# Date 2008-01-16 Time 01:09:15 PST -0800 (1200474555.98 s)
#phil __OFF__

Command line arguments: "../294.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29980
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 294

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.6953, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8871 1.97077
Completeness in resolution range: 0.94862
Completeness with d_max=infinity: 0.945689

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8871
                             d_min =   1.9708

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8871 1.97077
Completeness in resolution range: 0.94862
Completeness with d_max=infinity: 0.945689

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8875 -  4.2168 [2176/2203]  1956   220  10.1%
  bin  2:  4.2168 -  3.3596 [2070/2086]  1864   206  10.0%
  bin  3:  3.3596 -  2.9386 [2062/2081]  1857   205   9.9%
  bin  4:  2.9386 -  2.6717 [2041/2071]  1835   206  10.1%
  bin  5:  2.6717 -  2.4811 [2009/2028]  1810   199   9.9%
  bin  6:  2.4811 -  2.3354 [2023/2048]  1818   205  10.1%
  bin  7:  2.3354 -  2.2188 [2014/2048]  1819   195   9.7%
  bin  8:  2.2188 -  2.1225 [1988/2018]  1781   207  10.4%
  bin  9:  2.1225 -  2.0410 [1979/2021]  1789   190   9.6%
  bin 10:  2.0410 -  1.9708 [1227/2046]  1101   126  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_294/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 13
        2.18 -     2.86: 1153
        2.86 -     3.54: 4450
        3.54 -     4.22: 9256
        4.22 -     4.90: 13568
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.497 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.667 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.749 3.120 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.831 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28435 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_294/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_294/model_refine_001.geo

CPU time processing inputs: 9.36


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.69535 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4597   r_free= 0.4435   ksol= 0.00   Bsol= 0.00   scale= 0.810    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.259570                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7030 0.99   1411  156 0.3735 0.3540      6.5521      6.5212|
|  2:  4.7030 -  3.7526 0.99   1354  152 0.3534 0.3882      6.6842      6.7794|
|  3:  3.7526 -  3.2841 0.99   1324  147 0.4135 0.3725      6.6186      6.5861|
|  4:  3.2841 -  2.9864 0.99   1329  142 0.4494 0.4663      6.4954      6.4832|
|  5:  2.9864 -  2.7739 0.99   1308  151 0.4802 0.4541      6.3355      6.3352|
|  6:  2.7739 -  2.6112 0.99   1309  142 0.4888 0.5443       6.265      6.2512|
|  7:  2.6112 -  2.4811 0.99   1287  146 0.4848 0.4713      6.2168      6.1305|
|  8:  2.4811 -  2.3735 0.98   1287  145 0.5123 0.4755       6.182      6.1664|
|  9:  2.3735 -  2.2825 0.98   1311  140 0.5198 0.4844      6.0959       6.142|
| 10:  2.2825 -  2.2040 0.98   1295  143 0.5329 0.4472      6.1309      6.0456|
| 11:  2.2040 -  2.1353 0.99   1273  148 0.5201 0.4889       6.033      6.0343|
| 12:  2.1353 -  2.0744 0.97   1274  136 0.5172 0.4598      5.9631      5.9808|
| 13:  2.0744 -  2.0199 0.98   1280  138 0.5271 0.4736       5.893      5.8067|
| 14:  2.0199 -  1.9708 0.46    588   73 0.5066 0.4888      5.9001      5.7686|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8875 -  4.7030  1411   156  0.71  32.98   0.81     0.74      66638.54|
|  2:  4.7030 -  3.7526  1354   152  0.73  32.30   0.90     0.80      91129.33|
|  3:  3.7526 -  3.2841  1324   147  0.65  39.75   0.86     0.76      96221.13|
|  4:  3.2841 -  2.9864  1329   142  0.57  46.46   0.81     0.65      87470.37|
|  5:  2.9864 -  2.7739  1308   151  0.46  55.35   0.76     0.54      76199.69|
|  6:  2.7739 -  2.6112  1309   142  0.41  58.98   0.73     0.47      69809.07|
|  7:  2.6112 -  2.4811  1287   146  0.40  59.97   0.77     0.46      63905.60|
|  8:  2.4811 -  2.3735  1287   145  0.42  58.47   0.74     0.49      54566.95|
|  9:  2.3735 -  2.2825  1311   140  0.44  56.53   0.72     0.54      47922.31|
| 10:  2.2825 -  2.2040  1295   143  0.47  54.67   0.74     0.54      40563.32|
| 11:  2.2040 -  2.1353  1273   148  0.44  57.06   0.76     0.55      40328.39|
| 12:  2.1353 -  2.0744  1274   136  0.43  57.61   0.76     0.53      36826.25|
| 13:  2.0744 -  2.0199  1280   138  0.42  58.78   0.74     0.52      32368.06|
| 14:  2.0199 -  1.9708   588    73  0.48  53.53   0.76     0.49      23787.36|
|alpha:            min =        0.46 max =            0.80 mean =         0.58|
|beta:             min =    23787.36 max =        96221.13 mean =     60896.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           89.93 mean =        51.30|
|phase err.(test): min =        0.00 max =           89.93 mean =        51.61|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.655305              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.598   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.804968              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.984   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       27 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      179 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      695 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1512 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2648 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3927 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5129 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6589 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7709 |
|-----------------------------------------------------------------------------|
