:    5        |
|      4:    33.425 -  41.781:  105   |   9:    75.206 -  83.562:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1142 r_free = 0.1596             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1141 r_free = 0.1595             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1595   ksol= 0.32   Bsol= 43.09   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,2.63,3.78,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.157017                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1594   ksol= 0.33   Bsol= 42.02   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,2.50,3.85,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.156929                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.999437              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.854  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.362558              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.238   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1594      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2329 = 2.00 * 0.50 * 5.1715 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2064 = 2.00 * 0.50 * 5.1521 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8791 = 0.36 * 1.00 * 5.1521 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8832 = 0.36 * 1.00 * 5.1427 + 1.00 * 0.0187                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.61   11.88    None  None   None       |
|    all(noH): 2823   0      0.00    85.61   11.88    None  None   None       |
|    Sol.    : 438    0      1.69    77.41   33.98    None  None   None       |
|    Mac.    : 2385   0      0.00    85.61   7.83     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.561: 1734   |   5:    42.806 -  51.367:   84        |
|      1:     8.561 -  17.122:  551   |   6:    51.367 -  59.928:   46        |
|      2:    17.122 -  25.683:  141   |   7:    59.928 -  68.489:   16        |
|      3:    25.683 -  34.245:  130   |   8:    68.489 -  77.050:    4        |
|      4:    34.245 -  42.806:  114   |   9:    77.050 -  85.611:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1566             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1117 r_free = 0.1567             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1567   ksol= 0.33   Bsol= 42.02   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,2.50,3.85,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141944                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7070 0.99   1389  153 0.1028 0.1254      5.3978      5.5287|
|  2:  4.7070 -  3.7557 0.99   1328  152 0.0870 0.1159      5.4515      5.6422|
|  3:  3.7557 -  3.2867 0.99   1304  140 0.1074 0.1481       5.489      5.8532|
|  4:  3.2867 -  2.9888 0.99   1297  149 0.1213 0.1691      5.4547      5.6108|
|  5:  2.9888 -  2.7760 0.99   1293  145 0.1309 0.1704        5.33      5.5477|
|  6:  2.7760 -  2.6133 0.99   1297  138 0.1162 0.1880        5.19      5.4582|
|  7:  2.6133 -  2.4830 0.99   1279  144 0.1278 0.1598      5.1685      5.3531|
|  8:  2.4830 -  2.3754 0.98   1269  142 0.1147 0.1709      5.0642      5.3255|
|  9:  2.3754 -  2.2843 0.98   1257  140 0.1171 0.1707      5.0341      5.2692|
| 10:  2.2843 -  2.2057 1.00   1283  143 0.1114 0.1652      4.9502      5.1978|
| 11:  2.2057 -  2.1369 0.97   1254  137 0.1147 0.1739      4.9453      5.2629|
| 12:  2.1369 -  2.0760 0.98   1249  138 0.1103 0.1713      4.8677      5.2131|
| 13:  2.0760 -  2.0215 0.99   1292  141 0.1093 0.1712      4.7678       5.045|
| 14:  2.0215 -  1.9723 0.66    839   97 0.0974 0.1558      4.6516      4.8638|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7070  1389   153  0.94   9.01   0.98     0.96       7054.88|
|  2:  4.7070 -  3.7557  1328   152  0.95   7.83   1.02     1.01       9059.38|
|  3:  3.7557 -  3.2867  1304   140  0.93  11.37   1.03     1.02      10567.51|
|  4:  3.2867 -  2.9888  1297   149  0.92  13.42   1.01     0.99      10205.89|
|  5:  2.9888 -  2.7760  1293   145  0.90  15.85   1.00     0.97       8394.00|
|  6:  2.7760 -  2.6133  1297   138  0.90  15.58   0.98     0.96       6838.34|
|  7:  2.6133 -  2.4830  1279   144  0.90  15.87   0.99     0.95       6160.64|
|  8:  2.4830 -  2.3754  1269   142  0.91  14.77   1.00     0.98       5169.27|
|  9:  2.3754 -  2.2843  1257   140  0.91  15.06   1.01     0.98       5007.25|
| 10:  2.2843 -  2.2057  1283   143  0.90  15.47   1.00     0.96       4284.59|
| 11:  2.2057 -  2.1369  1254   137  0.90  16.19   1.00     0.97       4401.61|
| 12:  2.1369 -  2.0760  1249   138  0.91  15.03   1.02     1.01       3848.19|
| 13:  2.0760 -  2.0215  1292   141  0.91  15.71   1.01     0.99       3206.46|
| 14:  2.0215 -  1.9723   839    97  0.93  13.54   1.00     0.97       2519.76|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2519.76 max =        10567.51 mean =      6317.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.75 mean =        13.86|
|phase err.(test): min =        0.00 max =           89.75 mean =        13.38|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1567   ksol= 0.33   Bsol= 44.96   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.54,-0.44,0.97,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141911                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1567   ksol= 0.33   Bsol= 44.96   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.54,-0.44,0.97,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141911                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7070 0.99   1389  153 0.1028 0.1254      5.3981      5.5291|
|  2:  4.7070 -  3.7557 0.99   1328  152 0.0870 0.1159      5.4517      5.6423|
|  3:  3.7557 -  3.2867 0.99   1304  140 0.1074 0.1481      5.4891      5.8533|
|  4:  3.2867 -  2.9888 0.99   1297  149 0.1213 0.1691      5.4546      5.6107|
|  5:  2.9888 -  2.7760 0.99   1293  145 0.1309 0.1703      5.3299      5.5476|
|  6:  2.7760 -  2.6133 0.99   1297  138 0.1162 0.1878      5.1898      5.4578|
|  7:  2.6133 -  2.4830 0.99   1279  144 0.1278 0.1599      5.1685      5.3534|
|  8:  2.4830 -  2.3754 0.98   1269  142 0.1147 0.1708      5.0642      5.3253|
|  9:  2.3754 -  2.2843 0.98   1257  140 0.1171 0.1706      5.0341      5.2688|
| 10:  2.2843 -  2.2057 1.00   1283  143 0.1114 0.1654      4.9501      5.1987|
| 11:  2.2057 -  2.1369 0.97   1254  137 0.1147 0.1739      4.9454       5.263|
