# Date 2008-01-16 Time 00:52:21 PST -0800 (1200473541.28 s)
#phil __OFF__

Command line arguments: "../200.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27548
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 200

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 47.3993, 85.0941, 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: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8115 1.96061
Completeness in resolution range: 0.953654
Completeness with d_max=infinity: 0.950692

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8115
                             d_min =   1.9606

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8115 1.96061
Completeness in resolution range: 0.953654
Completeness with d_max=infinity: 0.950692

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8119 -  4.1950 [2163/2191]  1947   216  10.0%
  bin  2:  4.1950 -  3.3423 [2066/2089]  1859   207  10.0%
  bin  3:  3.3423 -  2.9235 [2045/2070]  1840   205  10.0%
  bin  4:  2.9235 -  2.6579 [2023/2039]  1821   202  10.0%
  bin  5:  2.6579 -  2.4683 [2005/2044]  1799   206  10.3%
  bin  6:  2.4683 -  2.3234 [2005/2037]  1813   192   9.6%
  bin  7:  2.3234 -  2.2074 [1985/2022]  1785   200  10.1%
  bin  8:  2.2074 -  2.1116 [1984/2026]  1786   198  10.0%
  bin  9:  2.1116 -  2.0305 [1973/2012]  1777   196   9.9%
  bin 10:  2.0305 -  1.9606 [1340/2011]  1203   137  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_200/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: 0.12 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:
        1.32 -     2.03: 16
        2.03 -     2.75: 362
        2.75 -     3.47: 4675
        3.47 -     4.18: 9510
        4.18 -     4.90: 14132
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.317 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.426 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.555 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.699 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  69 " - " O   HOH Z 357 "  1.750 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28690 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_200/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_200/model_refine_001.geo

CPU time processing inputs: 8.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 47.3993 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4828   r_free= 0.4721   ksol= 0.00   Bsol= 0.00   scale= 0.801    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.281072                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8119 -  4.6788 0.99   1399  158 0.3952 0.3867      6.5833      6.6244|
|  2:  4.6788 -  3.7333 0.99   1349  148 0.4004 0.3884      6.7718      6.7887|
|  3:  3.7333 -  3.2671 0.99   1319  149 0.4374 0.4173      6.6705      6.7203|
|  4:  3.2671 -  2.9710 0.99   1320  136 0.4597 0.4420       6.507      6.4667|
|  5:  2.9710 -  2.7596 0.98   1299  147 0.5113 0.5212      6.3828      6.4001|
|  6:  2.7596 -  2.5978 0.99   1292  144 0.5041 0.5353      6.2725      6.2105|
|  7:  2.5978 -  2.4683 0.99   1288  154 0.5278 0.4605      6.2691      6.1655|
|  8:  2.4683 -  2.3613 0.99   1310  133 0.5231 0.5148      6.1759      6.1681|
|  9:  2.3613 -  2.2707 0.99   1273  148 0.5334 0.5483      6.1199      6.1712|
| 10:  2.2707 -  2.1926 0.98   1272  139 0.5302 0.5321       6.118      6.0977|
| 11:  2.1926 -  2.1243 0.98   1276  147 0.5288 0.5561       6.037      6.0786|
| 12:  2.1243 -  2.0637 1.00   1285  141 0.5396 0.5363      5.9722      6.0064|
| 13:  2.0637 -  2.0095 0.96   1270  130 0.5582 0.5201      5.9044      5.8781|
| 14:  2.0095 -  1.9606 0.54    678   85 0.5317 0.4482      5.8893      5.7076|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8119 -  4.6788  1399   158  0.67  36.79   0.80     0.68      77282.04|
|  2:  4.6788 -  3.7333  1349   148  0.68  36.81   0.89     0.74     110999.13|
|  3:  3.7333 -  3.2671  1319   149  0.59  44.53   0.86     0.71     117017.76|
|  4:  3.2671 -  2.9710  1320   136  0.52  50.60   0.81     0.62      99598.15|
|  5:  2.9710 -  2.7596  1299   147  0.42  58.03   0.73     0.52      83674.65|
|  6:  2.7596 -  2.5978  1292   144  0.40  60.11   0.73     0.46      70742.43|
|  7:  2.5978 -  2.4683  1288   154  0.39  60.95   0.74     0.44      64478.22|
|  8:  2.4683 -  2.3613  1310   133  0.38  61.23   0.74     0.45      56716.14|
|  9:  2.3613 -  2.2707  1273   148  0.35  63.80   0.72     0.43      54330.59|
| 10:  2.2707 -  2.1926  1272   139  0.32  66.13   0.77     0.38      51491.07|
| 11:  2.1926 -  2.1243  1276   147  0.26  70.82   0.74     0.32      51039.86|
| 12:  2.1243 -  2.0637  1285   141  0.25  71.12   0.75     0.33      47764.40|
| 13:  2.0637 -  2.0095  1270   130  0.31  66.92   0.74     0.39      37716.13|
| 14:  2.0095 -  1.9606   678    85  0.49  53.46   0.73     0.52      22893.47|
|alpha:            min =        0.32 max =            0.74 mean =         0.50|
|beta:             min =    22893.47 max =       117017.76 mean =     69523.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.10|
|phase err.(test): min =        0.00 max =           89.91 mean =        57.18|
|-----------------------------------------------------------------------------|