|-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 |       53.595 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.027 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    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 = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4675   r_free= 0.4493   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.262497                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4513   r_free= 0.4355   ksol= 0.36   Bsol= 20.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.04,7.43,9.76,0.00,0.00,0.00); trace/3= 8.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.250089                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.678209              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.963   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.801563              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.847   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4513      final r-factor (work) = 0.3544          |
| start r-factor (free) = 0.4355      final r-factor (free) = 0.3719          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.7630 = 8.68 * 0.50 * 6.2611 + 1.00 * 53.5955                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.7598 = 8.68 * 0.50 * 6.1376 + 1.00 * 0.1282                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3544      final r-factor (work) = 0.3004          |
| start r-factor (free) = 0.3719      final r-factor (free) = 0.3451          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9340 = 0.80 * 1.00 * 6.1376 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8236 = 0.80 * 1.00 * 6.0006 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    60.71   11.82    None  None   None       |
|    all(noH): 2823   0      0.00    60.71   11.82    None  None   None       |
|    Sol.    : 438    0      0.00    60.71   26.59    None  None   None       |
|    Mac.    : 2385   0      0.00    52.86   9.11     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.071: 1045   |   5:    30.355 -  36.426:  100        |
|      1:     6.071 -  12.142:  773   |   6:    36.426 -  42.497:   65        |
|      2:    12.142 -  18.213:  406   |   7:    42.497 -  48.569:   45        |
|      3:    18.213 -  24.284:  235   |   8:    48.569 -  54.640:   16        |
|      4:    24.284 -  30.355:  135   |   9:    54.640 -  60.711:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3004 r_free = 0.3451             target_work(ml) = 5.970         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3001 r_free = 0.3458             target_work(ml) = 5.969         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3001   r_free= 0.3458   ksol= 0.36   Bsol= 20.00   scale= 1.094   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.04,7.43,9.76,0.00,0.00,0.00); trace/3= 8.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.968952                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2970   r_free= 0.3419   ksol= 0.34   Bsol= 40.07   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.00,3.92,6.56,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.968671                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.677546              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.933   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.400817              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.512  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2970      final r-factor (work) = 0.2073          |
| start r-factor (free) = 0.3419      final r-factor (free) = 0.2532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1610 = 3.68 * 0.50 * 6.0001 + 1.00 * 0.1282                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7569 = 3.68 * 0.50 * 5.8149 + 1.00 * 0.0646                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2073      final r-factor (work) = 0.1877          |
| start r-factor (free) = 0.2532      final r-factor (free) = 0.2391          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3466 = 0.40 * 1.00 * 5.8149 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1543 = 0.40 * 1.00 * 5.6091 + 1.00 * 0.9060                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.56  12.05    None  None   None       |
|    all(noH): 2823   0      0.00    102.56  12.05    None  None   None       |
|    Sol.    : 438    0      0.00    62.76   31.82    None  None   None       |
|    Mac.    : 2385   0      0.00    102.56  8.41     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 -  10.256: 1764   |   5:    51.282 -  61.538:   20        |
|      1:    10.256 -  20.513:  562   |   6:    61.538 -  71.794:    2        |
|      2:    20.513 -  30.769:  177   |   7:    71.794 -  82.051:    0        |
|      3:    30.769 -  41.025:  183   |   8:    82.051 -  92.307:    0        |
|      4:    41.025 -  51.282:  114   |   9:    92.307 - 102.563:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1877 r_free = 0.2391             target_work(ml) = 5.579         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1875 r_free = 0.2389             target_work(ml) = 5.579         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1875   r_free= 0.2389   ksol= 0.34   Bsol= 40.07   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.00,3.92,6.56,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.578693                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1859   r_free= 0.2390   ksol= 0.33   Bsol= 40.07   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.00,2.63,4.69,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.579542                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.320602              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.334  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 13.149643             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.490   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1859      final r-factor (work) = 0.1437          |
| start r-factor (free) = 0.2390      final r-factor (free) = 0.1895          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5859 = 2.32 * 0.50 * 5.6203 + 1.00 * 0.0646                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4040 = 2.32 * 0.50 * 5.4696 + 1.00 * 0.0576                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1437      final r-factor (work) = 0.1339          |