| 12:  2.1369 -  2.0760 0.98   1249  138 0.1102 0.1713      4.8676      5.2133|
| 13:  2.0760 -  2.0215 0.99   1292  141 0.1094 0.1710      4.7675      5.0444|
| 14:  2.0215 -  1.9723 0.66    839   97 0.0975 0.1556       4.651       4.863|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7070  1389   153  0.94   9.02   0.98     0.96       7060.18|
|  2:  4.7070 -  3.7557  1328   152  0.95   7.83   1.02     1.01       9063.62|
|  3:  3.7557 -  3.2867  1304   140  0.93  11.37   1.03     1.03      10569.43|
|  4:  3.2867 -  2.9888  1297   149  0.92  13.42   1.01     0.99      10203.51|
|  5:  2.9888 -  2.7760  1293   145  0.90  15.84   1.00     0.97       8388.31|
|  6:  2.7760 -  2.6133  1297   138  0.90  15.58   0.98     0.96       6836.64|
|  7:  2.6133 -  2.4830  1279   144  0.90  15.87   0.99     0.96       6160.42|
|  8:  2.4830 -  2.3754  1269   142  0.91  14.77   1.00     0.98       5168.44|
|  9:  2.3754 -  2.2843  1257   140  0.91  15.06   1.01     0.98       5007.83|
| 10:  2.2843 -  2.2057  1283   143  0.90  15.47   1.01     0.97       4284.65|
| 11:  2.2057 -  2.1369  1254   137  0.90  16.19   1.00     0.97       4403.97|
| 12:  2.1369 -  2.0760  1249   138  0.91  15.03   1.02     1.01       3848.53|
| 13:  2.0760 -  2.0215  1292   141  0.91  15.70   1.01     0.99       3204.32|
| 14:  2.0215 -  1.9723   839    97  0.93  13.53   1.00     0.97       2515.02|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2515.02 max =        10569.43 mean =      6317.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.75 mean =        13.86|
|phase err.(test): min =        0.00 max =           89.75 mean =        13.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.658)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.94    88.55   14.83    None  None   None       |
|    all(noH): 2823   0      2.94    88.55   14.83    None  None   None       |
|    Sol.    : 438    0      4.64    80.36   36.92    None  None   None       |
|    Mac.    : 2385   0      2.94    88.55   10.77    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:     2.944 -  11.505: 1734   |   5:    45.749 -  54.310:   84        |
|      1:    11.505 -  20.066:  551   |   6:    54.310 -  62.872:   46        |
|      2:    20.066 -  28.627:  141   |   7:    62.872 -  71.433:   16        |
|      3:    28.627 -  37.188:  130   |   8:    71.433 -  79.994:    4        |
|      4:    37.188 -  45.749:  114   |   9:    79.994 -  88.555:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 296         
Filter by distance & map next to the model:
   mapped sites are within: 0.387 - 3.995
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 296
   mapped sites are within: 0.705 - 3.995

peak=   11.282 closest distance to " CB  VAL A 230 " =    1.464
peak=   10.181 closest distance to " CB  VAL A 296 " =    1.589
peak=    6.836 closest distance to " O   HOH Z 130 " =    1.267
peak=    6.384 closest distance to " CG  LEU A   5 " =    1.205
peak=    6.157 closest distance to " NE2 GLN A  11 " =    1.223
peak=    5.972 closest distance to " CD2 LEU A   5 " =    1.252
peak=    5.755 closest distance to " O   HOH Z   9 " =    1.529
peak=    5.595 closest distance to " CG  PRO A  54 " =    1.357
peak=    5.586 closest distance to " O   HOH Z 142 " =    1.966
peak=    5.360 closest distance to " CG  LEU A 228 " =    1.169
peak=    5.308 closest distance to " O   HOH Z 427 " =    2.531
peak=    5.192 closest distance to " NH2 ARG A  56 " =    2.051
peak=    5.143 closest distance to " CB  PRO A  54 " =    1.022
peak=    4.844 closest distance to " O   HOH Z 232 " =    2.377
peak=    4.773 closest distance to " CB  ARG A 275 " =    0.927
peak=    4.699 closest distance to " CB  GLN A 223 " =    1.480
peak=    4.639 closest distance to " CB  VAL A 230 " =    1.138
peak=    4.636 closest distance to " CG  PRO A 243 " =    1.147
peak=    4.618 closest distance to " O   HOH Z 126 " =    2.114
peak=    4.602 closest distance to " CB  SER A  63 " =    1.240
peak=    4.575 closest distance to " CB  GLN A 183 " =    1.194
peak=    4.568 closest distance to " ND2 ASN A 187 " =    1.610
peak=    4.544 closest distance to " CG  PRO A 213 " =    1.232
peak=    4.534 closest distance to " CG  PRO A 198 " =    1.257
peak=    4.492 closest distance to " O   HOH Z 287 " =    2.034
peak=    4.477 closest distance to " O   HOH Z  78 " =    1.651
peak=    4.469 closest distance to " O   HOH Z 209 " =    2.265
peak=    4.411 closest distance to " CB  SER A   3 " =    1.358
peak=    4.378 closest distance to " O   HOH Z 272 " =    1.798
peak=    4.349 closest distance to " O   HOH Z 346 " =    1.632
peak=    4.296 closest distance to " C   PRO A 198 " =    1.520
peak=    4.278 closest distance to " CB  ASN A 148 " =    1.286
peak=    4.232 closest distance to " O   HOH Z   2 " =    1.612
peak=    4.217 closest distance to " CB BVAL A  41 " =    1.314
peak=    4.212 closest distance to " O   HOH Z 380 " =    1.808
peak=    4.200 closest distance to " CD2 LEU A 228 " =    1.105
peak=    4.176 closest distance to " O   HOH Z 298 " =    1.748
peak=    4.162 closest distance to " O   SER A  87 " =    2.329
peak=    4.158 closest distance to " CB  GLU A 152 " =    1.168
peak=    4.145 closest distance to " CB  ARG A  79 " =    1.353
peak=    4.118 closest distance to " O   HOH Z 193 " =    1.740
peak=    4.103 closest distance to " CB  TRP A 266 " =    1.018
peak=    4.087 closest distance to " O   HOH Z 425 " =    1.412
peak=    4.071 closest distance to " CB  VAL A 265 " =    1.294
peak=    4.062 closest distance to " CG2 VAL A 257 " =    0.858
peak=    4.049 closest distance to " O   HOH Z 316 " =    3.051
peak=    4.034 closest distance to " N   PHE A 130 " =    1.254
peak=    4.018 closest distance to " O   HOH Z 124 " =    1.379
peak=    4.005 closest distance to " CB  TRP A 179 " =    1.347
peak=    3.996 closest distance to " O   HOH Z 389 " =    1.799
peak=    3.990 closest distance to " CB  GLU A 128 " =    1.016
peak=    3.988 closest distance to " O   HOH Z 234 " =    3.583
peak=    3.967 closest distance to " CG1BVAL A  72 " =    1.525
peak=    3.966 closest distance to " O   HOH Z  55 " =    2.208
peak=    3.964 closest distance to " CB  VAL A 202 " =    1.647
peak=    3.957 closest distance to " O   HOH Z  61 " =    1.545
peak=    3.952 closest distance to " O   HOH Z 203 " =    1.663
peak=    3.952 closest distance to " O   HOH Z 422 " =    2.573
peak=    3.948 closest distance to " CB  ASN A  39 " =    0.915