============================== 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 = 14.933981             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.565   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.146174              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.534   (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 |  1.039 -  1.425:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.425 -  1.811:       11 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.811 -  2.198:      108 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.198 -  2.584:      572 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.584 -  2.970:     1368 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.970 -  3.356:     2499 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.356 -  3.742:     4016 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.742 -  4.128:     5234 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.128 -  4.514:     6815 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.514 -  4.900:     8111 |
|-----------------------------------------------------------------------------|
|-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 |       53.159 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.039 |       2.594 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    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 = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4878   r_free= 0.4812   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.282015                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4738   r_free= 0.4643   ksol= 0.36   Bsol= 12.59   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.89,9.08,8.33,0.00,0.00,0.00); trace/3= 8.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.274790                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.550774             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.023   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.250930              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.648   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4738      final r-factor (work) = 0.3870          |
| start r-factor (free) = 0.4643      final r-factor (free) = 0.4102          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 95.7284 = 13.55 * 0.50 * 6.2829 + 1.00 * 53.1591                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.0662 = 13.55 * 0.50 * 6.1849 + 1.00 * 0.1608                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3870      final r-factor (work) = 0.3408          |
| start r-factor (free) = 0.4102      final r-factor (free) = 0.3893          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7512 = 1.25 * 1.00 * 6.1849 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6388 = 1.25 * 1.00 * 6.0922 + 1.00 * 0.0178                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.96   13.07    None  None   None       |
|    all(noH): 2823   0      0.00    82.96   13.07    None  None   None       |
|    Sol.    : 438    0      0.00    82.96   27.47    None  None   None       |
|    Mac.    : 2385   0      0.00    71.89   10.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.296: 1287   |   5:    41.481 -  49.777:   60        |
|      1:     8.296 -  16.592:  729   |   6:    49.777 -  58.073:   34        |
|      2:    16.592 -  24.889:  393   |   7:    58.073 -  66.369:   14        |
|      3:    24.889 -  33.185:  183   |   8:    66.369 -  74.665:    9        |
|      4:    33.185 -  41.481:  111   |   9:    74.665 -  82.962:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3408 r_free = 0.3893             target_work(ml) = 6.067         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3399 r_free = 0.3890             target_work(ml) = 6.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3399   r_free= 0.3890   ksol= 0.36   Bsol= 12.59   scale= 1.104   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.89,9.08,8.33,0.00,0.00,0.00); trace/3= 8.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.066010                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3368   r_free= 0.3831   ksol= 0.34   Bsol= 34.74   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.23,5.23,5.26,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.064842                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.178846              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.260   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.448064              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.832  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3368      final r-factor (work) = 0.2404          |
| start r-factor (free) = 0.3831      final r-factor (free) = 0.2861          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.0117 = 7.18 * 0.50 * 6.0876 + 1.00 * 0.1608                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3750 = 7.18 * 0.50 * 5.9331 + 1.00 * 0.0784                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2404      final r-factor (work) = 0.2134          |
| start r-factor (free) = 0.2861      final r-factor (free) = 0.2639          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6775 = 0.45 * 1.00 * 5.9331 + 1.00 * 0.0191                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5779 = 0.45 * 1.00 * 5.7275 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.31   12.91    None  None   None       |
|    all(noH): 2823   0      0.00    88.31   12.91    None  None   None       |
|    Sol.    : 438    0      2.30    88.31   32.56    None  None   None       |
|    Mac.    : 2385   0      0.00    76.56   9.30     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 -   8.831: 1525   |   5:    44.153 -  52.984:   78        |
|      1:     8.831 -  17.661:  669   |   6:    52.984 -  61.814:   30        |
|      2:    17.661 -  26.492:  219   |   7:    61.814 -  70.645:   11        |
|      3:    26.492 -  35.322:  158   |   8:    70.645 -  79.475:    4        |
|      4:    35.322 -  44.153:  128   |   9:    79.475 -  88.306:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2134 r_free = 0.2639             target_work(ml) = 5.686         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2130 r_free = 0.2635             target_work(ml) = 5.685         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2130   r_free= 0.2635   ksol= 0.34   Bsol= 34.74   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.23,5.23,5.26,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.685089                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2107   r_free= 0.2616   ksol= 0.33   Bsol= 30.58   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,3.43,3.47,0.00,0.00,0.00); trace/3= 2.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.682657                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.532670              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.603  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.223778              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.530  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2107      final r-factor (work) = 0.1584          |
| start r-factor (free) = 0.2616      final r-factor (free) = 0.2046          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3397 = 2.53 * 0.50 * 5.7342 + 1.00 * 0.0782                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1071 = 2.53 * 0.50 * 5.5668 + 1.00 * 0.0577                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1584      final r-factor (work) = 0.1513          |
| start r-factor (free) = 0.2046      final r-factor (free) = 0.1934          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2574 = 0.22 * 1.00 * 5.5668 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2228 = 0.22 * 1.00 * 5.4168 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.05   12.91    None  None   None       |
|    all(noH): 2823   0      0.00    84.05   12.91    None  None   None       |
|    Sol.    : 438    0      2.01    84.05   34.07    None  None   None       |
|    Mac.    : 2385   0      0.00    76.18   9.02     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 -   8.405: 1532   |   5:    42.024 -  50.429:   95        |
|      1:     8.405 -  16.810:  680   |   6:    50.429 -  58.834:   44        |
|      2:    16.810 -  25.214:  179   |   7:    58.834 -  67.238:   15        |
|      3:    25.214 -  33.619:  135   |   8:    67.238 -  75.643:    5        |
|      4:    33.619 -  42.024:  136   |   9:    75.643 -  84.048:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1513 r_free = 0.1934             target_work(ml) = 5.387         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1510 r_free = 0.1935             target_work(ml) = 5.387         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1510   r_free= 0.1935   ksol= 0.33   Bsol= 30.58   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,3.43,3.47,0.00,0.00,0.00); trace/3= 2.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.386854                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1511   r_free= 0.1934   ksol= 0.32   Bsol= 30.58   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.15,2.50,2.62,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.386485                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.972956              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.343  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.334360              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.668  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1511      final r-factor (work) = 0.1275          |