| start r-factor (free) = 0.1895      final r-factor (free) = 0.1845          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 71.9725 = 13.15 * 1.00 * 5.4696 + 1.00 * 0.0493                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 69.8456 = 13.15 * 1.00 * 5.3103 + 1.00 * 0.0174                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.39   13.23    None  None   None       |
|    all(noH): 2823   0      0.00    87.39   13.23    None  None   None       |
|    Sol.    : 438    0      0.85    87.39   38.72    None  None   None       |
|    Mac.    : 2385   0      0.00    85.86   8.55     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 -   8.739: 1639   |   5:    43.694 -  52.433:   89        |
|      1:     8.739 -  17.478:  580   |   6:    52.433 -  61.172:   74        |
|      2:    17.478 -  26.217:  168   |   7:    61.172 -  69.911:   39        |
|      3:    26.217 -  34.955:  110   |   8:    69.911 -  78.650:   16        |
|      4:    34.955 -  43.694:  103   |   9:    78.650 -  87.388:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1339 r_free = 0.1845             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1338 r_free = 0.1844             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1338   r_free= 0.1844   ksol= 0.33   Bsol= 40.07   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.00,2.63,4.69,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.296944                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1339   r_free= 0.1841   ksol= 0.31   Bsol= 40.07   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.64,4.44,0.00,0.00,0.00); trace/3= 3.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.296022                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.700582              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.564  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.349717              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.559   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1339      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1841      final r-factor (free) = 0.1682          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8829 = 3.70 * 0.50 * 5.3102 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7715 = 3.70 * 0.50 * 5.2421 + 1.00 * 0.0721                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1170      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1682      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8543 = 0.35 * 1.00 * 5.2421 + 1.00 * 0.0210                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8579 = 0.35 * 1.00 * 5.1946 + 1.00 * 0.0412                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.92   12.36    None  None   None       |
|    all(noH): 2823   0      0.00    87.92   12.36    None  None   None       |
|    Sol.    : 438    0      1.09    79.94   35.55    None  None   None       |
|    Mac.    : 2385   0      0.00    87.92   8.10     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 -   8.792: 1719   |   5:    43.961 -  52.754:   90        |
|      1:     8.792 -  17.585:  552   |   6:    52.754 -  61.546:   48        |
|      2:    17.585 -  26.377:  153   |   7:    61.546 -  70.338:   22        |
|      3:    26.377 -  35.169:  127   |   8:    70.338 -  79.130:    9        |
|      4:    35.169 -  43.961:  100   |   9:    79.130 -  87.923:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1615             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1149 r_free = 0.1615             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1615   ksol= 0.31   Bsol= 40.07   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.64,4.44,0.00,0.00,0.00); trace/3= 3.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.174272                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1615   ksol= 0.32   Bsol= 45.84   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,2.64,4.34,0.00,0.00,0.00); trace/3= 3.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.173977                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.293886              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.877  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.271394              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.589   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1149      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0295 = 2.29 * 0.50 * 5.1942 + 1.00 * 0.0721                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9913 = 2.29 * 0.50 * 5.1705 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4171 = 0.27 * 1.00 * 5.1705 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4114 = 0.27 * 1.00 * 5.1612 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.52   11.99    None  None   None       |
|    all(noH): 2823   0      0.00    88.52   11.99    None  None   None       |
|    Sol.    : 438    0      1.50    75.32   34.21    None  None   None       |
|    Mac.    : 2385   0      0.00    88.52   7.91     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 -   8.852: 1762   |   5:    44.261 -  53.113:   80        |
|      1:     8.852 -  17.704:  525   |   6:    53.113 -  61.965:   40        |
|      2:    17.704 -  26.556:  151   |   7:    61.965 -  70.817:   16        |
|      3:    26.556 -  35.409:  138   |   8:    70.817 -  79.669:    7        |
|      4:    35.409 -  44.261:  102   |   9:    79.669 -  88.521:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1570             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1570             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1570   ksol= 0.32   Bsol= 45.84   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,2.64,4.34,0.00,0.00,0.00); trace/3= 3.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158405                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7030 0.99   1411  156 0.1042 0.1316      5.4192      5.5619|
|  2:  4.7030 -  3.7526 0.99   1354  152 0.0873 0.1083      5.4504      5.6214|
|  3:  3.7526 -  3.2841 0.99   1324  147 0.1072 0.1513      5.4754      5.8322|
|  4:  3.2841 -  2.9864 0.99   1329  142 0.1206 0.1637      5.4435      5.6246|