peak=    3.941 closest distance to " O   HOH Z 369 " =    2.243
peak=    3.940 closest distance to " CG  LEU A 167 " =    1.176
peak=    3.937 closest distance to " O   HOH Z  78 " =    2.086
peak=    3.920 closest distance to " OG BSER A 164 " =    2.137
peak=    3.919 closest distance to " O   HOH Z  30 " =    1.621
peak=    3.912 closest distance to " O   HOH Z 303 " =    2.143
peak=    3.898 closest distance to " O   HOH Z 371 " =    2.811
peak=    3.890 closest distance to " O   HOH Z 424 " =    1.661
peak=    3.870 closest distance to " CB  ARG A 139 " =    0.968
peak=    3.868 closest distance to " CB  SER A 216 " =    0.770
peak=    3.863 closest distance to " O   HOH Z 144 " =    2.301
peak=    3.862 closest distance to " O   HOH Z 130 " =    2.585
peak=    3.832 closest distance to " OD1 ASN A  69 " =    2.534
peak=    3.827 closest distance to " O   HOH Z  43 " =    2.113
peak=    3.820 closest distance to " NH2AARG A 190 " =    1.788
peak=    3.819 closest distance to " CB  ASN A 187 " =    1.135
peak=    3.816 closest distance to " O   HOH Z 189 " =    2.798
peak=    3.814 closest distance to " O   HOH Z 368 " =    2.000
peak=    3.813 closest distance to " O   HOH Z 425 " =    1.970
peak=    3.807 closest distance to " CA  TYR A  30 " =    0.976
peak=    3.804 closest distance to " O   HOH Z   1 " =    1.751
peak=    3.799 closest distance to " O   HOH Z  63 " =    1.279
peak=    3.797 closest distance to " O   HOH Z  10 " =    1.782
peak=    3.786 closest distance to " O   HOH Z 411 " =    3.692
peak=    3.776 closest distance to " O   HOH Z 263 " =    1.690
peak=    3.773 closest distance to " O   HOH Z 213 " =    2.145
peak=    3.759 closest distance to " CA  ASN A 215 " =    1.068
peak=    3.751 closest distance to " O   HOH Z 419 " =    2.033
peak=    3.745 closest distance to " O   HOH Z 371 " =    1.691
peak=    3.743 closest distance to " O   HOH Z 250 " =    1.416
peak=    3.740 closest distance to " CB  ASN A 142 " =    0.997
peak=    3.725 closest distance to " CB  SER A  26 " =    1.711
peak=    3.713 closest distance to " O   HOH Z 403 " =    1.633
peak=    3.704 closest distance to " O   HOH Z   3 " =    2.022
peak=    3.696 closest distance to " O   HOH Z 222 " =    2.397
peak=    3.688 closest distance to " O   HOH Z 273 " =    2.889
peak=    3.687 closest distance to " O   HOH Z   9 " =    1.776
peak=    3.675 closest distance to " CB  THR A 157 " =    1.091
peak=    3.667 closest distance to " O   HOH Z 193 " =    1.691
peak=    3.666 closest distance to " CB  ARG A  79 " =    0.874
peak=    3.659 closest distance to " O   HOH Z 214 " =    2.174
peak=    3.658 closest distance to " O   HOH Z  44 " =    1.704
peak=    3.653 closest distance to " CB  GLU A 277 " =    3.496
peak=    3.653 closest distance to " O   HOH Z 251 " =    1.740
peak=    3.646 closest distance to " CA  ALA A 299 " =    0.927
peak=    3.645 closest distance to " CZ  PHE A 218 " =    1.093
peak=    3.642 closest distance to " NH1AARG A 145 " =    1.141
peak=    3.642 closest distance to " N   ASN A  39 " =    1.132
peak=    3.638 closest distance to " O   HOH Z  97 " =    2.077
peak=    3.632 closest distance to " N   ARG A 156 " =    1.302
peak=    3.632 closest distance to " CA  PHE A 283 " =    1.298
peak=    3.628 closest distance to " O   HOH Z 145 " =    1.941
peak=    3.625 closest distance to " O   HOH Z 145 " =    3.622
peak=    3.617 closest distance to " CG  GLN A  88 " =    1.104
peak=    3.614 closest distance to " O   HOH Z 193 " =    1.943
peak=    3.608 closest distance to " O   HOH Z 423 " =    1.429
peak=    3.607 closest distance to " NZ  LYS A 117 " =    3.109
peak=    3.600 closest distance to " O   HOH Z  93 " =    2.454
peak=    3.587 closest distance to " O   HOH Z 405 " =    1.316
peak=    3.577 closest distance to " O   HOH Z 248 " =    1.552
peak=    3.576 closest distance to " CA  ASP A 162 " =    1.002
peak=    3.574 closest distance to " O   HOH Z 368 " =    3.581
peak=    3.574 closest distance to " O   HOH Z  61 " =    1.514
peak=    3.573 closest distance to " CA  LYS A 117 " =    1.213
peak=    3.567 closest distance to " O   HOH Z 128 " =    2.147
peak=    3.562 closest distance to " CA  THR A 264 " =    0.751
peak=    3.554 closest distance to " CG1 ILE A  33 " =    1.342
peak=    3.552 closest distance to " O   HOH Z 423 " =    1.663
peak=    3.551 closest distance to " O   HOH Z 424 " =    2.323
peak=    3.540 closest distance to " CB  GLN A  88 " =    1.239
peak=    3.527 closest distance to " O   HOH Z 126 " =    1.458
peak=    3.524 closest distance to " CB  ARG A 190 " =    1.639
peak=    3.524 closest distance to " O   HOH Z 366 " =    2.848
peak=    3.520 closest distance to " O   HOH Z  68 " =    2.171
peak=    3.517 closest distance to " NH1 ARG A 138 " =    1.102
peak=    3.511 closest distance to " O   HOH Z 146 " =    1.563
peak=    3.502 closest distance to " O   HOH Z 353 " =    2.456
peak=    3.501 closest distance to " NH2BARG A 145 " =    2.042
peak=    3.499 closest distance to " CA  SER A  87 " =    0.966
peak=    3.492 closest distance to " CD1 LEU A 300 " =    1.256
peak=    3.490 closest distance to " O   HOH Z 327 " =    1.566
peak=    3.488 closest distance to " OG  SER A  62 " =    2.785
peak=    3.485 closest distance to " CG BARG A 102 " =    1.842
peak=    3.484 closest distance to " O   HOH Z 359 " =    1.348
peak=    3.477 closest distance to " O   HOH Z  88 " =    2.757
peak=    3.471 closest distance to " O   HOH Z 132 " =    2.430
peak=    3.471 closest distance to " CG  MET A 185 " =    1.191
peak=    3.468 closest distance to " CG1 ILE A  49 " =    1.411
peak=    3.461 closest distance to " CG1 ILE A 120 " =    1.130
peak=    3.459 closest distance to " CB  ASP A 124 " =    0.710
peak=    3.458 closest distance to " CB  SER A  62 " =    1.260
peak=    3.454 closest distance to " O   HOH Z   1 " =    1.840
peak=    3.444 closest distance to " CB  GLN A 278 " =    0.896
peak=    3.439 closest distance to " O   HOH Z 305 " =    3.425
peak=    3.437 closest distance to " O   HOH Z 329 " =    3.877
peak=    3.434 closest distance to " CA  ALA A  51 " =    0.967
peak=    3.433 closest distance to " O   HOH Z 435 " =    2.076
peak=    3.431 closest distance to " CB  LYS A 117 " =    1.216
peak=    3.428 closest distance to " O   HOH Z 197 " =    3.198
peak=    3.426 closest distance to " CB  ALA A 291 " =    1.346
peak=    3.423 closest distance to " CB  ALA A 248 " =    1.351