| start r-factor (free) = 0.1934      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4073 = 1.97 * 0.50 * 5.4230 + 1.00 * 0.0577                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2972 = 1.97 * 0.50 * 5.3117 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1275      final r-factor (work) = 0.1229          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1649          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7893 = 0.33 * 1.00 * 5.3117 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7557 = 0.33 * 1.00 * 5.2210 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.54   13.15    None  None   None       |
|    all(noH): 2823   0      0.00    79.54   13.15    None  None   None       |
|    Sol.    : 438    0      2.29    78.79   35.96    None  None   None       |
|    Mac.    : 2385   0      0.00    79.54   8.96     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 -   7.954: 1471   |   5:    39.768 -  47.721:  105        |
|      1:     7.954 -  15.907:  726   |   6:    47.721 -  55.675:   73        |
|      2:    15.907 -  23.861:  179   |   7:    55.675 -  63.628:   36        |
|      3:    23.861 -  31.814:  110   |   8:    63.628 -  71.582:   14        |
|      4:    31.814 -  39.768:  104   |   9:    71.582 -  79.535:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1229 r_free = 0.1649             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1228 r_free = 0.1649             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1649   ksol= 0.32   Bsol= 30.58   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.15,2.50,2.62,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.210814                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1648   ksol= 0.32   Bsol= 37.10   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.95,2.17,2.40,0.00,0.00,0.00); trace/3= 1.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.210999                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.566385              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.721  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.482606              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.085  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1229      final r-factor (work) = 0.1173          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1467 = 1.57 * 0.50 * 5.2216 + 1.00 * 0.0572                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1206 = 1.57 * 0.50 * 5.1917 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1173      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1608      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5156 = 0.48 * 1.00 * 5.1917 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5078 = 0.48 * 1.00 * 5.1742 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.45   13.12    None  None   None       |
|    all(noH): 2823   0      0.00    81.45   13.12    None  None   None       |
|    Sol.    : 438    0      1.80    76.99   36.01    None  None   None       |
|    Mac.    : 2385   0      0.00    81.45   8.92     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 -   8.145: 1514   |   5:    40.723 -  48.868:  102        |
|      1:     8.145 -  16.289:  697   |   6:    48.868 -  57.012:   63        |
|      2:    16.289 -  24.434:  176   |   7:    57.012 -  65.157:   36        |
|      3:    24.434 -  32.578:  112   |   8:    65.157 -  73.301:    9        |
|      4:    32.578 -  40.723:  107   |   9:    73.301 -  81.446:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1160 r_free = 0.1613             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1160 r_free = 0.1614             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1614   ksol= 0.32   Bsol= 37.10   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.95,2.17,2.40,0.00,0.00,0.00); trace/3= 1.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175305                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8119 -  4.6788 0.99   1399  158 0.1020 0.1326      5.4128      5.5697|
|  2:  4.6788 -  3.7333 0.99   1349  148 0.0904 0.1112      5.4792      5.6508|
|  3:  3.7333 -  3.2671 0.99   1319  149 0.1080 0.1557      5.4912       5.856|
|  4:  3.2671 -  2.9710 0.99   1320  136 0.1243 0.1576      5.4686      5.6457|
|  5:  2.9710 -  2.7596 0.98   1299  147 0.1370 0.1662      5.3506      5.4837|
|  6:  2.7596 -  2.5978 0.99   1292  144 0.1329 0.2103      5.2611      5.5434|
|  7:  2.5978 -  2.4683 0.99   1288  154 0.1206 0.1636      5.1705      5.3887|
|  8:  2.4683 -  2.3613 0.99   1310  133 0.1223 0.1784      5.1197      5.3705|
|  9:  2.3613 -  2.2707 0.99   1273  148 0.1246 0.1867      5.0618      5.3363|
| 10:  2.2707 -  2.1926 0.98   1272  139 0.1178 0.1778      5.0068      5.1982|
| 11:  2.1926 -  2.1243 0.98   1276  147 0.1186 0.1705      4.9398      5.2505|
| 12:  2.1243 -  2.0637 1.00   1285  141 0.1124 0.1763       4.866      5.1495|
| 13:  2.0637 -  2.0095 0.96   1270  130 0.1185 0.1804      4.8156      5.0853|
| 14:  2.0095 -  1.9606 0.54    678   85 0.1149 0.1702      4.7447      4.9333|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8119 -  4.6788  1399   158  0.94   9.31   0.98     0.96       7651.01|
|  2:  4.6788 -  3.7333  1349   148  0.95   8.33   1.02     1.01       9552.89|
|  3:  3.7333 -  3.2671  1319   149  0.93  11.29   1.03     1.03      10673.40|
|  4:  3.2671 -  2.9710  1320   136  0.92  13.74   1.02     1.01      10475.92|
|  5:  2.9710 -  2.7596  1299   147  0.90  16.30   0.99     0.97       8534.35|
|  6:  2.7596 -  2.5978  1292   144  0.89  16.79   0.98     0.95       7651.08|
|  7:  2.5978 -  2.4683  1288   154  0.90  15.73   0.99     0.95       6360.79|
|  8:  2.4683 -  2.3613  1310   133  0.90  15.92   1.00     0.97       5963.85|
|  9:  2.3613 -  2.2707  1273   148  0.90  16.50   1.01     0.98       5342.32|
| 10:  2.2707 -  2.1926  1272   139  0.90  16.20   1.00     0.98       4842.64|
| 11:  2.1926 -  2.1243  1276   147  0.90  15.82   1.00     0.97       4251.79|
| 12:  2.1243 -  2.0637  1285   141  0.91  15.21   1.01     1.00       3820.72|
| 13:  2.0637 -  2.0095  1270   130  0.90  16.39   1.01     1.00       3494.03|
| 14:  2.0095 -  1.9606   678    85  0.90  16.16   0.98     0.95       2995.15|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2995.15 max =        10673.40 mean =      6706.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.43|
|phase err.(test): min =        0.00 max =           89.90 mean =        13.93|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1614   ksol= 0.32   Bsol= 40.02   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,0.29,0.57,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175356                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1614   ksol= 0.32   Bsol= 40.02   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,0.29,0.57,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175356                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8119 -  4.6788 0.99   1399  158 0.1021 0.1329      5.4137      5.5712|
|  2:  4.6788 -  3.7333 0.99   1349  148 0.0905 0.1113      5.4802      5.6519|
|  3:  3.7333 -  3.2671 0.99   1319  149 0.1080 0.1558      5.4918      5.8567|
|  4:  3.2671 -  2.9710 0.99   1320  136 0.1243 0.1576      5.4686      5.6456|
|  5:  2.9710 -  2.7596 0.98   1299  147 0.1370 0.1661      5.3502      5.4834|
|  6:  2.7596 -  2.5978 0.99   1292  144 0.1328 0.2100      5.2607      5.5428|
|  7:  2.5978 -  2.4683 0.99   1288  154 0.1206 0.1637      5.1701      5.3888|
|  8:  2.4683 -  2.3613 0.99   1310  133 0.1223 0.1782      5.1195      5.3699|
|  9:  2.3613 -  2.2707 0.99   1273  148 0.1246 0.1868      5.0617      5.3366|
| 10:  2.2707 -  2.1926 0.98   1272  139 0.1177 0.1779      5.0067      5.1981|
| 11:  2.1926 -  2.1243 0.98   1276  147 0.1185 0.1705      4.9398      5.2506|
| 12:  2.1243 -  2.0637 1.00   1285  141 0.1124 0.1763      4.8659      5.1496|
| 13:  2.0637 -  2.0095 0.96   1270  130 0.1185 0.1803      4.8155      5.0848|
| 14:  2.0095 -  1.9606 0.54    678   85 0.1148 0.1701      4.7443      4.9326|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8119 -  4.6788  1399   158  0.94   9.33   0.98     0.96       7674.78|
|  2:  4.6788 -  3.7333  1349   148  0.95   8.34   1.02     1.01       9575.99|
|  3:  3.7333 -  3.2671  1319   149  0.93  11.30   1.03     1.03      10691.59|
|  4:  3.2671 -  2.9710  1320   136  0.92  13.75   1.02     1.01      10477.47|
|  5:  2.9710 -  2.7596  1299   147  0.90  16.30   1.00     0.97       8528.33|
|  6:  2.7596 -  2.5978  1292   144  0.89  16.77   0.98     0.95       7644.68|
|  7:  2.5978 -  2.4683  1288   154  0.90  15.72   0.99     0.95       6357.73|
|  8:  2.4683 -  2.3613  1310   133  0.90  15.92   1.00     0.98       5962.09|
|  9:  2.3613 -  2.2707  1273   148  0.90  16.50   1.01     0.99       5341.67|
| 10:  2.2707 -  2.1926  1272   139  0.90  16.20   1.01     0.98       4841.97|
| 11:  2.1926 -  2.1243  1276   147  0.90  15.82   1.01     0.97       4251.85|
| 12:  2.1243 -  2.0637  1285   141  0.91  15.20   1.01     1.00       3820.14|
| 13:  2.0637 -  2.0095  1270   130  0.90  16.38   1.01     1.01       3491.25|
| 14:  2.0095 -  1.9606   678    85  0.90  16.14   0.99     0.95       2990.00|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2990.00 max =        10691.59 mean =      6709.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.43|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.93|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.89    83.34   15.01    None  None   None       |
|    all(noH): 2823   0      1.89    83.34   15.01    None  None   None       |
|    Sol.    : 438    0      3.69    78.88   37.90    None  None   None       |
|    Mac.    : 2385   0      1.89    83.34   10.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.893 -  10.037: 1514   |   5:    42.616 -  50.760:  102        |
|      1:    10.037 -  18.182:  697   |   6:    50.760 -  58.905:   63        |
|      2:    18.182 -  26.326:  176   |   7:    58.905 -  67.049:   36        |
|      3:    26.326 -  34.471:  112   |   8:    67.049 -  75.194:    9        |
|      4:    34.471 -  42.616:  107   |   9:    75.194 -  83.339:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.582 - 4.267
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 322
   mapped sites are within: 0.736 - 4.267