|  5:  2.9864 -  2.7739 0.99   1308  151 0.1336 0.1566      5.3328      5.5003|
|  6:  2.7739 -  2.6112 0.99   1309  142 0.1245 0.2045      5.2199      5.5273|
|  7:  2.6112 -  2.4811 0.99   1287  146 0.1307 0.1627       5.202      5.3313|
|  8:  2.4811 -  2.3735 0.98   1287  145 0.1164 0.1709      5.0773      5.3186|
|  9:  2.3735 -  2.2825 0.98   1311  140 0.1211 0.1932      5.0288      5.3729|
| 10:  2.2825 -  2.2040 0.98   1295  143 0.1147 0.1550      4.9612      5.1226|
| 11:  2.2040 -  2.1353 0.99   1273  148 0.1178 0.1864      4.9506      5.3236|
| 12:  2.1353 -  2.0744 0.97   1274  136 0.1193 0.1546       4.909      5.1331|
| 13:  2.0744 -  2.0199 0.98   1280  138 0.1115 0.1776      4.7702      5.0097|
| 14:  2.0199 -  1.9708 0.46    588   73 0.0946 0.1623      4.6179      4.9011|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8875 -  4.7030  1411   156  0.94   9.47   0.98     0.96       7612.09|
|  2:  4.7030 -  3.7526  1354   152  0.95   8.04   1.02     1.00       9100.86|
|  3:  3.7526 -  3.2841  1324   147  0.93  11.36   1.03     1.02      10251.02|
|  4:  3.2841 -  2.9864  1329   142  0.92  13.31   1.01     1.00      10176.51|
|  5:  2.9864 -  2.7739  1308   151  0.90  15.88   1.00     0.97       8397.78|
|  6:  2.7739 -  2.6112  1309   142  0.89  16.80   0.98     0.95       7283.58|
|  7:  2.6112 -  2.4811  1287   146  0.90  15.72   0.99     0.94       6315.80|
|  8:  2.4811 -  2.3735  1287   145  0.91  15.12   1.00     0.98       5378.40|
|  9:  2.3735 -  2.2825  1311   140  0.91  15.45   1.01     0.98       4882.42|
| 10:  2.2825 -  2.2040  1295   143  0.90  15.93   1.01     0.97       4361.70|
| 11:  2.2040 -  2.1353  1273   148  0.90  16.74   1.00     0.97       4563.10|
| 12:  2.1353 -  2.0744  1274   136  0.91  15.95   1.01     1.01       4115.22|
| 13:  2.0744 -  2.0199  1280   138  0.90  16.03   1.00     0.98       3219.27|
| 14:  2.0199 -  1.9708   588    73  0.93  12.66   0.99     0.96       2286.03|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2286.03 max =        10251.02 mean =      6482.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.18|
|phase err.(test): min =        0.00 max =           88.37 mean =        13.68|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1570   ksol= 0.32   Bsol= 48.84   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-0.37,1.34,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158387                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1570   ksol= 0.32   Bsol= 48.84   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-0.37,1.34,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158387                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7030 0.99   1411  156 0.1042 0.1317      5.4188       5.562|
|  2:  4.7030 -  3.7526 0.99   1354  152 0.0873 0.1083      5.4507      5.6218|
|  3:  3.7526 -  3.2841 0.99   1324  147 0.1072 0.1513      5.4755      5.8322|
|  4:  3.2841 -  2.9864 0.99   1329  142 0.1206 0.1637      5.4434      5.6246|
|  5:  2.9864 -  2.7739 0.99   1308  151 0.1336 0.1566      5.3327      5.5002|
|  6:  2.7739 -  2.6112 0.99   1309  142 0.1245 0.2045      5.2198      5.5273|
|  7:  2.6112 -  2.4811 0.99   1287  146 0.1307 0.1627       5.202      5.3313|
|  8:  2.4811 -  2.3735 0.98   1287  145 0.1164 0.1709      5.0773      5.3185|
|  9:  2.3735 -  2.2825 0.98   1311  140 0.1211 0.1932      5.0288      5.3729|
| 10:  2.2825 -  2.2040 0.98   1295  143 0.1147 0.1550      4.9612      5.1226|
| 11:  2.2040 -  2.1353 0.99   1273  148 0.1178 0.1864      4.9506      5.3236|
| 12:  2.1353 -  2.0744 0.97   1274  136 0.1193 0.1546       4.909      5.1331|
| 13:  2.0744 -  2.0199 0.98   1280  138 0.1115 0.1776      4.7702      5.0097|
| 14:  2.0199 -  1.9708 0.46    588   73 0.0946 0.1623      4.6179      4.9011|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8875 -  4.7030  1411   156  0.94   9.47   0.98     0.96       7611.37|
|  2:  4.7030 -  3.7526  1354   152  0.95   8.05   1.02     1.00       9105.05|
|  3:  3.7526 -  3.2841  1324   147  0.93  11.36   1.03     1.02      10255.76|
|  4:  3.2841 -  2.9864  1329   142  0.92  13.31   1.01     1.00      10176.05|
|  5:  2.9864 -  2.7739  1308   151  0.90  15.88   1.00     0.97       8396.57|
|  6:  2.7739 -  2.6112  1309   142  0.89  16.80   0.98     0.95       7282.43|
|  7:  2.6112 -  2.4811  1287   146  0.90  15.71   0.99     0.94       6314.96|
|  8:  2.4811 -  2.3735  1287   145  0.91  15.12   1.00     0.98       5378.13|
|  9:  2.3735 -  2.2825  1311   140  0.91  15.45   1.01     0.98       4882.29|
| 10:  2.2825 -  2.2040  1295   143  0.90  15.93   1.01     0.97       4361.64|
| 11:  2.2040 -  2.1353  1273   148  0.90  16.74   1.00     0.97       4562.93|
| 12:  2.1353 -  2.0744  1274   136  0.91  15.95   1.01     1.01       4115.15|
| 13:  2.0744 -  2.0199  1280   138  0.90  16.03   1.00     0.98       3219.19|
| 14:  2.0199 -  1.9708   588    73  0.93  12.66   0.99     0.96       2285.92|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2285.92 max =        10255.76 mean =      6483.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.18|
|phase err.(test): min =        0.00 max =           88.37 mean =        13.68|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.01    91.53   15.00    None  None   None       |
|    all(noH): 2823   0      3.01    91.53   15.00    None  None   None       |
|    Sol.    : 438    0      4.51    78.32   37.22    None  None   None       |
|    Mac.    : 2385   0      3.01    91.53   10.92    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:     3.007 -  11.859: 1762   |   5:    47.268 -  56.120:   80        |
|      1:    11.859 -  20.711:  525   |   6:    56.120 -  64.972:   40        |
|      2:    20.711 -  29.563:  151   |   7:    64.972 -  73.824:   16        |
|      3:    29.563 -  38.416:  138   |   8:    73.824 -  82.676:    7        |
|      4:    38.416 -  47.268:  102   |   9:    82.676 -  91.528:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.209 - 4.144
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 294 from: 302
   mapped sites are within: 0.704 - 4.144

peak=   11.343 closest distance to " CB  VAL A 230 " =    1.468