peak=    3.421 closest distance to " OG  SER A  62 " =    2.914
peak=    3.420 closest distance to " O   HOH Z  40 " =    2.023
peak=    3.417 closest distance to " O   HOH Z 344 " =    2.943
peak=    3.416 closest distance to " CB  LEU A 143 " =    1.089
peak=    3.413 closest distance to " O   HOH Z 158 " =    3.235
peak=    3.412 closest distance to " CG2 THR A 221 " =    1.229
peak=    3.411 closest distance to " O   HOH Z  21 " =    1.711
peak=    3.394 closest distance to " CA  ARG A  36 " =    1.008
peak=    3.393 closest distance to " ND1 HIS A  86 " =    1.809
peak=    3.388 closest distance to " O   HOH Z 128 " =    1.898
peak=    3.376 closest distance to " CA  ALA A  21 " =    1.188
peak=    3.375 closest distance to " CA  ALA A 233 " =    0.957
peak=    3.373 closest distance to " CD  LYS A 166 " =    1.327
peak=    3.369 closest distance to " OD2 ASP A 286 " =    2.732
peak=    3.364 closest distance to " OG BSER A  99 " =    2.201
peak=    3.358 closest distance to " O   HOH Z 130 " =    1.900
peak=    3.350 closest distance to " CD1 ILE A 106 " =    1.048
peak=    3.348 closest distance to " CB  HIS A 108 " =    0.839
peak=    3.343 closest distance to " N   GLN A 278 " =    1.093
peak=    3.341 closest distance to " CA  ALA A 158 " =    1.208
peak=    3.340 closest distance to " O   HOH Z 423 " =    2.334
peak=    3.335 closest distance to " CD1 ILE A  33 " =    1.653
peak=    3.335 closest distance to " CD BLYS A 290 " =    1.155
peak=    3.330 closest distance to " O   HOH Z 128 " =    2.107
peak=    3.327 closest distance to " OE2 GLU A  53 " =    1.886
peak=    3.324 closest distance to " O   HOH Z 402 " =    1.375
peak=    3.322 closest distance to " CA  SER A 146 " =    1.776
peak=    3.319 closest distance to " O  BHOH Z 338 " =    2.468
peak=    3.318 closest distance to " ND2 ASN A 249 " =    0.832
peak=    3.318 closest distance to " CD2 TYR A 186 " =    1.025
peak=    3.314 closest distance to " O   HOH Z  40 " =    1.984
peak=    3.314 closest distance to " N   SER A 135 " =    1.205
peak=    3.312 closest distance to " O   HOH Z 345 " =    3.346
peak=    3.312 closest distance to " NZ  LYS A  76 " =    1.582
peak=    3.310 closest distance to " CG AARG A 275 " =    1.122
peak=    3.308 closest distance to " CB  VAL A 296 " =    1.045
peak=    3.306 closest distance to " CB  ASN A 224 " =    1.049
peak=    3.299 closest distance to " O   HOH Z 426 " =    1.850
peak=    3.296 closest distance to " CE3 TRP A 150 " =    0.983
peak=    3.294 closest distance to " CA  VAL A  41 " =    0.766
peak=    3.294 closest distance to " O   HOH Z 147 " =    1.687
peak=    3.290 closest distance to " CA  ARG A 102 " =    1.105
peak=    3.290 closest distance to " O   HOH Z   6 " =    2.090
peak=    3.287 closest distance to " NH1BARG A 145 " =    1.316
peak=    3.287 closest distance to " CB  ASP A 140 " =    0.828
peak=    3.281 closest distance to " NH2BARG A 190 " =    1.594
peak=    3.281 closest distance to " O   HOH Z 180 " =    2.105
peak=    3.280 closest distance to " O   HOH Z 322 " =    1.945
peak=    3.279 closest distance to " CB  ASN A 110 " =    1.014
peak=    3.279 closest distance to " CG1 ILE A 151 " =    1.125
peak=    3.276 closest distance to " CD1 LEU A 228 " =    1.977
peak=    3.273 closest distance to " O   HOH Z  59 " =    1.722
peak=    3.273 closest distance to " O   HOH Z  88 " =    3.156
peak=    3.271 closest distance to " O   HOH Z 245 " =    1.349
peak=    3.266 closest distance to " O   HOH Z 437 " =    2.220
peak=    3.258 closest distance to " CB  PRO A  90 " =    1.171
peak=    3.253 closest distance to " CE1 TYR A 186 " =    1.300
peak=    3.249 closest distance to " O   HOH Z 284 " =    3.010
peak=    3.246 closest distance to " NE2 GLN A 223 " =    1.620
peak=    3.244 closest distance to " O   HOH Z 227 " =    1.775
peak=    3.243 closest distance to " CD  ARG A  14 " =    1.364
peak=    3.241 closest distance to " NE  ARG A  56 " =    3.455
peak=    3.239 closest distance to " CB  ASN A 215 " =    1.143
peak=    3.239 closest distance to " OG ASER A  99 " =    1.506
peak=    3.232 closest distance to " NZ  LYS A  48 " =    1.168
peak=    3.228 closest distance to " O   HOH Z 412 " =    1.853
peak=    3.224 closest distance to " CB  TRP A 150 " =    1.468
peak=    3.220 closest distance to " CG  GLN A  77 " =    2.331
peak=    3.220 closest distance to " OE2 GLU A   2 " =    1.830
peak=    3.220 closest distance to " CB  ALA A  34 " =    1.040
peak=    3.219 closest distance to " CZ3 TRP A 266 " =    1.130
peak=    3.216 closest distance to " O   HOH Z 383 " =    1.809
peak=    3.211 closest distance to " CB  SER A 212 " =    1.230
peak=    3.209 closest distance to " O   HOH Z 133 " =    2.374
peak=    3.206 closest distance to " N   ASP A 162 " =    1.207
peak=    3.206 closest distance to " CA  ALA A  84 " =    1.427
peak=    3.205 closest distance to " NH2 ARG A 156 " =    1.044
peak=    3.203 closest distance to " CD1 LEU A 261 " =    1.225
peak=    3.202 closest distance to " O   HOH Z 257 " =    2.272
peak=    3.195 closest distance to " CG1 VAL A 153 " =    0.896
peak=    3.195 closest distance to " O   HOH Z 438 " =    2.391
peak=    3.194 closest distance to " N   ALA A   1 " =    2.140
peak=    3.193 closest distance to " CG  GLN A 278 " =    1.276
peak=    3.191 closest distance to " O   HOH Z 238 " =    3.735
peak=    3.185 closest distance to " CD2 TYR A  30 " =    0.867
peak=    3.180 closest distance to " CG  GLN A  89 " =    1.440
peak=    3.180 closest distance to " CB  ALA A   9 " =    1.525
peak=    3.177 closest distance to " CB  MET A  40 " =    0.811
peak=    3.177 closest distance to " CG2 ILE A 106 " =    0.861
peak=    3.173 closest distance to " O   HOH Z 291 " =    1.512
peak=    3.171 closest distance to " CB  VAL A 250 " =    1.066
peak=    3.170 closest distance to " O   HOH Z  89 " =    2.044
peak=    3.169 closest distance to " O   HOH Z 438 " =    3.184
peak=    3.169 closest distance to " CG  LEU A 281 " =    1.047
peak=    3.168 closest distance to " O   HOH Z  78 " =    2.308
peak=    3.163 closest distance to " CA  MET A 105 " =    0.924
peak=    3.159 closest distance to " O   HOH Z 139 " =    2.738
peak=    3.158 closest distance to " N   ALA A 233 " =    0.988
peak=    3.158 closest distance to " CA  GLY A 267 " =    0.988
peak=    3.158 closest distance to " O   LEU A 228 " =    1.965
peak=    3.152 closest distance to " CD2 LEU A 255 " =    1.506