peak=   11.011 closest distance to " CB  VAL A 230 " =    1.423
peak=    6.168 closest distance to " CB  VAL A 296 " =    1.111
peak=    5.626 closest distance to " CG  LEU A   5 " =    1.268
peak=    5.501 closest distance to " CD2 LEU A   5 " =    1.203
peak=    5.434 closest distance to " O   HOH Z 193 " =    1.851
peak=    5.429 closest distance to " CD1AILE A 234 " =    1.043
peak=    5.330 closest distance to " O   HOH Z 402 " =    1.527
peak=    5.281 closest distance to " CG1 VAL A 296 " =    1.154
peak=    5.198 closest distance to " CG2 VAL A 296 " =    1.033
peak=    5.148 closest distance to " CB  ARG A 275 " =    0.978
peak=    5.112 closest distance to " NH2 ARG A  56 " =    2.128
peak=    5.053 closest distance to " O   HOH Z 142 " =    1.707
peak=    5.047 closest distance to " O   HOH Z 126 " =    1.908
peak=    5.015 closest distance to " O   HOH Z 124 " =    1.672
peak=    5.004 closest distance to " CG  PRO A 213 " =    1.287
peak=    4.999 closest distance to " O   HOH Z 278 " =    1.237
peak=    4.992 closest distance to " O   HOH Z 120 " =    1.024
peak=    4.883 closest distance to " O   HOH Z 209 " =    2.299
peak=    4.842 closest distance to " CB  GLN A 223 " =    1.410
peak=    4.831 closest distance to " O   HOH Z  85 " =    1.639
peak=    4.800 closest distance to " O   HOH Z 102 " =    1.312
peak=    4.799 closest distance to " CG  PRO A  54 " =    1.293
peak=    4.771 closest distance to " O   HOH Z 272 " =    1.911
peak=    4.753 closest distance to " NE2 GLN A  11 " =    1.058
peak=    4.671 closest distance to " O   HOH Z 128 " =    2.142
peak=    4.638 closest distance to " O   HOH Z 406 " =    1.318
peak=    4.621 closest distance to " O   SER A  87 " =    2.240
peak=    4.619 closest distance to " CA  TYR A  30 " =    1.015
peak=    4.610 closest distance to " CB  SER A  63 " =    1.154
peak=    4.603 closest distance to " O   HOH Z 232 " =    2.240
peak=    4.549 closest distance to " CG  LEU A 228 " =    1.166
peak=    4.497 closest distance to " CG  PRO A 198 " =    1.169
peak=    4.491 closest distance to " CD2 LEU A 228 " =    1.270
peak=    4.483 closest distance to " O   HOH Z 368 " =    2.140
peak=    4.483 closest distance to " CB  GLN A 183 " =    1.317
peak=    4.477 closest distance to " O   HOH Z 414 " =    1.728
peak=    4.474 closest distance to " O   HOH Z  80 " =    1.782
peak=    4.461 closest distance to " O   HOH Z 236 " =    1.443
peak=    4.407 closest distance to " CB  PRO A  54 " =    0.929
peak=    4.390 closest distance to " O   HOH Z 316 " =    2.615
peak=    4.381 closest distance to " O   HOH Z 234 " =    3.691
peak=    4.375 closest distance to " CG  ARG A  66 " =    1.083
peak=    4.362 closest distance to " CB  SER A   3 " =    1.279
peak=    4.331 closest distance to " C   PRO A 198 " =    1.492
peak=    4.321 closest distance to " O   HOH Z  59 " =    2.196
peak=    4.316 closest distance to " O   HOH Z 403 " =    1.867
peak=    4.307 closest distance to " O   HOH Z  48 " =    1.805
peak=    4.296 closest distance to " CA  VAL A  41 " =    0.817
peak=    4.291 closest distance to " CA  ALA A  21 " =    1.190
peak=    4.254 closest distance to " NZ  LYS A 117 " =    3.074
peak=    4.238 closest distance to " O   HOH Z  97 " =    1.938
peak=    4.217 closest distance to " O   HOH Z 369 " =    2.234
peak=    4.215 closest distance to " O   HOH Z 411 " =    3.535
peak=    4.213 closest distance to " O   HOH Z 247 " =    1.323
peak=    4.209 closest distance to " O   HOH Z 346 " =    1.474
peak=    4.202 closest distance to " O   HOH Z 345 " =    2.610
peak=    4.195 closest distance to " CB  VAL A 230 " =    1.149
peak=    4.192 closest distance to " CD2 TRP A 179 " =    1.381
peak=    4.189 closest distance to " O   HOH Z 394 " =    1.440
peak=    4.189 closest distance to " O   HOH Z 327 " =    1.736
peak=    4.171 closest distance to " CD  ARG A 269 " =    1.109
peak=    4.153 closest distance to " O   HOH Z 423 " =    1.782
peak=    4.130 closest distance to " CB  GLU A 152 " =    1.081
peak=    4.118 closest distance to " O   HOH Z 279 " =    1.132
peak=    4.097 closest distance to " O   HOH Z 357 " =    1.914
peak=    4.091 closest distance to " CG AARG A 275 " =    1.150
peak=    4.077 closest distance to " CB  SER A  26 " =    1.711
peak=    4.061 closest distance to " O   HOH Z 249 " =    1.036
peak=    4.043 closest distance to " CB  TRP A 179 " =    1.095
peak=    4.004 closest distance to " O   HOH Z 303 " =    2.120
peak=    3.972 closest distance to " N   ASN A  39 " =    1.229
peak=    3.969 closest distance to " O   HOH Z  78 " =    1.612
peak=    3.962 closest distance to " O   HOH Z 134 " =    1.560
peak=    3.948 closest distance to " O   HOH Z  47 " =    1.708
peak=    3.947 closest distance to " CB  ALA A   9 " =    1.579
peak=    3.933 closest distance to " OE1 GLU A   2 " =    2.164
peak=    3.930 closest distance to " O   HOH Z  97 " =    2.338
peak=    3.924 closest distance to " O   HOH Z  63 " =    2.439
peak=    3.923 closest distance to " O   HOH Z 156 " =    3.174
peak=    3.918 closest distance to " O   HOH Z 419 " =    1.675
peak=    3.916 closest distance to " O   HOH Z 426 " =    1.421
peak=    3.916 closest distance to " O   HOH Z 408 " =    1.666
peak=    3.903 closest distance to " O   HOH Z  48 " =    1.705
peak=    3.901 closest distance to " CA  ASN A 176 " =    0.949
peak=    3.887 closest distance to " O   HOH Z 203 " =    1.633
peak=    3.883 closest distance to " O   HOH Z 154 " =    1.485
peak=    3.873 closest distance to " O   HOH Z  54 " =    1.478
peak=    3.862 closest distance to " O   HOH Z 298 " =    1.864
peak=    3.859 closest distance to " O   HOH Z 130 " =    2.775
peak=    3.847 closest distance to " CA  ALA A  51 " =    1.122
peak=    3.837 closest distance to " ND2 ASN A 187 " =    1.664
peak=    3.834 closest distance to " CG  GLN A  77 " =    2.310
peak=    3.833 closest distance to " O   HOH Z  40 " =    1.698
peak=    3.825 closest distance to " CB  VAL A 265 " =    1.212
peak=    3.823 closest distance to " CB  GLU A 128 " =    1.133
peak=    3.823 closest distance to " O   TRP A 274 " =    1.899
peak=    3.822 closest distance to " CG1 ILE A  33 " =    1.271
peak=    3.812 closest distance to " O   HOH Z 245 " =    1.387
peak=    3.806 closest distance to " CB  ASN A 148 " =    1.340
peak=    3.800 closest distance to " O   HOH Z  43 " =    2.248
peak=    3.791 closest distance to " CG2 ILE A  20 " =    1.410
peak=    3.790 closest distance to " O   HOH Z 214 " =    2.919
peak=    3.778 closest distance to " CG  PRO A 243 " =    1.192
peak=    3.773 closest distance to " O   HOH Z 284 " =    2.921
peak=    3.768 closest distance to " CB BVAL A  41 " =    1.087
peak=    3.768 closest distance to " O   HOH Z 427 " =    2.518
peak=    3.763 closest distance to " O   HOH Z 189 " =    2.397
peak=    3.763 closest distance to " CG1BVAL A  72 " =    1.658
peak=    3.762 closest distance to " O   HOH Z 271 " =    2.386
peak=    3.758 closest distance to " O   HOH Z 404 " =    1.449
peak=    3.758 closest distance to " O   HOH Z 227 " =    1.591
peak=    3.735 closest distance to " CB  PRO A 198 " =    0.999
peak=    3.730 closest distance to " CD BLYS A 290 " =    1.087
peak=    3.724 closest distance to " O   HOH Z 344 " =    2.638
peak=    3.703 closest distance to " O   HOH Z 345 " =    1.680
peak=    3.703 closest distance to " O   ASP A 124 " =    1.471
peak=    3.700 closest distance to " O   HOH Z  15 " =    2.265
peak=    3.700 closest distance to " OD2 ASP A 298 " =    3.969
peak=    3.698 closest distance to " O   HOH Z  61 " =    1.649
peak=    3.685 closest distance to " O   HOH Z 250 " =    1.338
peak=    3.680 closest distance to " O   HOH Z 128 " =    1.805
peak=    3.677 closest distance to " O   HOH Z 422 " =    2.580
peak=    3.673 closest distance to " O   HOH Z 273 " =    2.759
peak=    3.670 closest distance to " O   HOH Z  54 " =    2.355
peak=    3.662 closest distance to " O   HOH Z 280 " =    2.490
peak=    3.659 closest distance to " O   HOH Z 417 " =    3.337
peak=    3.659 closest distance to " CA  ASP A 140 " =    1.109
peak=    3.657 closest distance to " O   HOH Z 389 " =    1.777
peak=    3.651 closest distance to " O   HOH Z 366 " =    2.832
peak=    3.651 closest distance to " CD1 LEU A  96 " =    0.736
peak=    3.644 closest distance to " O   GLY A  91 " =    1.557
peak=    3.638 closest distance to " O   HOH Z 425 " =    1.399
peak=    3.636 closest distance to " CB  GLU A 277 " =    3.543
peak=    3.629 closest distance to " CB  ARG A  79 " =    1.270
peak=    3.626 closest distance to " O   HOH Z 155 " =    1.588
peak=    3.622 closest distance to " O   HOH Z 367 " =    3.503
peak=    3.615 closest distance to " O   HOH Z 118 " =    1.454
peak=    3.612 closest distance to " O   HOH Z 406 " =    1.061
peak=    3.610 closest distance to " NH2 ARG A 156 " =    1.090
peak=    3.605 closest distance to " CB  THR A  31 " =    1.545
peak=    3.599 closest distance to " CG2 ILE A 120 " =    1.316
peak=    3.599 closest distance to " CE  LYS A 119 " =    0.996
peak=    3.594 closest distance to " O   HOH Z 322 " =    2.140
peak=    3.593 closest distance to " O   HOH Z  43 " =    1.524
peak=    3.593 closest distance to " OG1 THR A 294 " =    2.288
peak=    3.591 closest distance to " O   HOH Z 192 " =    1.723
peak=    3.586 closest distance to " CD  ARG A 159 " =    0.774
peak=    3.558 closest distance to " O   HOH Z 118 " =    1.365
peak=    3.558 closest distance to " O   HOH Z 197 " =    2.634
peak=    3.557 closest distance to " CA  ARG A  36 " =    0.968
peak=    3.556 closest distance to " O   HOH Z 416 " =    2.791
peak=    3.555 closest distance to " CB  TYR A 169 " =    0.746
peak=    3.554 closest distance to " CB  ALA A 248 " =    1.329
peak=    3.551 closest distance to " O   HOH Z  66 " =    2.043
peak=    3.544 closest distance to " O   HOH Z 420 " =    1.904
peak=    3.540 closest distance to " CB  ALA A 295 " =    1.187
peak=    3.539 closest distance to " CG2 THR A 221 " =    1.218
peak=    3.537 closest distance to " CB  SER A 273 " =    0.891
peak=    3.535 closest distance to " O   HOH Z 112 " =    1.687
peak=    3.532 closest distance to " CB  MET A  47 " =    1.154