peak=    9.731 closest distance to " CG2 VAL A 296 " =    1.507
peak=    6.519 closest distance to " CG  LEU A   5 " =    1.248
peak=    5.788 closest distance to " NE2 GLN A  11 " =    1.176
peak=    5.766 closest distance to " CD2 LEU A   5 " =    1.173
peak=    5.664 closest distance to " NH2 ARG A  56 " =    2.114
peak=    5.640 closest distance to " CG  PRO A  54 " =    1.353
peak=    5.376 closest distance to " CB  ARG A 275 " =    0.948
peak=    5.259 closest distance to " O   HOH Z 142 " =    1.815
peak=    5.217 closest distance to " CG  LEU A 228 " =    1.211
peak=    5.101 closest distance to " CB  GLN A 223 " =    1.503
peak=    4.883 closest distance to " CB  PRO A  54 " =    1.004
peak=    4.880 closest distance to " O   HOH Z 346 " =    1.604
peak=    4.837 closest distance to " O   HOH Z 232 " =    2.335
peak=    4.725 closest distance to " CG  PRO A 243 " =    1.150
peak=    4.672 closest distance to " O   HOH Z   9 " =    1.412
peak=    4.648 closest distance to " O   HOH Z 402 " =    1.448
peak=    4.628 closest distance to " CB  GLN A 183 " =    1.212
peak=    4.515 closest distance to " CG  PRO A 280 " =    0.897
peak=    4.513 closest distance to " CB  VAL A 230 " =    1.208
peak=    4.508 closest distance to " CB  ARG A  79 " =    1.415
peak=    4.473 closest distance to " O   HOH Z 248 " =    1.394
peak=    4.471 closest distance to " O   HOH Z 265 " =    2.123
peak=    4.460 closest distance to " O   HOH Z  61 " =    1.737
peak=    4.454 closest distance to " O   HOH Z 313 " =    1.972
peak=    4.453 closest distance to " ND2 ASN A 187 " =    1.640
peak=    4.445 closest distance to " CG  PRO A 198 " =    1.246
peak=    4.434 closest distance to " O   HOH Z 209 " =    2.297
peak=    4.432 closest distance to " CG  PRO A 213 " =    1.221
peak=    4.400 closest distance to " O   HOH Z 427 " =    2.968
peak=    4.345 closest distance to " O   SER A  87 " =    2.245
peak=    4.331 closest distance to " CB  ASN A 142 " =    1.097
peak=    4.311 closest distance to " O   HOH Z 272 " =    1.858
peak=    4.310 closest distance to " O   HOH Z  78 " =    1.659
peak=    4.295 closest distance to " CB  VAL A 265 " =    1.371
peak=    4.290 closest distance to " O   HOH Z 188 " =    2.776
peak=    4.272 closest distance to " CZ  PHE A 218 " =    1.127
peak=    4.230 closest distance to " O   HOH Z 287 " =    2.124
peak=    4.214 closest distance to " CB  ASN A 187 " =    2.095
peak=    4.210 closest distance to " C   PRO A 198 " =    1.547
peak=    4.207 closest distance to " O   HOH Z 369 " =    2.274
peak=    4.184 closest distance to " CD2 TRP A 179 " =    1.343
peak=    4.183 closest distance to " CB  GLU A 152 " =    1.140
peak=    4.146 closest distance to " O   HOH Z 193 " =    1.661
peak=    4.146 closest distance to " O   HOH Z  43 " =    2.060
peak=    4.131 closest distance to " CB  ASN A 148 " =    1.380
peak=    4.117 closest distance to " CB  SER A  63 " =    1.242
peak=    4.110 closest distance to " O   HOH Z 303 " =    2.081
peak=    4.096 closest distance to " N   ASN A  39 " =    1.185
peak=    4.085 closest distance to " N   PHE A 130 " =    1.240
peak=    4.052 closest distance to " O   HOH Z 126 " =    1.543
peak=    4.040 closest distance to " CB  VAL A 202 " =    1.586
peak=    4.029 closest distance to " O   HOH Z 234 " =    3.701
peak=    4.002 closest distance to " O   HOH Z 251 " =    1.563
peak=    3.996 closest distance to " CB  TRP A 266 " =    1.060
peak=    3.978 closest distance to " CB  ASN A  39 " =    0.911
peak=    3.977 closest distance to " O   HOH Z 423 " =    1.802
peak=    3.976 closest distance to " OG ASER A 258 " =    2.969
peak=    3.951 closest distance to " O   HOH Z 422 " =    2.477
peak=    3.934 closest distance to " O   HOH Z 130 " =    2.641
peak=    3.927 closest distance to " CD2 LEU A 228 " =    1.252
peak=    3.926 closest distance to " O   HOH Z  85 " =    1.491
peak=    3.920 closest distance to " O   HOH Z 411 " =    3.910
peak=    3.906 closest distance to " CA  TYR A  30 " =    0.951
peak=    3.889 closest distance to " O   HOH Z 403 " =    1.649
peak=    3.881 closest distance to " CG2 VAL A 257 " =    0.857
peak=    3.880 closest distance to " CB  ARG A 190 " =    1.680
peak=    3.878 closest distance to " CB  ALA A   9 " =    1.593
peak=    3.864 closest distance to " ND2 ASN A 249 " =    0.937
peak=    3.861 closest distance to " CB  GLU A 277 " =    3.584
peak=    3.845 closest distance to " O   HOH Z  97 " =    2.380
peak=    3.844 closest distance to " CB  GLU A  46 " =    0.982
peak=    3.839 closest distance to " O  BHOH Z 338 " =    2.416
peak=    3.834 closest distance to " O   HOH Z 258 " =    2.247
peak=    3.830 closest distance to " O   HOH Z 298 " =    1.702
peak=    3.808 closest distance to " CB  GLN A  88 " =    1.201
peak=    3.802 closest distance to " OG BSER A 164 " =    2.201
peak=    3.790 closest distance to " CG  LEU A 167 " =    1.256
peak=    3.771 closest distance to " O   HOH Z 128 " =    2.103
peak=    3.765 closest distance to " O   HOH Z 261 " =    2.030
peak=    3.762 closest distance to " O   HOH Z  21 " =    1.836
peak=    3.754 closest distance to " CE  LYS A  76 " =    0.922
peak=    3.743 closest distance to " CG1 ILE A  49 " =    1.571
peak=    3.742 closest distance to " O   HOH Z 425 " =    1.388
peak=    3.738 closest distance to " CA  ASN A 215 " =    0.966
peak=    3.732 closest distance to " NZ  LYS A  48 " =    1.151
peak=    3.726 closest distance to " O   HOH Z 273 " =    2.974
peak=    3.721 closest distance to " O   HOH Z  40 " =    1.679
peak=    3.713 closest distance to " O   HOH Z 128 " =    2.115
peak=    3.706 closest distance to " O   HOH Z  59 " =    1.924
peak=    3.704 closest distance to " O   HOH Z 359 " =    1.391
peak=    3.700 closest distance to " CA  ALA A  51 " =    0.935
peak=    3.698 closest distance to " CB  SER A   3 " =    1.213
peak=    3.690 closest distance to " CA  ARG A  36 " =    1.048
peak=    3.689 closest distance to " CB  THR A  31 " =    1.494
peak=    3.688 closest distance to " O   HOH Z   3 " =    2.028
peak=    3.686 closest distance to " O   HOH Z 286 " =    2.436