peak=    3.151 closest distance to " CA  LEU A 101 " =    1.627
peak=    3.143 closest distance to " N   SER A  97 " =    0.800
peak=    3.143 closest distance to " CG2 ILE A 120 " =    1.146
peak=    3.139 closest distance to " O   HOH Z 175 " =    2.096
peak=    3.138 closest distance to " O   HOH Z  59 " =    2.079
peak=    3.134 closest distance to " CG2 ILE A  20 " =    1.556
peak=    3.125 closest distance to " CB  ILE A 120 " =    1.267
peak=    3.125 closest distance to " O   HOH Z  85 " =    1.355
peak=    3.123 closest distance to " CB  LEU A 300 " =    0.868
peak=    3.121 closest distance to " CA  ARG A 195 " =    1.171
peak=    3.121 closest distance to " O   HOH Z 124 " =    1.924
peak=    3.120 closest distance to " CB  ALA A 114 " =    1.431
peak=    3.118 closest distance to " N   ASN A 127 " =    1.359
peak=    3.112 closest distance to " O   PRO A  90 " =    1.626
peak=    3.111 closest distance to " CD2 TRP A 179 " =    1.364
peak=    3.109 closest distance to " O   HOH Z 124 " =    1.618
peak=    3.103 closest distance to " N   VAL A 126 " =    1.245
peak=    3.101 closest distance to " O   PHE A 192 " =    1.415
peak=    3.095 closest distance to " CA  LYS A 290 " =    1.252
peak=    3.094 closest distance to " CA  ILE A 106 " =    0.705
peak=    3.092 closest distance to " O   HOH Z 272 " =    2.071
peak=    3.089 closest distance to " CB  GLN A 205 " =    1.194
peak=    3.089 closest distance to " O   HOH Z 145 " =    1.505
peak=    3.088 closest distance to " O   HOH Z 132 " =    1.371
peak=    3.071 closest distance to " CB  THR A  52 " =    1.177
peak=    3.069 closest distance to " CB  ALA A 114 " =    1.203
peak=    3.068 closest distance to " CA  ASP A 140 " =    1.278
peak=    3.058 closest distance to " CB  ILE A  20 " =    1.487
peak=    3.054 closest distance to " O   HOH Z 359 " =    3.995
peak=    3.053 closest distance to " CB  ALA A 180 " =    1.270
peak=    3.005 closest distance to " O   HOH Z 113 " =    1.952

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.743 - 5.425
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.743 - 5.425

peak=   -5.280 closest distance to " CG2 VAL A 230 " =    0.743
peak=   -4.447 closest distance to " CD  ARG A 156 " =    2.025
peak=   -4.436 closest distance to " CD  ARG A  14 " =    3.274
peak=   -4.327 closest distance to " CB  PRO A 243 " =    2.631
peak=   -4.315 closest distance to " CD1 LEU A 255 " =    2.833
peak=   -4.314 closest distance to " OG BSER A 134 " =    1.234
peak=   -4.218 closest distance to " O   HOH Z 266 " =    4.868
peak=   -4.115 closest distance to " O   HOH Z 351 " =    1.482
peak=   -4.059 closest distance to " C   HIS A 108 " =    1.197
peak=   -4.011 closest distance to " CG  GLN A  58 " =    1.045
peak=   -4.006 closest distance to " O   HOH Z 290 " =    1.113
peak=   -3.992 closest distance to " CB  ALA A 248 " =    2.047
peak=   -3.967 closest distance to " O   VAL A  67 " =    2.520
peak=   -3.953 closest distance to " O   HOH Z  65 " =    1.021
peak=   -3.946 closest distance to " O   HOH Z 185 " =    2.121
peak=   -3.917 closest distance to " NH2 ARG A  79 " =    1.924
peak=   -3.908 closest distance to " CB  PHE A 192 " =    1.787
peak=   -3.872 closest distance to " OG  SER A   3 " =    1.368
peak=   -3.867 closest distance to " O   HOH Z 114 " =    2.951
peak=   -3.864 closest distance to " O   PRO A 198 " =    1.215
peak=   -3.831 closest distance to " O   HOH Z 140 " =    1.444
peak=   -3.819 closest distance to " O   HOH Z  43 " =    1.874
peak=   -3.807 closest distance to " N   THR A 157 " =    1.398
peak=   -3.796 closest distance to " CG  ASP A 231 " =    0.767
peak=   -3.792 closest distance to " CG2 VAL A 296 " =    1.993
peak=   -3.787 closest distance to " CZ3 TRP A 179 " =    1.237
peak=   -3.785 closest distance to " O   HOH Z 191 " =    5.425
peak=   -3.762 closest distance to " CZ  TYR A 169 " =    1.718
peak=   -3.750 closest distance to " N   GLN A  58 " =    1.820
peak=   -3.744 closest distance to " CE  MET A 105 " =    2.466
peak=   -3.743 closest distance to " O   HOH Z  11 " =    1.864
peak=   -3.735 closest distance to " CE2 PHE A 218 " =    2.475
peak=   -3.712 closest distance to " O   ARG A 145 " =    1.563
peak=   -3.704 closest distance to " CG  GLN A 223 " =    2.046
peak=   -3.701 closest distance to " CA  VAL A  67 " =    2.774
peak=   -3.699 closest distance to " O   HOH Z 359 " =    1.670
peak=   -3.697 closest distance to " N   ALA A  43 " =    2.567
peak=   -3.693 closest distance to " O   HOH Z 389 " =    1.958
peak=   -3.678 closest distance to " O   PRO A 163 " =    2.047
peak=   -3.653 closest distance to " O   HOH Z 134 " =    3.050
peak=   -3.653 closest distance to " ND2 ASN A  45 " =    1.100
peak=   -3.646 closest distance to " C   ILE A 239 " =    2.115
peak=   -3.646 closest distance to " O   HOH Z  52 " =    1.448
peak=   -3.629 closest distance to " O   HOH Z 407 " =    3.117
peak=   -3.621 closest distance to " O   HOH Z 231 " =    1.922
peak=   -3.616 closest distance to " CB  PRO A 163 " =    2.442
peak=   -3.603 closest distance to " CD2 LEU A 237 " =    2.751
peak=   -3.601 closest distance to " CB  ALA A 244 " =    2.096
peak=   -3.584 closest distance to " CZ  PHE A  59 " =    1.400
peak=   -3.583 closest distance to " O   ALA A 161 " =    1.646
peak=   -3.583 closest distance to " CB  ALA A  43 " =    2.433
peak=   -3.580 closest distance to " O   HOH Z 389 " =    1.441
peak=   -3.577 closest distance to " ND2 ASN A 249 " =    2.409
peak=   -3.576 closest distance to " C   MET A 188 " =    1.429
peak=   -3.576 closest distance to " N   HIS A 115 " =    2.163
peak=   -3.570 closest distance to " CG  TRP A 266 " =    1.929
peak=   -3.569 closest distance to " CZ2 TRP A 274 " =    0.898
peak=   -3.564 closest distance to " C   ASP A 231 " =    2.555
peak=   -3.563 closest distance to " CB  ASN A  39 " =    2.229
peak=   -3.551 closest distance to " O   HOH Z 166 " =    1.567
peak=   -3.546 closest distance to " O   HOH Z 359 " =    3.398
peak=   -3.544 closest distance to " OD2 ASP A 191 " =    1.262
peak=   -3.537 closest distance to " CA  GLY A 203 " =    2.334
peak=   -3.532 closest distance to " N   ALA A 226 " =    2.039
peak=   -3.521 closest distance to " OG  SER A  62 " =    4.517
peak=   -3.516 closest distance to " CA  GLY A 133 " =    1.985
peak=   -3.513 closest distance to " C   LEU A 222 " =    0.774
peak=   -3.510 closest distance to " O   HOH Z 377 " =    0.939