peak=    3.531 closest distance to " CZ AARG A 102 " =    1.678
peak=    3.526 closest distance to " O   HOH Z 359 " =    1.506
peak=    3.521 closest distance to " CB  ASN A  39 " =    0.813
peak=    3.519 closest distance to " OD2 ASP A 286 " =    2.607
peak=    3.518 closest distance to " CA  LYS A 117 " =    1.329
peak=    3.513 closest distance to " O   HOH Z 248 " =    1.669
peak=    3.509 closest distance to " O   HOH Z 253 " =    1.660
peak=    3.505 closest distance to " OG BSER A 164 " =    2.205
peak=    3.496 closest distance to " O   HOH Z  68 " =    1.614
peak=    3.495 closest distance to " CB  ALA A 100 " =    1.156
peak=    3.493 closest distance to " O   HOH Z  21 " =    1.820
peak=    3.487 closest distance to " OD1 ASN A  69 " =    2.657
peak=    3.485 closest distance to " O   HOH Z 148 " =    3.149
peak=    3.482 closest distance to " CA  ALA A 295 " =    1.010
peak=    3.481 closest distance to " O   HOH Z 344 " =    1.721
peak=    3.478 closest distance to " O   HOH Z  48 " =    2.308
peak=    3.466 closest distance to " CD  LYS A 166 " =    1.352
peak=    3.465 closest distance to " O   HOH Z 244 " =    1.608
peak=    3.465 closest distance to " CG  GLN A  58 " =    2.611
peak=    3.463 closest distance to " O   HOH Z 287 " =    1.662
peak=    3.458 closest distance to " O   HOH Z  44 " =    1.919
peak=    3.449 closest distance to " CB  VAL A 202 " =    1.512
peak=    3.440 closest distance to " NZ  LYS A 119 " =    1.551
peak=    3.438 closest distance to " NH2BARG A 145 " =    2.386
peak=    3.436 closest distance to " CA  ARG A  66 " =    0.853
peak=    3.435 closest distance to " CG2AVAL A 121 " =    2.160
peak=    3.432 closest distance to " O   HOH Z 383 " =    1.874
peak=    3.428 closest distance to " CB  ARG A 139 " =    0.897
peak=    3.428 closest distance to " O   HOH Z 193 " =    2.087
peak=    3.428 closest distance to " O   HOH Z 132 " =    0.953
peak=    3.424 closest distance to " O   HOH Z 109 " =    2.192
peak=    3.420 closest distance to " O   HOH Z   4 " =    1.511
peak=    3.417 closest distance to " CG2 THR A 294 " =    1.545
peak=    3.412 closest distance to " CB  ARG A  79 " =    0.796
peak=    3.410 closest distance to " CZ  PHE A 218 " =    1.156
peak=    3.407 closest distance to " O   HOH Z 250 " =    1.533
peak=    3.404 closest distance to " O   HOH Z 261 " =    1.869
peak=    3.401 closest distance to " O   HOH Z  66 " =    2.152
peak=    3.401 closest distance to " OD1 ASP A 286 " =    1.806
peak=    3.400 closest distance to " O   HOH Z 435 " =    1.891
peak=    3.398 closest distance to " CD  GLN A 194 " =    1.540
peak=    3.393 closest distance to " O   HOH Z 261 " =    2.104
peak=    3.392 closest distance to " O   HOH Z 222 " =    2.374
peak=    3.387 closest distance to " O   HOH Z 421 " =    1.775
peak=    3.380 closest distance to " O   HOH Z 299 " =    4.267
peak=    3.378 closest distance to " O   HOH Z  89 " =    1.492
peak=    3.378 closest distance to " O   HOH Z 132 " =    2.699
peak=    3.373 closest distance to " O   HOH Z 188 " =    0.897
peak=    3.368 closest distance to " NZ  LYS A  76 " =    1.376
peak=    3.366 closest distance to " O   HOH Z 361 " =    3.053
peak=    3.364 closest distance to " CE1 HIS A 108 " =    1.136
peak=    3.363 closest distance to " C   ALA A 299 " =    0.910
peak=    3.363 closest distance to " OD1 ASP A 238 " =    0.975
peak=    3.361 closest distance to " CD2 LEU A 297 " =    0.958
peak=    3.342 closest distance to " OE1 GLN A  11 " =    1.739
peak=    3.337 closest distance to " CD  LYS A 119 " =    1.960
peak=    3.336 closest distance to " CA  GLY A  80 " =    0.926
peak=    3.335 closest distance to " O   HOH Z 298 " =    2.195
peak=    3.334 closest distance to " CB  GLN A 278 " =    0.909
peak=    3.334 closest distance to " O   HOH Z 215 " =    1.489
peak=    3.334 closest distance to " O   HOH Z 261 " =    1.807
peak=    3.325 closest distance to " CE1 TYR A 186 " =    1.285
peak=    3.322 closest distance to " O   HOH Z 353 " =    2.775
peak=    3.318 closest distance to " CA  ASN A 217 " =    1.306
peak=    3.318 closest distance to " CA  GLN A 194 " =    1.027
peak=    3.317 closest distance to " O   HOH Z  63 " =    2.171
peak=    3.317 closest distance to " O   HOH Z 411 " =    1.907
peak=    3.313 closest distance to " O   HOH Z 313 " =    1.736
peak=    3.306 closest distance to " NE1 TRP A 274 " =    0.888
peak=    3.298 closest distance to " CA  ASP A 191 " =    1.130
peak=    3.298 closest distance to " CB  ALA A   1 " =    1.215
peak=    3.294 closest distance to " OG BSER A 210 " =    1.327
peak=    3.292 closest distance to " CG2 ILE A 106 " =    0.809
peak=    3.292 closest distance to " CA  VAL A 126 " =    0.979
peak=    3.287 closest distance to " O   HOH Z 428 " =    3.725
peak=    3.283 closest distance to " CB  TRP A 266 " =    1.083
peak=    3.275 closest distance to " O   HOH Z 374 " =    2.457
peak=    3.269 closest distance to " O   HOH Z  40 " =    2.036
peak=    3.263 closest distance to " CB  SER A 141 " =    1.084
peak=    3.263 closest distance to " CB  GLN A 205 " =    1.108
peak=    3.261 closest distance to " N   SER A 135 " =    1.239
peak=    3.259 closest distance to " CA  LEU A 101 " =    1.367
peak=    3.258 closest distance to " CG2 VAL A 257 " =    0.831
peak=    3.257 closest distance to " NH1 ARG A  14 " =    1.115
peak=    3.251 closest distance to " CB  ASN A 110 " =    1.060
peak=    3.249 closest distance to " O   HOH Z 291 " =    1.671
peak=    3.246 closest distance to " O   HOH Z 380 " =    1.938
peak=    3.244 closest distance to " O   HOH Z 303 " =    1.539
peak=    3.240 closest distance to " O   HOH Z 238 " =    0.880
peak=    3.239 closest distance to " O   HOH Z 263 " =    1.476
peak=    3.239 closest distance to " CB  TYR A 247 " =    0.997
peak=    3.237 closest distance to " O   HOH Z 155 " =    2.802
peak=    3.232 closest distance to " O   HOH Z 136 " =    1.282
peak=    3.229 closest distance to " O   HOH Z 284 " =    1.650
peak=    3.227 closest distance to " CA  ASP A 162 " =    1.078
peak=    3.227 closest distance to " CB  ASN A 215 " =    1.046
peak=    3.227 closest distance to " CB  SER A  62 " =    1.157
peak=    3.226 closest distance to " O   HOH Z 423 " =    3.268
peak=    3.225 closest distance to " O   HOH Z   1 " =    1.881
peak=    3.222 closest distance to " O   HOH Z 273 " =    3.319
peak=    3.222 closest distance to " O   HOH Z 334 " =    1.329
peak=    3.220 closest distance to " O   HOH Z 329 " =    3.639
peak=    3.216 closest distance to " O   HOH Z 214 " =    1.247
peak=    3.216 closest distance to " O   HOH Z  38 " =    1.248
peak=    3.214 closest distance to " O   HOH Z 113 " =    1.870
peak=    3.213 closest distance to " CE BMET A  47 " =    1.179
peak=    3.207 closest distance to " CZ2 TRP A 274 " =    1.523
peak=    3.203 closest distance to " CG2 ILE A 234 " =    2.043
peak=    3.196 closest distance to " CG  MET A 185 " =    1.185
peak=    3.196 closest distance to " CA  ALA A 158 " =    1.282
peak=    3.196 closest distance to " CG  PRO A 280 " =    0.800
peak=    3.194 closest distance to " CD2 TYR A  30 " =    0.843
peak=    3.192 closest distance to " OH  TYR A 116 " =    1.072
peak=    3.181 closest distance to " O   HOH Z 173 " =    2.365
peak=    3.181 closest distance to " O   HOH Z 180 " =    2.191
peak=    3.180 closest distance to " CB  ARG A 259 " =    1.953
peak=    3.180 closest distance to " CB  PRO A 213 " =    1.859
peak=    3.180 closest distance to " CA  SER A  32 " =    1.660
peak=    3.180 closest distance to " CG  MET A  93 " =    1.057
peak=    3.178 closest distance to " O   HOH Z 267 " =    1.942
peak=    3.178 closest distance to " OG  SER A  62 " =    2.843
peak=    3.171 closest distance to " O   HOH Z 185 " =    1.628
peak=    3.169 closest distance to " CD2 HIS A  81 " =    1.103
peak=    3.164 closest distance to " O   HOH Z 227 " =    2.191
peak=    3.163 closest distance to " O   HOH Z 412 " =    3.718
peak=    3.161 closest distance to " O   HOH Z 337 " =    3.544
peak=    3.160 closest distance to " O   HOH Z  11 " =    1.399
peak=    3.155 closest distance to " O   HOH Z 163 " =    1.335
peak=    3.153 closest distance to " O   HOH Z 404 " =    1.995
peak=    3.149 closest distance to " CA  ARG A 195 " =    1.130
peak=    3.148 closest distance to " O   HOH Z 295 " =    1.409
peak=    3.147 closest distance to " CZ2 TRP A 150 " =    1.047
peak=    3.143 closest distance to " CG  MET A 188 " =    1.206
peak=    3.142 closest distance to " O   HOH Z 194 " =    2.121
peak=    3.140 closest distance to " OD1 ASN A  60 " =    1.576
peak=    3.133 closest distance to " C   ALA A   1 " =    1.751
peak=    3.131 closest distance to " O   HOH Z 162 " =    1.674
peak=    3.129 closest distance to " C   ARG A  56 " =    1.342
peak=    3.128 closest distance to " O   HOH Z  59 " =    2.037
peak=    3.123 closest distance to " O   HOH Z  39 " =    2.596
peak=    3.122 closest distance to " O   HOH Z 214 " =    2.295
peak=    3.116 closest distance to " CB  VAL A 268 " =    0.826
peak=    3.116 closest distance to " CA  PHE A  59 " =    0.861
peak=    3.115 closest distance to " O   HOH Z 130 " =    1.145
peak=    3.110 closest distance to " O   HOH Z 145 " =    2.351
peak=    3.104 closest distance to " NH1 ARG A 269 " =    0.855
peak=    3.103 closest distance to " CB  PRO A 243 " =    1.171
peak=    3.099 closest distance to " CA  LYS A 290 " =    1.151
peak=    3.096 closest distance to " CB  ARG A 190 " =    1.794
peak=    3.095 closest distance to " O   HOH Z 147 " =    1.793
peak=    3.070 closest distance to " O   HOH Z  59 " =    2.306
peak=    3.066 closest distance to " OG BSER A 164 " =    1.989
peak=    3.060 closest distance to " CH2 TRP A 274 " =    2.081
peak=    3.057 closest distance to " O   HOH Z 381 " =    1.453
peak=    3.057 closest distance to " NH2BARG A 190 " =    1.900
peak=    3.050 closest distance to " O   HOH Z 197 " =    1.933
peak=    3.032 closest distance to " O   HOH Z  88 " =    3.452
peak=    3.014 closest distance to " O   HOH Z 215 " =    1.543
peak=    3.008 closest distance to " O   HOH Z 438 " =    2.195