peak=    3.682 closest distance to " CG AARG A 275 " =    1.154
peak=    3.677 closest distance to " O   HOH Z 353 " =    2.612
peak=    3.673 closest distance to " O   HOH Z  44 " =    1.806
peak=    3.664 closest distance to " CA  SER A  87 " =    0.976
peak=    3.658 closest distance to " O   HOH Z 250 " =    1.396
peak=    3.657 closest distance to " CB  ASN A 110 " =    1.037
peak=    3.645 closest distance to " O   HOH Z  80 " =    1.644
peak=    3.643 closest distance to " O   HOH Z  97 " =    2.023
peak=    3.634 closest distance to " O   HOH Z 158 " =    3.192
peak=    3.632 closest distance to " O   HOH Z  63 " =    1.905
peak=    3.627 closest distance to " CG2 ILE A 120 " =    1.249
peak=    3.622 closest distance to " O   HOH Z 371 " =    2.895
peak=    3.603 closest distance to " O   HOH Z 337 " =    3.490
peak=    3.594 closest distance to " O   HOH Z 435 " =    2.057
peak=    3.594 closest distance to " CB  SER A  26 " =    1.769
peak=    3.590 closest distance to " O   HOH Z 299 " =    4.089
peak=    3.582 closest distance to " CG  MET A 185 " =    1.194
peak=    3.581 closest distance to " CD  LYS A 166 " =    1.284
peak=    3.573 closest distance to " O   ASP A 124 " =    1.182
peak=    3.566 closest distance to " CB BVAL A  41 " =    1.164
peak=    3.564 closest distance to " O   HOH Z 368 " =    2.065
peak=    3.562 closest distance to " O   HOH Z 180 " =    2.083
peak=    3.557 closest distance to " CB  ASN A 187 " =    1.066
peak=    3.555 closest distance to " CD  ARG A 269 " =    0.983
peak=    3.552 closest distance to " N   ASP A 162 " =    1.182
peak=    3.547 closest distance to " O   HOH Z 214 " =    2.325
peak=    3.546 closest distance to " CG2 ILE A  20 " =    1.497
peak=    3.532 closest distance to " O   ASN A  74 " =    1.458
peak=    3.532 closest distance to " O   HOH Z  92 " =    2.383
peak=    3.532 closest distance to " CZ  PHE A  38 " =    1.062
peak=    3.529 closest distance to " CA  PHE A 283 " =    1.107
peak=    3.521 closest distance to " O   HOH Z  30 " =    1.415
peak=    3.518 closest distance to " O   HOH Z 280 " =    2.983
peak=    3.518 closest distance to " O   HOH Z   9 " =    1.911
peak=    3.512 closest distance to " CB  VAL A 296 " =    1.012
peak=    3.510 closest distance to " O   HOH Z 352 " =    1.320
peak=    3.507 closest distance to " O   HOH Z 392 " =    2.907
peak=    3.504 closest distance to " O   HOH Z  10 " =    1.721
peak=    3.500 closest distance to " CA  ALA A 233 " =    1.219
peak=    3.498 closest distance to " CZ3 TRP A 266 " =    1.068
peak=    3.495 closest distance to " CG BARG A 102 " =    1.768
peak=    3.491 closest distance to " CB  ASP A 124 " =    0.752
peak=    3.490 closest distance to " OD1 ASN A  69 " =    2.384
peak=    3.486 closest distance to " CE1 TYR A 186 " =    1.325
peak=    3.486 closest distance to " O   HOH Z 145 " =    2.245
peak=    3.481 closest distance to " O   HOH Z 322 " =    1.989
peak=    3.480 closest distance to " O   HOH Z 329 " =    4.144
peak=    3.478 closest distance to " CD  LYS A  76 " =    1.955
peak=    3.474 closest distance to " CB  PHE A 204 " =    0.885
peak=    3.466 closest distance to " O   HOH Z 366 " =    2.771
peak=    3.461 closest distance to " O   HOH Z  88 " =    3.314
peak=    3.452 closest distance to " NZ  LYS A 117 " =    2.958
peak=    3.449 closest distance to " CG1 VAL A 153 " =    0.909
peak=    3.448 closest distance to " CA  ARG A 195 " =    1.179
peak=    3.448 closest distance to " O   HOH Z 368 " =    3.493
peak=    3.445 closest distance to " O   HOH Z 419 " =    1.888
peak=    3.440 closest distance to " CB  GLU A 128 " =    0.883
peak=    3.435 closest distance to " CG  GLN A  88 " =    1.078
peak=    3.421 closest distance to " CB  TRP A 179 " =    1.372
peak=    3.415 closest distance to " CB  SER A 273 " =    0.904
peak=    3.411 closest distance to " CA  LYS A 117 " =    1.221
peak=    3.406 closest distance to " CD2 TYR A 186 " =    1.105
peak=    3.403 closest distance to " CB  ARG A 139 " =    0.980
peak=    3.399 closest distance to " O   HOH Z 421 " =    2.009
peak=    3.398 closest distance to " O   HOH Z 183 " =    1.754
peak=    3.395 closest distance to " CB  PRO A  90 " =    1.100
peak=    3.394 closest distance to " O   HOH Z  68 " =    2.168
peak=    3.393 closest distance to " CA  ASP A 191 " =    1.211
peak=    3.387 closest distance to " O   LEU A 228 " =    1.771
peak=    3.379 closest distance to " CB  ASN A 215 " =    1.164
peak=    3.374 closest distance to " CB  SER A 212 " =    1.304
peak=    3.374 closest distance to " CD2 LEU A 297 " =    0.978
peak=    3.373 closest distance to " N   SER A 135 " =    1.358
peak=    3.373 closest distance to " CD1 LEU A 261 " =    1.177
peak=    3.364 closest distance to " O   HOH Z 124 " =    1.240
peak=    3.362 closest distance to " O   HOH Z  88 " =    2.593
peak=    3.360 closest distance to " CG1BVAL A  72 " =    1.584
peak=    3.355 closest distance to " CB  HIS A 108 " =    0.819
peak=    3.353 closest distance to " CB  GLN A 278 " =    0.945
peak=    3.349 closest distance to " CG  GLN A  58 " =    0.945
peak=    3.343 closest distance to " CA  ASP A 162 " =    1.010
peak=    3.339 closest distance to " OE1 GLU A   2 " =    2.028
peak=    3.338 closest distance to " CA  THR A 264 " =    0.830
peak=    3.337 closest distance to " O   HOH Z  88 " =    2.777
peak=    3.333 closest distance to " CA  ALA A 291 " =    0.837
peak=    3.328 closest distance to " O   HOH Z 148 " =    3.458
peak=    3.328 closest distance to " O   HOH Z 389 " =    1.719
peak=    3.322 closest distance to " O   HOH Z 290 " =    1.128
peak=    3.321 closest distance to " O   HOH Z 132 " =    2.551
peak=    3.320 closest distance to " CG  ARG A  66 " =    2.508
peak=    3.320 closest distance to " N   ARG A 156 " =    1.314
peak=    3.319 closest distance to " O   HOH Z 141 " =    1.725
peak=    3.317 closest distance to " NE2 GLN A  77 " =    3.121
peak=    3.316 closest distance to " CA  LYS A 290 " =    1.154
peak=    3.314 closest distance to " O   HOH Z 407 " =    2.455
peak=    3.313 closest distance to " CA  TYR A 116 " =    1.464
peak=    3.312 closest distance to " O   SER A 164 " =    1.279