peak=   -3.505 closest distance to " CA  GLY A  98 " =    1.830
peak=   -3.502 closest distance to " O   HOH Z 394 " =    1.449
peak=   -3.499 closest distance to " CB  ASP A 132 " =    2.324
peak=   -3.499 closest distance to " CE BMET A  47 " =    1.588
peak=   -3.499 closest distance to " O   HOH Z 211 " =    1.498
peak=   -3.493 closest distance to " ND2 ASN A 187 " =    1.462
peak=   -3.479 closest distance to " CG1 VAL A 112 " =    2.664
peak=   -3.474 closest distance to " CA  GLY A 241 " =    2.219
peak=   -3.463 closest distance to " O   SER A  22 " =    2.265
peak=   -3.457 closest distance to " O   HOH Z 423 " =    2.310
peak=   -3.452 closest distance to " CD  LYS A 289 " =    2.495
peak=   -3.452 closest distance to " CE2 TYR A  30 " =    2.837
peak=   -3.444 closest distance to " CB  ALA A 161 " =    2.508
peak=   -3.443 closest distance to " OG  SER A  87 " =    1.382
peak=   -3.441 closest distance to " O   SER A 135 " =    1.442
peak=   -3.439 closest distance to " CD1 LEU A 228 " =    2.120
peak=   -3.437 closest distance to " O   HOH Z 313 " =    1.656
peak=   -3.430 closest distance to " ND2 ASN A 252 " =    1.772
peak=   -3.427 closest distance to " O   HOH Z 198 " =    2.159
peak=   -3.420 closest distance to " OG ASER A 216 " =    1.065
peak=   -3.419 closest distance to " CG  PHE A 283 " =    2.614
peak=   -3.417 closest distance to " CG1 VAL A 112 " =    2.766
peak=   -3.415 closest distance to " CB  TYR A  15 " =    2.135
peak=   -3.415 closest distance to " CE  LYS A  76 " =    2.778
peak=   -3.414 closest distance to " CD1 PHE A  59 " =    1.983
peak=   -3.411 closest distance to " CG1 VAL A 230 " =    1.851
peak=   -3.408 closest distance to " ND2 ASN A  45 " =    1.755
peak=   -3.405 closest distance to " CD2 TYR A 293 " =    1.979
peak=   -3.400 closest distance to " NE2 GLN A 278 " =    1.886
peak=   -3.393 closest distance to " O   LEU A 101 " =    2.750
peak=   -3.384 closest distance to " OD1 ASN A 301 " =    1.986
peak=   -3.382 closest distance to " CB  ALA A 248 " =    2.389
peak=   -3.381 closest distance to " O   HOH Z 102 " =    1.610
peak=   -3.377 closest distance to " O   HOH Z  51 " =    1.058
peak=   -3.371 closest distance to " O   HOH Z 103 " =    1.750
peak=   -3.363 closest distance to " O   HOH Z 134 " =    3.564
peak=   -3.363 closest distance to " O   HOH Z 345 " =    2.065
peak=   -3.360 closest distance to " O   PRO A 198 " =    1.329
peak=   -3.358 closest distance to " CB  ALA A 291 " =    2.426
peak=   -3.355 closest distance to " O   VAL A 189 " =    2.573
peak=   -3.346 closest distance to " O   HOH Z 131 " =    4.024
peak=   -3.339 closest distance to " OG  SER A  63 " =    1.148
peak=   -3.339 closest distance to " O   HOH Z 118 " =    1.703
peak=   -3.335 closest distance to " O   HOH Z  13 " =    1.743
peak=   -3.335 closest distance to " O   HOH Z 369 " =    2.137
peak=   -3.329 closest distance to " CB  ASN A  69 " =    1.218
peak=   -3.326 closest distance to " N   SER A 212 " =    1.936
peak=   -3.326 closest distance to " OE1 GLN A  88 " =    1.180
peak=   -3.325 closest distance to " NH2AARG A 275 " =    5.152
peak=   -3.316 closest distance to " OG  SER A 206 " =    1.732
peak=   -3.316 closest distance to " N   PHE A  59 " =    2.086
peak=   -3.315 closest distance to " O   HOH Z 417 " =    2.555
peak=   -3.312 closest distance to " CG2 VAL A 202 " =    2.633
peak=   -3.312 closest distance to " CG1 VAL A 268 " =    2.823
peak=   -3.310 closest distance to " O   PRO A 243 " =    2.572
peak=   -3.307 closest distance to " O   HOH Z   9 " =    1.563
peak=   -3.306 closest distance to " CA  TRP A  70 " =    2.471
peak=   -3.305 closest distance to " O   HOH Z 339 " =    1.805
peak=   -3.304 closest distance to " O   HOH Z  56 " =    2.321
peak=   -3.299 closest distance to " OG1 THR A 178 " =    1.188
peak=   -3.286 closest distance to " O   HOH Z 111 " =    4.330
peak=   -3.282 closest distance to " CD1 LEU A 101 " =    2.280
peak=   -3.276 closest distance to " O   HOH Z 317 " =    1.434
peak=   -3.266 closest distance to " C   GLY A 229 " =    1.258
peak=   -3.266 closest distance to " O   SER A 271 " =    2.145
peak=   -3.264 closest distance to " CE3 TRP A 150 " =    2.002
peak=   -3.263 closest distance to " N   VAL A  72 " =    1.608
peak=   -3.258 closest distance to " O   HOH Z 165 " =    2.148
peak=   -3.258 closest distance to " O   GLN A 240 " =    2.021
peak=   -3.257 closest distance to " CG  GLU A 152 " =    1.482
peak=   -3.256 closest distance to " O   HOH Z  60 " =    2.119
peak=   -3.254 closest distance to " N   ALA A 248 " =    1.549
peak=   -3.251 closest distance to " O   GLY A  80 " =    2.477
peak=   -3.251 closest distance to " OD1 ASN A 148 " =    1.501
peak=   -3.244 closest distance to " O   HOH Z 385 " =    2.073
peak=   -3.239 closest distance to " O   HOH Z  90 " =    2.728
peak=   -3.237 closest distance to " O   HOH Z 427 " =    1.666
peak=   -3.234 closest distance to " O   ALA A 292 " =    1.995
peak=   -3.231 closest distance to " CB  ASN A 301 " =    2.033
peak=   -3.230 closest distance to " CD1 TYR A 247 " =    2.738
peak=   -3.227 closest distance to " O   HOH Z  63 " =    1.824
peak=   -3.224 closest distance to " O   HOH Z 210 " =    0.989
peak=   -3.224 closest distance to " O   HOH Z 243 " =    1.828
peak=   -3.224 closest distance to " OD2 ASP A 171 " =    2.207
peak=   -3.223 closest distance to " CB  ALA A   1 " =    2.791
peak=   -3.220 closest distance to " C   LEU A 143 " =    1.081
peak=   -3.216 closest distance to " C   ASN A 285 " =    2.186
peak=   -3.214 closest distance to " N   MET A 188 " =    1.770
peak=   -3.213 closest distance to " CG  GLN A 278 " =    2.045
peak=   -3.211 closest distance to " O   HOH Z 149 " =    2.175
peak=   -3.201 closest distance to " CA  GLY A  57 " =    2.151
peak=   -3.199 closest distance to " CG2 THR A 178 " =    2.190
peak=   -3.198 closest distance to " NH1 ARG A  36 " =    2.018
peak=   -3.197 closest distance to " O   HOH Z 423 " =    1.246
peak=   -3.193 closest distance to " CA  ASN A 127 " =    1.321
peak=   -3.191 closest distance to " CB  VAL A 230 " =    1.011
peak=   -3.187 closest distance to " CD2 LEU A 237 " =    2.738
peak=   -3.187 closest distance to " O   HOH Z 377 " =    1.449
peak=   -3.186 closest distance to " CB  PRO A  90 " =    1.606
peak=   -3.184 closest distance to " CG  LEU A 228 " =    0.989
peak=   -3.182 closest distance to " CD2 LEU A   5 " =    1.121