                           ----------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: 0.557 - 5.804
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 205
   mapped sites are within: 0.718 - 5.804

peak=   -5.069 closest distance to " CG2 VAL A 230 " =    0.718
peak=   -4.473 closest distance to " CD  ARG A 156 " =    2.057
peak=   -4.412 closest distance to " C   HIS A 108 " =    1.187
peak=   -4.410 closest distance to " OXT GLY A 302 " =    2.828
peak=   -4.346 closest distance to " SG  CYS A 254 " =    3.188
peak=   -4.284 closest distance to " CG2BVAL A  41 " =    2.628
peak=   -4.247 closest distance to " O   HOH Z 290 " =    0.886
peak=   -4.214 closest distance to " O   HOH Z 266 " =    4.516
peak=   -4.205 closest distance to " CG1 VAL A 296 " =    0.986
peak=   -4.136 closest distance to " CD1 LEU A 101 " =    2.504
peak=   -4.098 closest distance to " O   HOH Z  13 " =    1.647
peak=   -4.094 closest distance to " O   HOH Z 166 " =    1.842
peak=   -4.078 closest distance to " CE2 TYR A  30 " =    2.790
peak=   -4.074 closest distance to " O   PRO A 163 " =    2.024
peak=   -4.069 closest distance to " O   HOH Z 103 " =    1.781
peak=   -4.068 closest distance to " O   HOH Z 351 " =    1.439
peak=   -4.012 closest distance to " O   GLY A  80 " =    2.415
peak=   -4.007 closest distance to " C   THR A 279 " =    1.201
peak=   -3.989 closest distance to " O   ASN A  45 " =    1.798
peak=   -3.986 closest distance to " CB  ALA A 161 " =    2.459
peak=   -3.952 closest distance to " OG BSER A 134 " =    1.333
peak=   -3.901 closest distance to " O   HOH Z 362 " =    5.804
peak=   -3.864 closest distance to " O   HOH Z 423 " =    2.253
peak=   -3.839 closest distance to " ND2 ASN A  45 " =    0.990
peak=   -3.834 closest distance to " CD  GLN A  58 " =    1.323
peak=   -3.824 closest distance to " O   HOH Z 250 " =    1.380
peak=   -3.822 closest distance to " N   ALA A 226 " =    1.932
peak=   -3.799 closest distance to " O   MET A  40 " =    2.721
peak=   -3.770 closest distance to " O   ASN A 187 " =    1.415
peak=   -3.769 closest distance to " ND2 ASN A 187 " =    1.490
peak=   -3.764 closest distance to " O   VAL A  67 " =    2.673
peak=   -3.757 closest distance to " O   HOH Z 435 " =    2.629
peak=   -3.741 closest distance to " ND2 ASN A  39 " =    1.107
peak=   -3.741 closest distance to " O   HOH Z  11 " =    1.848
peak=   -3.727 closest distance to " CD1 PHE A 130 " =    2.229
peak=   -3.725 closest distance to " CB  ALA A 248 " =    1.947
peak=   -3.721 closest distance to " O   VAL A  67 " =    1.868
peak=   -3.714 closest distance to " N   ALA A 248 " =    1.667
peak=   -3.706 closest distance to " N   GLN A  58 " =    2.013
peak=   -3.691 closest distance to " O   HOH Z 426 " =    1.748
peak=   -3.687 closest distance to " O   PRO A 198 " =    1.240
peak=   -3.685 closest distance to " O   ALA A 256 " =    1.369
peak=   -3.658 closest distance to " O   ALA A  51 " =    1.494
peak=   -3.645 closest distance to " NH2 ARG A  66 " =    1.503
peak=   -3.631 closest distance to " CB  GLN A  11 " =    1.853
peak=   -3.626 closest distance to " CD1 PHE A  59 " =    1.934
peak=   -3.625 closest distance to " O   HOH Z 407 " =    2.801
peak=   -3.623 closest distance to " NH2 ARG A  79 " =    1.970
peak=   -3.619 closest distance to " CE  LYS A 166 " =    2.962
peak=   -3.615 closest distance to " O   HOH Z  92 " =    1.788
peak=   -3.613 closest distance to " O   HOH Z 431 " =    1.927
peak=   -3.612 closest distance to " OG ASER A 134 " =    1.155
peak=   -3.608 closest distance to " OD2 ASP A  50 " =    1.341
peak=   -3.607 closest distance to " O   HOH Z 118 " =    3.247
peak=   -3.593 closest distance to " OD1 ASN A  39 " =    2.194
peak=   -3.591 closest distance to " CD2 LEU A 300 " =    2.714
peak=   -3.585 closest distance to " O   HOH Z  56 " =    2.110
peak=   -3.581 closest distance to " O   HOH Z 165 " =    1.977
peak=   -3.573 closest distance to " CD1 TYR A 247 " =    2.313
peak=   -3.558 closest distance to " CA  VAL A 296 " =    0.935
peak=   -3.554 closest distance to " CG  GLN A 223 " =    2.353
peak=   -3.552 closest distance to " CG  ASP A 231 " =    0.869
peak=   -3.550 closest distance to " O   HOH Z 193 " =    1.746
peak=   -3.549 closest distance to " O   SER A 210 " =    1.877
peak=   -3.546 closest distance to " O   HOH Z  60 " =    1.902
peak=   -3.538 closest distance to " O   HOH Z 426 " =    2.418
peak=   -3.538 closest distance to " O   SER A 146 " =    0.959
peak=   -3.537 closest distance to " O   HOH Z 120 " =    1.090
peak=   -3.527 closest distance to " CD  LYS A 289 " =    2.513
peak=   -3.526 closest distance to " C   MET A 188 " =    1.573
peak=   -3.523 closest distance to " NE2 GLN A  88 " =    1.138
peak=   -3.520 closest distance to " O   HOH Z  11 " =    1.677
peak=   -3.504 closest distance to " N   THR A  52 " =    1.654
peak=   -3.501 closest distance to " OG  SER A  97 " =    2.300
peak=   -3.501 closest distance to " OG  SER A   3 " =    1.400
peak=   -3.498 closest distance to " CD1 PHE A  59 " =    2.198
peak=   -3.486 closest distance to " OD2 ASP A 191 " =    1.495
peak=   -3.485 closest distance to " CG2 ILE A 263 " =    2.217
peak=   -3.482 closest distance to " CZ  TYR A 169 " =    1.903
peak=   -3.476 closest distance to " CB  PHE A 208 " =    2.276
peak=   -3.475 closest distance to " O   HOH Z 191 " =    5.301
peak=   -3.464 closest distance to " O   HOH Z  71 " =    1.286
peak=   -3.459 closest distance to " O   HOH Z  63 " =    1.061
peak=   -3.458 closest distance to " O   HOH Z 377 " =    1.589
peak=   -3.454 closest distance to " CD  ARG A 139 " =    1.592
peak=   -3.448 closest distance to " CG  ASP A  50 " =    2.472
peak=   -3.448 closest distance to " CB  PRO A 163 " =    2.752
peak=   -3.447 closest distance to " NH2AARG A 275 " =    4.639
peak=   -3.440 closest distance to " O   GLY A 196 " =    1.000
peak=   -3.437 closest distance to " CA  GLY A 133 " =    1.875
peak=   -3.423 closest distance to " O   VAL A 197 " =    1.279
peak=   -3.423 closest distance to " O   TRP A  92 " =    1.875
peak=   -3.417 closest distance to " O   HOH Z 388 " =    1.987
peak=   -3.414 closest distance to " O   ALA A 160 " =    1.466
peak=   -3.409 closest distance to " O   PHE A 218 " =    1.618
peak=   -3.407 closest distance to " ND2 ASN A  69 " =    1.707
peak=   -3.404 closest distance to " O   HOH Z  34 " =    1.830
peak=   -3.387 closest distance to " O   HOH Z  44 " =    2.168
peak=   -3.386 closest distance to " O   VAL A 174 " =    1.915
peak=   -3.383 closest distance to " CG  GLU A   2 " =    1.833