peak=    3.301 closest distance to " O   HOH Z 344 " =    2.874
peak=    3.300 closest distance to " CG2 ILE A 239 " =    0.751
peak=    3.299 closest distance to " NH2BARG A 190 " =    1.689
peak=    3.297 closest distance to " CB  SER A 210 " =    0.704
peak=    3.297 closest distance to " CB  ARG A 138 " =    0.933
peak=    3.297 closest distance to " NH1AARG A 145 " =    1.184
peak=    3.294 closest distance to " O   HOH Z 380 " =    2.036
peak=    3.293 closest distance to " CA  ALA A 129 " =    1.591
peak=    3.292 closest distance to " O   HOH Z 172 " =    3.601
peak=    3.291 closest distance to " CD1 ILE A  33 " =    1.687
peak=    3.290 closest distance to " CB  LYS A 117 " =    1.173
peak=    3.290 closest distance to " CG  GLU A  37 " =    0.864
peak=    3.288 closest distance to " O   HOH Z 410 " =    2.932
peak=    3.288 closest distance to " O   HOH Z 294 " =    1.522
peak=    3.283 closest distance to " O   HOH Z 327 " =    1.883
peak=    3.276 closest distance to " CB  ILE A  20 " =    1.396
peak=    3.273 closest distance to " CG2 ILE A  49 " =    1.356
peak=    3.267 closest distance to " CG  MET A 185 " =    0.969
peak=    3.266 closest distance to " CA  PHE A  59 " =    0.935
peak=    3.263 closest distance to " CB  ALA A 233 " =    1.365
peak=    3.250 closest distance to " O   GLN A 278 " =    1.226
peak=    3.248 closest distance to " CD1 LEU A  96 " =    0.709
peak=    3.246 closest distance to " CA  ASN A 127 " =    1.049
peak=    3.244 closest distance to " CB  ASN A 148 " =    1.940
peak=    3.242 closest distance to " CG  LEU A 281 " =    1.001
peak=    3.241 closest distance to " OG1 THR A 221 " =    1.312
peak=    3.240 closest distance to " CE3 TRP A 150 " =    1.004
peak=    3.236 closest distance to " O   HOH Z 164 " =    1.982
peak=    3.232 closest distance to " CB  THR A  52 " =    0.850
peak=    3.232 closest distance to " O   HOH Z 171 " =    4.006
peak=    3.230 closest distance to " CB  TYR A 247 " =    1.004
peak=    3.229 closest distance to " O   HOH Z 112 " =    1.097
peak=    3.224 closest distance to " O   HOH Z   1 " =    1.791
peak=    3.221 closest distance to " OG  SER A  62 " =    2.795
peak=    3.218 closest distance to " O   HOH Z 227 " =    2.193
peak=    3.215 closest distance to " O   HOH Z  80 " =    2.108
peak=    3.214 closest distance to " CA  ASN A 217 " =    1.258
peak=    3.208 closest distance to " O   HOH Z 173 " =    2.178
peak=    3.207 closest distance to " O   HOH Z 213 " =    2.091
peak=    3.205 closest distance to " O   HOH Z   1 " =    1.701
peak=    3.203 closest distance to " CG1 VAL A 296 " =    1.248
peak=    3.203 closest distance to " O   HOH Z 244 " =    1.646
peak=    3.202 closest distance to " O   HOH Z 425 " =    2.068
peak=    3.202 closest distance to " O   HOH Z 409 " =    3.193
peak=    3.200 closest distance to " CG AARG A 275 " =    1.091
peak=    3.198 closest distance to " CD1 LEU A 228 " =    2.041
peak=    3.196 closest distance to " NH1 ARG A  66 " =    1.375
peak=    3.194 closest distance to " O   HOH Z 187 " =    2.255
peak=    3.193 closest distance to " O   GLY A  91 " =    1.451
peak=    3.191 closest distance to " NH1 ARG A 138 " =    1.199
peak=    3.187 closest distance to " O   HOH Z 156 " =    3.382
peak=    3.186 closest distance to " O   HOH Z 233 " =    1.676
peak=    3.186 closest distance to " CB  ALA A 180 " =    1.230
peak=    3.179 closest distance to " CB  ALA A 114 " =    1.221
peak=    3.177 closest distance to " OE2 GLU A  53 " =    2.039
peak=    3.172 closest distance to " CB  SER A 216 " =    0.799
peak=    3.172 closest distance to " CG  MET A 113 " =    0.992
peak=    3.170 closest distance to " O   HOH Z 293 " =    1.840
peak=    3.170 closest distance to " CA  ASP A 149 " =    1.053
peak=    3.167 closest distance to " CA  ILE A 234 " =    0.921
peak=    3.166 closest distance to " CD1 ILE A 199 " =    1.123
peak=    3.166 closest distance to " CB  ARG A 219 " =    0.896
peak=    3.165 closest distance to " O   PHE A 192 " =    1.382
peak=    3.163 closest distance to " O   HOH Z 415 " =    3.623
peak=    3.161 closest distance to " C   ALA A 299 " =    0.877
peak=    3.160 closest distance to " O   HOH Z 162 " =    3.250
peak=    3.156 closest distance to " O   HOH Z  47 " =    1.924
peak=    3.155 closest distance to " NE2 HIS A 207 " =    1.148
peak=    3.155 closest distance to " CA  VAL A  41 " =    0.704
peak=    3.153 closest distance to " CD  LYS A 119 " =    1.841
peak=    3.151 closest distance to " O   HOH Z 188 " =    1.421
peak=    3.146 closest distance to " CB  THR A 157 " =    1.216
peak=    3.146 closest distance to " O   HOH Z 345 " =    3.216
peak=    3.145 closest distance to " O   ASN A 284 " =    1.737
peak=    3.142 closest distance to " CA  LEU A 282 " =    1.234
peak=    3.141 closest distance to " O   ALA A   1 " =    1.702
peak=    3.136 closest distance to " O   HOH Z 263 " =    1.692
peak=    3.131 closest distance to " CA  ARG A 102 " =    1.159
peak=    3.130 closest distance to " CG1 ILE A 120 " =    1.102
peak=    3.119 closest distance to " CD1 ILE A 106 " =    1.103
peak=    3.114 closest distance to " O   PRO A 198 " =    1.260
peak=    3.111 closest distance to " CG  PHE A 204 " =    0.967
peak=    3.111 closest distance to " O   HOH Z 355 " =    1.723
peak=    3.110 closest distance to " CB  ALA A 291 " =    1.213
peak=    3.100 closest distance to " O   LYS A 290 " =    2.414
peak=    3.097 closest distance to " CB  LEU A 300 " =    0.901
peak=    3.097 closest distance to " O   HOH Z 424 " =    1.462
peak=    3.094 closest distance to " O   HOH Z 361 " =    3.475
peak=    3.093 closest distance to " O   HOH Z 282 " =    1.955
peak=    3.090 closest distance to " O   HOH Z 109 " =    2.453
peak=    3.087 closest distance to " O   HOH Z 423 " =    2.854
peak=    3.084 closest distance to " O   HOH Z 203 " =    1.617
peak=    3.083 closest distance to " O   HOH Z 403 " =    2.116
peak=    3.080 closest distance to " N   CYS A 260 " =    0.778
peak=    3.073 closest distance to " OG BSER A 134 " =    3.012
peak=    3.069 closest distance to " OG1 THR A 264 " =    0.731