peak=   -3.180 closest distance to " CB  ALA A   7 " =    2.110
peak=   -3.178 closest distance to " CG  PRO A 163 " =    2.648
peak=   -3.176 closest distance to " O   HOH Z 166 " =    2.074
peak=   -3.176 closest distance to " CA  ASP A 298 " =    1.083
peak=   -3.170 closest distance to " O   HOH Z 281 " =    2.742
peak=   -3.169 closest distance to " CD  GLU A 277 " =    1.150
peak=   -3.168 closest distance to " CE  LYS A 166 " =    1.236
peak=   -3.165 closest distance to " CG1 VAL A 197 " =    2.256
peak=   -3.163 closest distance to " CG2 THR A  42 " =    1.835
peak=   -3.158 closest distance to " O   HOH Z 298 " =    1.212
peak=   -3.157 closest distance to " CD  PRO A 213 " =    1.997
peak=   -3.157 closest distance to " C   ALA A 158 " =    1.383
peak=   -3.144 closest distance to " OE2 GLU A 152 " =    1.103
peak=   -3.139 closest distance to " CZ  ARG A 259 " =    0.894
peak=   -3.136 closest distance to " O   ALA A  51 " =    1.351
peak=   -3.133 closest distance to " O   HOH Z 250 " =    1.503
peak=   -3.131 closest distance to " CB  ALA A 291 " =    2.169
peak=   -3.129 closest distance to " CD  ARG A 139 " =    1.565
peak=   -3.126 closest distance to " OD2 ASP A  27 " =    1.569
peak=   -3.121 closest distance to " O   HOH Z 313 " =    1.092
peak=   -3.111 closest distance to " O   HOH Z 390 " =    2.393
peak=   -3.110 closest distance to " CH2 TRP A 179 " =    1.938
peak=   -3.110 closest distance to " C   LYS A  76 " =    1.556
peak=   -3.107 closest distance to " OG  SER A 271 " =    1.153
peak=   -3.102 closest distance to " OG  SER A  97 " =    2.205
peak=   -3.092 closest distance to " O   HOH Z 311 " =    3.743
peak=   -3.089 closest distance to " O   HOH Z  28 " =    2.337
peak=   -3.082 closest distance to " CG  ARG A 269 " =    2.344
peak=   -3.078 closest distance to " O   HOH Z 111 " =    2.363
peak=   -3.078 closest distance to " O   HOH Z 216 " =    1.699
peak=   -3.077 closest distance to " O   HOH Z 193 " =    1.990
peak=   -3.072 closest distance to " NH1AARG A 275 " =    1.882
peak=   -3.035 closest distance to " O   HOH Z 189 " =    1.913
peak=   -3.029 closest distance to " CD2 PHE A  61 " =    2.037
peak=   -3.022 closest distance to " O   HOH Z 357 " =    2.096

================= 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    :  0.4532 0.4446   6.255496e+00   6.236370e+00
   1_bss:  0.4452 0.4310   6.249284e+00   6.221540e+00
   1_xyz:  0.3542 0.3737   6.099914e+00   6.128720e+00
   1_adp:  0.3008 0.3436   5.982831e+00   6.076271e+00
   1_occ:  0.3002 0.3427   5.981779e+00   6.076928e+00
   2_bss:  0.2950 0.3362   5.979379e+00   6.070811e+00
   2_xyz:  0.2099 0.2608   5.680202e+00   5.840146e+00
   2_adp:  0.1860 0.2393   5.578942e+00   5.764468e+00
   2_occ:  0.1858 0.2387   5.577965e+00   5.763611e+00
   3_bss:  0.1842 0.2360   5.573924e+00   5.757977e+00
   3_xyz:  0.1377 0.1871   5.318843e+00   5.543040e+00
   3_adp:  0.1271 0.1761   5.251761e+00   5.485370e+00
   3_occ:  0.1270 0.1759   5.251528e+00   5.485009e+00
   4_bss:  0.1272 0.1753   5.250164e+00   5.482159e+00
   4_xyz:  0.1154 0.1635   5.173871e+00   5.421938e+00
   4_adp:  0.1142 0.1596   5.157835e+00   5.398704e+00
   4_occ:  0.1141 0.1595   5.157017e+00   5.397413e+00
   5_bss:  0.1141 0.1594   5.156929e+00   5.397287e+00
   5_xyz:  0.1127 0.1573   5.145424e+00   5.385879e+00
   5_adp:  0.1120 0.1566   5.143198e+00   5.385639e+00
   5_occ:  0.1117 0.1567   5.141944e+00   5.384494e+00
   5_bss:  0.1117 0.1567   5.141911e+00   5.384469e+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:  0.358   5.161   7.267  10.367   8.061   0.000   0.000   0.000
   1_xyz:  0.358   5.161   7.267  10.367   8.061   0.000   0.000   0.000
   1_adp:  0.358   5.161   7.267  10.367   8.061   0.000   0.000   0.000
   1_occ:  0.358   5.161   7.267  10.367   8.061   0.000   0.000   0.000
   2_bss:  0.340  29.138   3.661   5.698   4.686   0.000   0.000   0.000
   2_xyz:  0.340  29.138   3.661   5.698   4.686   0.000   0.000   0.000
   2_adp:  0.340  29.138   3.661   5.698   4.686   0.000   0.000   0.000
   2_occ:  0.340  29.138   3.661   5.698   4.686   0.000   0.000   0.000
   3_bss:  0.331  39.840   2.618   3.275   3.933   0.000   0.000   0.000
   3_xyz:  0.331  39.840   2.618   3.275   3.933   0.000   0.000   0.000
   3_adp:  0.331  39.840   2.618   3.275   3.933   0.000   0.000   0.000
   3_occ:  0.331  39.840   2.618   3.275   3.933   0.000   0.000   0.000
   4_bss:  0.324  43.087   2.341   2.634   3.778   0.000   0.000   0.000
   4_xyz:  0.324  43.087   2.341   2.634   3.778   0.000   0.000   0.000
   4_adp:  0.324  43.087   2.341   2.634   3.778   0.000   0.000   0.000
   4_occ:  0.324  43.087   2.341   2.634   3.778   0.000   0.000   0.000
   5_bss:  0.326  42.016   2.342   2.501   3.846   0.000   0.000   0.000
   5_xyz:  0.326  42.016   2.342   2.501   3.846   0.000   0.000   0.000
   5_adp:  0.326  42.016   2.342   2.501   3.846   0.000   0.000   0.000
   5_occ:  0.326  42.016   2.342   2.501   3.846   0.000   0.000   0.000
   5_bss:  0.326  44.959  -0.537  -0.436   0.974   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.266 0.4929  0.5653    59996.476
   1_bss:  52.196 0.4914  0.7212    56940.449
   1_xyz:  41.888 0.6187  0.8918    39848.180
   1_adp:  36.474 0.6846  1.0079    33060.649
   1_occ:  36.541 0.6837  1.0054    33053.699
   2_bss:  35.936 0.6907  0.8850    32264.872
   2_xyz:  26.007 0.8005  0.9898    17354.375
   2_adp:  23.112 0.8313  1.0092    14544.086
   2_occ:  23.073 0.8317  1.0094    14502.825
   3_bss:  22.848 0.8338  0.9612    14248.643
   3_xyz:  17.546 0.8842  0.9921     8762.157
   3_adp:  16.201 0.8964  0.9928     7820.196
   3_occ:  16.200 0.8964  0.9925     7806.609
   4_bss:  16.132 0.8969  0.9797     7744.566
   4_xyz:  14.739 0.9087  0.9854     6773.396
   4_adp:  14.190 0.9134  0.9854     6501.359
   4_occ:  14.168 0.9136  0.9854     6478.706
   5_bss:  14.168 0.9136  0.9847     6477.844
   5_xyz:  13.875 0.9163  0.9841     6341.706
   5_adp:  13.836 0.9167  0.9805     6332.770
   5_occ:  13.815 0.9169  0.9803     6318.143
   5_bss:  13.814 0.9169  0.9820     6318.082
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3335e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3335e+01
   1_xyz:   1.584  0.012  0.102 18.029  0.006  4.117   1.2566e-01
   1_adp:   1.584  0.012  0.102 18.029  0.006  4.117   1.2566e-01
   1_occ:   1.584  0.012  0.102 18.029  0.006  4.117   1.2566e-01