peak=   -3.379 closest distance to " O   HOH Z 166 " =    2.038
peak=   -3.379 closest distance to " C   VAL A 265 " =    0.825
peak=   -3.375 closest distance to " C   ALA A 158 " =    1.217
peak=   -3.375 closest distance to " CD1 LEU A 228 " =    2.154
peak=   -3.372 closest distance to " O   HOH Z 196 " =    2.150
peak=   -3.370 closest distance to " N   SER A 276 " =    1.354
peak=   -3.370 closest distance to " N   THR A 157 " =    1.523
peak=   -3.359 closest distance to " O   HOH Z 234 " =    4.106
peak=   -3.356 closest distance to " NE2 GLN A 194 " =    1.741
peak=   -3.349 closest distance to " CG1 VAL A 112 " =    2.669
peak=   -3.347 closest distance to " N   THR A 235 " =    1.284
peak=   -3.343 closest distance to " O   HOH Z 283 " =    1.722
peak=   -3.340 closest distance to " O   HOH Z 172 " =    5.040
peak=   -3.338 closest distance to " CD2 TYR A 293 " =    2.049
peak=   -3.337 closest distance to " O   HOH Z 372 " =    2.192
peak=   -3.336 closest distance to " O   HOH Z 427 " =    1.403
peak=   -3.336 closest distance to " NE2 GLN A  88 " =    1.977
peak=   -3.336 closest distance to " C   GLY A  91 " =    1.285
peak=   -3.333 closest distance to " O   GLY A  75 " =    1.695
peak=   -3.329 closest distance to " O   ALA A 161 " =    1.678
peak=   -3.329 closest distance to " O   HOH Z 174 " =    4.306
peak=   -3.326 closest distance to " CB  ASN A  39 " =    2.170
peak=   -3.323 closest distance to " O   HOH Z  17 " =    1.121
peak=   -3.317 closest distance to " CB  PHE A 192 " =    1.980
peak=   -3.307 closest distance to " OG BSER A 134 " =    1.638
peak=   -3.305 closest distance to " CA  ASP A 298 " =    1.054
peak=   -3.304 closest distance to " CG  GLU A  53 " =    1.416
peak=   -3.295 closest distance to " O   HOH Z 126 " =    1.877
peak=   -3.292 closest distance to " OD1 ASP A 200 " =    1.254
peak=   -3.290 closest distance to " O   HOH Z 313 " =    1.295
peak=   -3.286 closest distance to " O   HOH Z  61 " =    1.516
peak=   -3.277 closest distance to " OXT GLY A 302 " =    3.344
peak=   -3.276 closest distance to " O   HOH Z 353 " =    2.127
peak=   -3.276 closest distance to " O   HOH Z 227 " =    1.100
peak=   -3.268 closest distance to " CD  ARG A 195 " =    5.098
peak=   -3.267 closest distance to " CB  ASP A 162 " =    2.587
peak=   -3.265 closest distance to " O   ILE A 120 " =    1.153
peak=   -3.256 closest distance to " O   HOH Z 210 " =    0.907
peak=   -3.252 closest distance to " O   GLY A 118 " =    2.215
peak=   -3.250 closest distance to " CG2 THR A 221 " =    2.359
peak=   -3.247 closest distance to " O  BHOH Z 338 " =    1.378
peak=   -3.243 closest distance to " O   GLY A  80 " =    2.565
peak=   -3.237 closest distance to " O   HOH Z 183 " =    1.527
peak=   -3.228 closest distance to " N   GLN A 122 " =    1.404
peak=   -3.224 closest distance to " O   LYS A 117 " =    1.547
peak=   -3.223 closest distance to " CE  MET A 105 " =    2.140
peak=   -3.217 closest distance to " CZ  PHE A 130 " =    0.911
peak=   -3.210 closest distance to " OD1 ASN A 173 " =    1.712
peak=   -3.209 closest distance to " O   SER A  95 " =    1.498
peak=   -3.208 closest distance to " CB  ASP A 132 " =    2.297
peak=   -3.206 closest distance to " CD2 LEU A 167 " =    1.722
peak=   -3.201 closest distance to " O   SER A 271 " =    2.027
peak=   -3.198 closest distance to " O   HOH Z 252 " =    4.249
peak=   -3.197 closest distance to " N   VAL A 230 " =    1.066
peak=   -3.196 closest distance to " CA  GLY A  23 " =    1.847
peak=   -3.189 closest distance to " O   HOH Z 113 " =    2.130
peak=   -3.188 closest distance to " N   ARG A  66 " =    1.804
peak=   -3.188 closest distance to " CG2 VAL A 296 " =    1.469
peak=   -3.186 closest distance to " O   ARG A 219 " =    1.787
peak=   -3.183 closest distance to " CE3 TRP A 150 " =    2.099
peak=   -3.182 closest distance to " OD2 ASP A 286 " =    2.366
peak=   -3.180 closest distance to " CE BMET A  47 " =    1.369
peak=   -3.177 closest distance to " N   HIS A 115 " =    2.011
peak=   -3.174 closest distance to " CB  ALA A 291 " =    2.191
peak=   -3.170 closest distance to " CG  ASP A 132 " =    2.257
peak=   -3.167 closest distance to " CG1 VAL A  78 " =    3.071
peak=   -3.167 closest distance to " CD2 TRP A 274 " =    1.005
peak=   -3.162 closest distance to " O   HOH Z 193 " =    1.542
peak=   -3.157 closest distance to " O   HOH Z 110 " =    1.506
peak=   -3.150 closest distance to " CG2 VAL A 189 " =    2.079
peak=   -3.149 closest distance to " O   HOH Z 265 " =    2.027
peak=   -3.142 closest distance to " O   HOH Z 198 " =    1.871
peak=   -3.142 closest distance to " OD1 ASN A 249 " =    1.326
peak=   -3.141 closest distance to " O   LEU A 228 " =    2.363
peak=   -3.141 closest distance to " O   HOH Z 203 " =    1.613
peak=   -3.140 closest distance to " OD1 ASN A 249 " =    1.874
peak=   -3.138 closest distance to " CG  GLU A 277 " =    1.148
peak=   -3.137 closest distance to " O   HOH Z  52 " =    1.825
peak=   -3.134 closest distance to " O   HOH Z 166 " =    1.835
peak=   -3.129 closest distance to " OG1 THR A  82 " =    1.339
peak=   -3.124 closest distance to " O   HOH Z 422 " =    1.514
peak=   -3.122 closest distance to " CA  GLY A 241 " =    2.350
peak=   -3.116 closest distance to " CG  ARG A 269 " =    2.197
peak=   -3.111 closest distance to " O   LEU A 167 " =    1.651
peak=   -3.109 closest distance to " NH2 ARG A  79 " =    1.775
peak=   -3.108 closest distance to " OD1 ASN A 301 " =    2.053
peak=   -3.108 closest distance to " O   HOH Z  97 " =    1.260
peak=   -3.107 closest distance to " O   HOH Z 310 " =    3.583
peak=   -3.105 closest distance to " CA  GLY A 133 " =    2.222
peak=   -3.104 closest distance to " O   HOH Z 134 " =    2.654
peak=   -3.103 closest distance to " CD2 LEU A 237 " =    2.566
peak=   -3.097 closest distance to " O   HOH Z 424 " =    3.018
peak=   -3.090 closest distance to " O   HOH Z 360 " =    2.443
peak=   -3.087 closest distance to " CG  PHE A 283 " =    2.686
peak=   -3.078 closest distance to " O   HOH Z  55 " =    2.439
peak=   -3.068 closest distance to " C   ASN A 148 " =    0.994
peak=   -3.059 closest distance to " OD2 ASP A 171 " =    2.417
peak=   -3.058 closest distance to " O   PRO A 198 " =    1.237
peak=   -3.057 closest distance to " O   HOH Z 111 " =    4.676
peak=   -3.049 closest distance to " OH  TYR A 169 " =    0.852
peak=   -3.045 closest distance to " O   HOH Z 151 " =    1.547
peak=   -3.026 closest distance to " O   HOH Z 429 " =    2.102
peak=   -3.022 closest distance to " NH1 ARG A  66 " =    4.904