   2_bss:   1.584  0.012  0.102 18.029  0.006  4.117   1.2566e-01
   2_xyz:   1.110  0.009  0.079 15.838  0.004  4.119   8.0683e-02
   2_adp:   1.110  0.009  0.079 15.838  0.004  4.119   8.0683e-02
   2_occ:   1.110  0.009  0.079 15.838  0.004  4.119   8.0683e-02
   3_bss:   1.110  0.009  0.079 15.838  0.004  4.119   8.0683e-02
   3_xyz:   1.040  0.007  0.078 15.884  0.004  4.116   6.5352e-02
   3_adp:   1.040  0.007  0.078 15.884  0.004  4.116   6.5352e-02
   3_occ:   1.040  0.007  0.078 15.884  0.004  4.116   6.5352e-02
   4_bss:   1.040  0.007  0.078 15.884  0.004  4.116   6.5352e-02
   4_xyz:   1.006  0.007  0.078 15.678  0.004  4.108   6.2879e-02
   4_adp:   1.006  0.007  0.078 15.678  0.004  4.108   6.2879e-02
   4_occ:   1.006  0.007  0.078 15.678  0.004  4.108   6.2879e-02
   5_bss:   1.006  0.007  0.078 15.678  0.004  4.108   6.2879e-02
   5_xyz:   0.941  0.006  0.073 15.323  0.004  4.109   5.5790e-02
   5_adp:   0.941  0.006  0.073 15.323  0.004  4.109   5.5790e-02
   5_occ:   0.941  0.006  0.073 15.323  0.004  4.109   5.5790e-02
   5_bss:   0.941  0.006  0.073 15.323  0.004  4.109   5.5790e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9138e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9138e+00
   1_xyz:  12.455  0.155  0.404 87.942  0.031  2.204   8.9876e-02
   1_adp:  12.455  0.155  0.404 87.942  0.031  2.204   8.9876e-02
   1_occ:  12.455  0.155  0.404 87.942  0.031  2.204   8.9876e-02
   2_bss:  12.455  0.155  0.404 87.942  0.031  2.204   8.9876e-02
   2_xyz:   7.881  0.085  0.263 88.652  0.034  2.272   1.6207e-01
   2_adp:   7.881  0.085  0.263 88.652  0.034  2.272   1.6207e-01
   2_occ:   7.881  0.085  0.263 88.652  0.034  2.272   1.6207e-01
   3_bss:   7.881  0.085  0.263 88.652  0.034  2.272   1.6207e-01
   3_xyz:   8.626  0.056  0.350 81.853  0.030  2.294   8.3380e-02
   3_adp:   8.626  0.056  0.350 81.853  0.030  2.294   8.3380e-02
   3_occ:   8.626  0.056  0.350 81.853  0.030  2.294   8.3380e-02
   4_bss:   8.626  0.056  0.350 81.853  0.030  2.294   8.3380e-02
   4_xyz:   6.362  0.045  0.371 83.221  0.038  2.288   4.9173e-02
   4_adp:   6.362  0.045  0.371 83.221  0.038  2.288   4.9173e-02
   4_occ:   6.362  0.045  0.371 83.221  0.038  2.288   4.9173e-02
   5_bss:   6.362  0.045  0.371 83.221  0.038  2.288   4.9173e-02
   5_xyz:   6.347  0.043  0.317 83.844  0.039  2.310   3.7472e-02
   5_adp:   6.347  0.043  0.317 83.844  0.039  2.310   3.7472e-02
   5_occ:   6.347  0.043  0.317 83.844  0.039  2.310   3.7472e-02
   5_bss:   6.347  0.043  0.317 83.844  0.039  2.310   3.7472e-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:  73.13   0.00  12.02  68.83   0.00   9.47  73.13   0.00  25.93
   1_occ:  73.13   0.00  12.02  68.83   0.00   9.47  73.13   0.00  25.93
   2_bss:  73.13   0.00  12.02  68.83   0.00   9.47  73.13   0.00  25.93
   2_xyz:  73.13   0.00  12.02  68.83   0.00   9.47  73.13   0.00  25.93
   2_adp:  78.84   0.00  11.96  72.27   0.00   8.32  78.84   1.18  31.79
   2_occ:  78.84   0.00  11.96  72.27   0.00   8.32  78.84   1.18  31.79
   3_bss:  78.84   0.00  11.96  72.27   0.00   8.32  78.84   1.18  31.79
   3_xyz:  78.84   0.00  11.96  72.27   0.00   8.32  78.84   1.18  31.79
   3_adp:  82.80   0.00  12.42  82.80   0.00   8.12  80.90   1.39  35.82
   3_occ:  82.80   0.00  12.42  82.80   0.00   8.12  80.90   1.39  35.82
   4_bss:  82.80   0.00  12.42  82.80   0.00   8.12  80.90   1.39  35.82
   4_xyz:  82.80   0.00  12.42  82.80   0.00   8.12  80.90   1.39  35.82
   4_adp:  83.56   0.00  12.01  83.56   0.00   7.90  78.57   1.80  34.39
   4_occ:  83.56   0.00  12.01  83.56   0.00   7.90  78.57   1.80  34.39
   5_bss:  83.56   0.00  12.01  83.56   0.00   7.90  78.57   1.80  34.39
   5_xyz:  83.56   0.00  12.01  83.56   0.00   7.90  78.57   1.80  34.39
   5_adp:  85.61   0.00  11.88  85.61   0.00   7.83  77.41   1.69  33.98
   5_occ:  85.61   0.00  11.88  85.61   0.00   7.83  77.41   1.69  33.98
   5_bss:  88.55   2.94  14.83  88.55   2.94  10.77  80.36   4.64  36.92
------------------------------------------------------------------------
 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:    1.221    0.023    0.403
   1_adp:    1.221    0.023    0.403
   1_occ:    1.221    0.023    0.403
   2_bss:    1.221    0.023    0.403
   2_xyz:    1.394    0.035    0.560
   2_adp:    1.394    0.035    0.560
   2_occ:    1.394    0.035    0.560
   3_bss:    1.394    0.035    0.560
   3_xyz:    1.593    0.014    0.617
   3_adp:    1.593    0.014    0.617
   3_occ:    1.593    0.014    0.617
   4_bss:    1.593    0.014    0.617
   4_xyz:    1.659    0.029    0.639
   4_adp:    1.659    0.029    0.639
   4_occ:    1.659    0.029    0.639
   5_bss:    1.659    0.029    0.639
   5_xyz:    1.679    0.062    0.650
   5_adp:    1.679    0.062    0.650
   5_occ:    1.679    0.062    0.650
   5_bss:    1.679    0.062    0.650
------------------------------------------------------------------------

CPU time actual refinement: 357.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_511/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_511/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_511/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_511/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_511/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 357.58 
  Macro-tasks:
    bulk solvent and scale       = 43.84  
    individual site refinement   = 154.04 
    weights calculation          = 32.94  
    collect and process          = 6.65   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 237.62 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 110.61 
    alpha_beta                      = 8.18   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 124.30 
    fmodel                         = 7.68   
    r_factors                      = 0.24   
    phase_errors                   = 10.76  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 264.94 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.853 micro seconds
Total CPU time: 6.19 minutes
from_scatterers_fft:    702 calls, 110.29 s
gradients_fft:          646 calls, 109.47 s

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

# Date 2008-01-16 Time 01:46:10 PST -0800 (1200476770.34 s)
Start R-work = 0.4532, R-free = 0.4446 (no bulk solvent and anisotropic scale)
Final R-work = 0.1292, R-free = 0.1734 (no bulk solvent and anisotropic scale)

Start R-work = 0.4452, R-free = 0.4310
Final R-work = 0.1117, R-free = 0.1567