================= 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    :  0.4828 0.4721   6.281072e+00   6.272507e+00
   1_bss:  0.4738 0.4643   6.274790e+00   6.264192e+00
   1_xyz:  0.3870 0.4102   6.152572e+00   6.194391e+00
   1_adp:  0.3408 0.3893   6.067450e+00   6.159042e+00
   1_occ:  0.3399 0.3890   6.066010e+00   6.158263e+00
   2_bss:  0.3368 0.3831   6.064842e+00   6.156108e+00
   2_xyz:  0.2404 0.2861   5.782837e+00   5.933320e+00
   2_adp:  0.2134 0.2639   5.685733e+00   5.853337e+00
   2_occ:  0.2130 0.2635   5.685089e+00   5.853133e+00
   3_bss:  0.2107 0.2616   5.682657e+00   5.850204e+00
   3_xyz:  0.1584 0.2046   5.439805e+00   5.643173e+00
   3_adp:  0.1513 0.1934   5.387492e+00   5.582868e+00
   3_occ:  0.1510 0.1935   5.386854e+00   5.582945e+00
   4_bss:  0.1511 0.1934   5.386485e+00   5.580193e+00
   4_xyz:  0.1275 0.1676   5.239547e+00   5.448842e+00
   4_adp:  0.1229 0.1649   5.211323e+00   5.428933e+00
   4_occ:  0.1228 0.1649   5.210814e+00   5.428657e+00
   5_bss:  0.1229 0.1648   5.210999e+00   5.427606e+00
   5_xyz:  0.1173 0.1608   5.179288e+00   5.406352e+00
   5_adp:  0.1160 0.1613   5.175319e+00   5.408540e+00
   5_occ:  0.1160 0.1614   5.175305e+00   5.408797e+00
   5_bss:  0.1160 0.1614   5.175356e+00   5.408916e+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:  0.361  12.593   7.885   9.077   8.334   0.000   0.000   0.000
   1_xyz:  0.361  12.593   7.885   9.077   8.334   0.000   0.000   0.000
   1_adp:  0.361  12.593   7.885   9.077   8.334   0.000   0.000   0.000
   1_occ:  0.361  12.593   7.885   9.077   8.334   0.000   0.000   0.000
   2_bss:  0.339  34.739   4.231   5.234   5.260   0.000   0.000   0.000
   2_xyz:  0.339  34.739   4.231   5.234   5.260   0.000   0.000   0.000
   2_adp:  0.339  34.739   4.231   5.234   5.260   0.000   0.000   0.000
   2_occ:  0.339  34.739   4.231   5.234   5.260   0.000   0.000   0.000
   3_bss:  0.327  30.583   2.043   3.428   3.467   0.000   0.000   0.000
   3_xyz:  0.327  30.583   2.043   3.428   3.467   0.000   0.000   0.000
   3_adp:  0.327  30.583   2.043   3.428   3.467   0.000   0.000   0.000
   3_occ:  0.327  30.583   2.043   3.428   3.467   0.000   0.000   0.000
   4_bss:  0.317  30.583   1.149   2.501   2.618   0.000   0.000   0.000
   4_xyz:  0.317  30.583   1.149   2.501   2.618   0.000   0.000   0.000
   4_adp:  0.317  30.583   1.149   2.501   2.618   0.000   0.000   0.000
   4_occ:  0.317  30.583   1.149   2.501   2.618   0.000   0.000   0.000
   5_bss:  0.321  37.097   0.954   2.169   2.403   0.000   0.000   0.000
   5_xyz:  0.321  37.097   0.954   2.169   2.403   0.000   0.000   0.000
   5_adp:  0.321  37.097   0.954   2.169   2.403   0.000   0.000   0.000
   5_occ:  0.321  37.097   0.954   2.169   2.403   0.000   0.000   0.000
   5_bss:  0.323  40.019  -0.863   0.292   0.571   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.110 0.4314  0.5030    69506.314
   1_bss:  57.450 0.4248  0.6317    67181.437
   1_xyz:  48.230 0.5405  0.7928    49601.033
   1_adp:  43.306 0.6022  0.9211    43123.197
   1_occ:  43.208 0.6034  0.9209    42942.758
   2_bss:  42.785 0.6084  0.8207    42234.732
   2_xyz:  30.079 0.7557  0.9859    21970.802
   2_adp:  26.363 0.7971  1.0242    17920.087
   2_occ:  26.332 0.7974  1.0245    17898.586
   3_bss:  26.211 0.7985  0.9544    17716.671
   3_xyz:  19.871 0.8627  1.0003    10862.745
   3_adp:  18.292 0.8782  1.0119     9663.136
   3_occ:  18.287 0.8782  1.0120     9658.924
   4_bss:  18.206 0.8789  0.9795     9567.007
   4_xyz:  15.344 0.9040  0.9906     7232.548
   4_adp:  14.890 0.9080  0.9914     6982.865
   4_occ:  14.877 0.9081  0.9915     6978.562
   5_bss:  14.866 0.9083  0.9825     6987.696
   5_xyz:  14.374 0.9124  0.9836     6674.151
   5_adp:  14.377 0.9125  0.9809     6699.696
   5_occ:  14.379 0.9125  0.9808     6704.809
   5_bss:  14.379 0.9125  0.9828     6708.140
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3159e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3159e+01
   1_xyz:   1.822  0.015  0.115 18.294  0.007  4.107   1.6084e-01
   1_adp:   1.822  0.015  0.115 18.294  0.007  4.107   1.6084e-01
   1_occ:   1.822  0.015  0.115 18.294  0.007  4.107   1.6084e-01
   2_bss:   1.822  0.015  0.115 18.294  0.007  4.107   1.6084e-01
   2_xyz:   1.145  0.008  0.081 16.400  0.004  4.122   7.8446e-02
   2_adp:   1.145  0.008  0.081 16.400  0.004  4.122   7.8446e-02
   2_occ:   1.145  0.008  0.081 16.400  0.004  4.122   7.8446e-02
   3_bss:   1.145  0.008  0.081 16.400  0.004  4.122   7.8446e-02
   3_xyz:   0.963  0.006  0.070 15.640  0.003  4.116   5.7675e-02
   3_adp:   0.963  0.006  0.070 15.640  0.003  4.116   5.7675e-02
   3_occ:   0.963  0.006  0.070 15.640  0.003  4.116   5.7675e-02
   4_bss:   0.963  0.006  0.070 15.640  0.003  4.116   5.7675e-02
   4_xyz:   0.975  0.006  0.073 15.399  0.004  4.120   5.7294e-02
   4_adp:   0.975  0.006  0.073 15.399  0.004  4.120   5.7294e-02
   4_occ:   0.975  0.006  0.073 15.399  0.004  4.120   5.7294e-02
   5_bss:   0.975  0.006  0.073 15.399  0.004  4.120   5.7294e-02
   5_xyz:   0.947  0.005  0.072 15.242  0.003  4.114   5.4517e-02
   5_adp:   0.947  0.005  0.072 15.242  0.003  4.114   5.4517e-02
   5_occ:   0.947  0.005  0.072 15.242  0.003  4.114   5.4517e-02
   5_bss:   0.947  0.005  0.072 15.242  0.003  4.114   5.4517e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.039   6.8856e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.039   6.8856e+00
   1_xyz:  16.700  0.187  0.573 85.678  0.048  2.100   1.1266e-01
   1_adp:  16.700  0.187  0.573 85.678  0.048  2.100   1.1266e-01
   1_occ:  16.700  0.187  0.573 85.678  0.048  2.100   1.1266e-01
   2_bss:  16.700  0.187  0.573 85.678  0.048  2.100   1.1266e-01
   2_xyz:   7.153  0.080  0.382 82.898  0.043  2.289   6.3480e-02
   2_adp:   7.153  0.080  0.382 82.898  0.043  2.289   6.3480e-02
   2_occ:   7.153  0.080  0.382 82.898  0.043  2.289   6.3480e-02
   3_bss:   7.153  0.080  0.382 82.898  0.043  2.289   6.3480e-02
   3_xyz:   6.747  0.051  0.247 81.857  0.034  2.319   4.2284e-02
   3_adp:   6.747  0.051  0.247 81.857  0.034  2.319   4.2284e-02
   3_occ:   6.747  0.051  0.247 81.857  0.034  2.319   4.2284e-02
   4_bss:   6.747  0.051  0.247 81.857  0.034  2.319   4.2284e-02
   4_xyz:   6.585  0.034  0.375 82.256  0.030  2.285   3.9096e-02
   4_adp:   6.585  0.034  0.375 82.256  0.030  2.285   3.9096e-02
   4_occ:   6.585  0.034  0.375 82.256  0.030  2.285   3.9096e-02
   5_bss:   6.585  0.034  0.375 82.256  0.030  2.285   3.9096e-02
   5_xyz:   6.472  0.043  0.373 82.476  0.030  2.334   3.0349e-02
   5_adp:   6.472  0.043  0.373 82.476  0.030  2.334   3.0349e-02
   5_occ:   6.472  0.043  0.373 82.476  0.030  2.334   3.0349e-02
   5_bss:   6.472  0.043  0.373 82.476  0.030  2.334   3.0349e-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:  82.96   0.00  13.07  71.89   0.00  10.42  82.96   0.00  27.47
   1_occ:  82.96   0.00  13.07  71.89   0.00  10.42  82.96   0.00  27.47
   2_bss:  82.96   0.00  13.07  71.89   0.00  10.42  82.96   0.00  27.47
   2_xyz:  82.96   0.00  13.07  71.89   0.00  10.42  82.96   0.00  27.47
   2_adp:  88.31   0.00  12.91  76.56   0.00   9.30  88.31   2.30  32.56
   2_occ:  88.31   0.00  12.91  76.56   0.00   9.30  88.31   2.30  32.56
   3_bss:  88.31   0.00  12.91  76.56   0.00   9.30  88.31   2.30  32.56
   3_xyz:  88.31   0.00  12.91  76.56   0.00   9.30  88.31   2.30  32.56
   3_adp:  84.05   0.00  12.91  76.18   0.00   9.02  84.05   2.01  34.07
   3_occ:  84.05   0.00  12.91  76.18   0.00   9.02  84.05   2.01  34.07
   4_bss:  84.05   0.00  12.91  76.18   0.00   9.02  84.05   2.01  34.07
   4_xyz:  84.05   0.00  12.91  76.18   0.00   9.02  84.05   2.01  34.07
   4_adp:  79.54   0.00  13.15  79.54   0.00   8.96  78.79   2.29  35.96
   4_occ:  79.54   0.00  13.15  79.54   0.00   8.96  78.79   2.29  35.96
   5_bss:  79.54   0.00  13.15  79.54   0.00   8.96  78.79   2.29  35.96
   5_xyz:  79.54   0.00  13.15  79.54   0.00   8.96  78.79   2.29  35.96
   5_adp:  81.45   0.00  13.12  81.45   0.00   8.92  76.99   1.80  36.01
   5_occ:  81.45   0.00  13.12  81.45   0.00   8.92  76.99   1.80  36.01
   5_bss:  83.34   1.89  15.01  83.34   1.89  10.81  78.88   3.69  37.90
------------------------------------------------------------------------
 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:    1.223    0.039    0.426
   1_adp:    1.223    0.039    0.426
   1_occ:    1.223    0.039    0.426
   2_bss:    1.223    0.039    0.426
   2_xyz:    1.654    0.037    0.601
   2_adp:    1.654    0.037    0.601
   2_occ:    1.654    0.037    0.601
   3_bss:    1.654    0.037    0.601
   3_xyz:    1.629    0.048    0.651
   3_adp:    1.629    0.048    0.651
   3_occ:    1.629    0.048    0.651
   4_bss:    1.629    0.048    0.651
   4_xyz:    1.764    0.056    0.705
   4_adp:    1.764    0.056    0.705
   4_occ:    1.764    0.056    0.705
   5_bss:    1.764    0.056    0.705
   5_xyz:    1.825    0.035    0.719
   5_adp:    1.825    0.035    0.719
   5_occ:    1.825    0.035    0.719
   5_bss:    1.825    0.035    0.719
------------------------------------------------------------------------

CPU time actual refinement: 287.01


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_200/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_200/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_200/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_200/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_200/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 286.88 
  Macro-tasks:
    bulk solvent and scale       = 34.70  
    individual site refinement   = 117.15 
    weights calculation          = 28.55  
    collect and process          = 5.54   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 186.06 
  Micro-tasks:
    mask                            = 2.01   
    f_calc                          = 89.11  
    alpha_beta                      = 7.15   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 97.21  
    fmodel                         = 6.11   
    r_factors                      = 0.19   
    phase_errors                   = 8.69   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 211.71 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.056 micro seconds
Total CPU time: 4.98 minutes
from_scatterers_fft:    638 calls, 88.75 s
gradients_fft:          582 calls, 85.86 s

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

# Date 2008-01-16 Time 00:57:20 PST -0800 (1200473840.62 s)
Start R-work = 0.4828, R-free = 0.4721 (no bulk solvent and anisotropic scale)
Final R-work = 0.1339, R-free = 0.1769 (no bulk solvent and anisotropic scale)

Start R-work = 0.4738, R-free = 0.4643
Final R-work = 0.1160, R-free = 0.1614