peak=    3.066 closest distance to " CB  SER A  62 " =    1.189
peak=    3.066 closest distance to " CB  ILE A 120 " =    1.347
peak=    3.037 closest distance to " O   HOH Z 222 " =    2.326
peak=    3.032 closest distance to " CA  ILE A 106 " =    0.732

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.679 - 5.469
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 202
   mapped sites are within: 0.768 - 5.469

peak=   -4.635 closest distance to " CD  ARG A  14 " =    3.166
peak=   -4.582 closest distance to " CG  GLN A  58 " =    0.991
peak=   -4.482 closest distance to " OG BSER A 134 " =    1.249
peak=   -4.372 closest distance to " O   HOH Z 387 " =    2.657
peak=   -4.268 closest distance to " CB  PHE A 192 " =    1.998
peak=   -4.261 closest distance to " C   HIS A 108 " =    1.185
peak=   -4.222 closest distance to " O   VAL A  67 " =    2.524
peak=   -4.145 closest distance to " CD  ARG A 156 " =    2.107
peak=   -4.143 closest distance to " O   HOH Z 351 " =    1.481
peak=   -4.136 closest distance to " O   PRO A 163 " =    2.089
peak=   -4.083 closest distance to " O   HOH Z 290 " =    1.182
peak=   -4.065 closest distance to " O   HOH Z 394 " =    1.528
peak=   -4.042 closest distance to " CE  MET A 105 " =    2.402
peak=   -4.028 closest distance to " OE1 GLN A 223 " =    2.183
peak=   -4.018 closest distance to " O   HOH Z 266 " =    5.469
peak=   -4.002 closest distance to " O   PRO A 198 " =    1.154
peak=   -4.001 closest distance to " O   HOH Z 211 " =    1.429
peak=   -4.000 closest distance to " CD1 LEU A 101 " =    2.360
peak=   -3.991 closest distance to " CB  ALA A  43 " =    2.454
peak=   -3.983 closest distance to " O   HOH Z 166 " =    1.937
peak=   -3.918 closest distance to " CA  VAL A  67 " =    2.894
peak=   -3.870 closest distance to " CD1 LEU A 255 " =    2.745
peak=   -3.842 closest distance to " O   HOH Z  11 " =    1.890
peak=   -3.838 closest distance to " O   HOH Z 193 " =    1.317
peak=   -3.838 closest distance to " CG2 ILE A  49 " =    2.819
peak=   -3.833 closest distance to " CG  LEU A   5 " =    0.895
peak=   -3.828 closest distance to " O   HOH Z 100 " =    0.998
peak=   -3.809 closest distance to " CB  ALA A 161 " =    2.472
peak=   -3.808 closest distance to " CB  ALA A 248 " =    2.336
peak=   -3.794 closest distance to " ND2 ASN A  45 " =    1.159
peak=   -3.779 closest distance to " CD2 TYR A 293 " =    1.997
peak=   -3.760 closest distance to " ND2 ASN A 249 " =    2.233
peak=   -3.747 closest distance to " O   HOH Z 231 " =    2.222
peak=   -3.745 closest distance to " OXT GLY A 302 " =    2.868
peak=   -3.729 closest distance to " CG2 VAL A 296 " =    1.815
peak=   -3.724 closest distance to " CE2 TYR A  30 " =    2.742
peak=   -3.721 closest distance to " CA  ASP A 298 " =    1.108
peak=   -3.720 closest distance to " O   HOH Z 114 " =    3.133
peak=   -3.720 closest distance to " CD1 ILE A 199 " =    2.409
peak=   -3.674 closest distance to " CG  ASP A 231 " =    0.768
peak=   -3.657 closest distance to " CD1 ILE A 263 " =    2.735
peak=   -3.654 closest distance to " O   HOH Z 429 " =    1.977
peak=   -3.642 closest distance to " CG  TRP A 266 " =    1.885
peak=   -3.624 closest distance to " NH2AARG A 275 " =    4.967
peak=   -3.618 closest distance to " N   ALA A 226 " =    1.979
peak=   -3.607 closest distance to " CG2 VAL A 202 " =    2.701
peak=   -3.607 closest distance to " N   THR A 157 " =    1.491
peak=   -3.586 closest distance to " CZ3 TRP A 179 " =    1.264
peak=   -3.580 closest distance to " ND2 ASN A 187 " =    1.534
peak=   -3.580 closest distance to " CA  GLY A 241 " =    2.363
peak=   -3.577 closest distance to " NE2 GLN A  88 " =    1.087
peak=   -3.563 closest distance to " CE BMET A  47 " =    1.294
peak=   -3.548 closest distance to " CG2 THR A 178 " =    2.343
peak=   -3.541 closest distance to " CA  GLY A 133 " =    1.928
peak=   -3.527 closest distance to " CG1 VAL A 112 " =    2.817
peak=   -3.494 closest distance to " N   ALA A 248 " =    1.565
peak=   -3.480 closest distance to " O   HOH Z 359 " =    3.125
peak=   -3.478 closest distance to " CA  GLY A  98 " =    1.872
peak=   -3.466 closest distance to " O   HOH Z 185 " =    2.371
peak=   -3.462 closest distance to " CB  ASP A 132 " =    2.381
peak=   -3.461 closest distance to " O   HOH Z 139 " =    3.111
peak=   -3.450 closest distance to " NE2 GLN A 278 " =    1.786
peak=   -3.438 closest distance to " CG2 VAL A 296 " =    0.806
peak=   -3.436 closest distance to " O   HOH Z 421 " =    3.054
peak=   -3.432 closest distance to " O   ALA A 227 " =    1.551
peak=   -3.432 closest distance to " CG1 VAL A 112 " =    2.674
peak=   -3.426 closest distance to " C   MET A 188 " =    1.443
peak=   -3.425 closest distance to " O   HOH Z 103 " =    1.698
peak=   -3.424 closest distance to " CE3 TRP A 150 " =    2.125
peak=   -3.422 closest distance to " CB  PRO A 163 " =    2.485
peak=   -3.420 closest distance to " O   HOH Z 191 " =    5.469
peak=   -3.410 closest distance to " O   HOH Z 285 " =    1.988
peak=   -3.407 closest distance to " O   HOH Z 166 " =    2.180
peak=   -3.405 closest distance to " CB  SER A 210 " =    1.110
peak=   -3.402 closest distance to " CG2 ILE A 263 " =    2.320
peak=   -3.399 closest distance to " OH  TYR A 172 " =    1.840
peak=   -3.399 closest distance to " CD  PRO A 213 " =    2.064
peak=   -3.397 closest distance to " O   HOH Z 238 " =    1.012
peak=   -3.397 closest distance to " N   HIS A 115 " =    2.207
peak=   -3.394 closest distance to " O   HOH Z 371 " =    2.153
peak=   -3.389 closest distance to " O   VAL A 189 " =    2.638
peak=   -3.377 closest distance to " O   HOH Z 136 " =    2.487
peak=   -3.377 closest distance to " OE1 GLN A  88 " =    0.990
peak=   -3.373 closest distance to " N   GLN A  58 " =    1.944
peak=   -3.372 closest distance to " O   HOH Z 357 " =    2.067
peak=   -3.367 closest distance to " O   HOH Z 407 " =    2.906
peak=   -3.365 closest distance to " O   HOH Z 286 " =    1.881
peak=   -3.365 closest distance to " O   SER A 210 " =    1.953
peak=   -3.363 closest distance to " O   GLY A 196 " =    1.275
peak=   -3.362 closest distance to " O   HOH Z 295 " =    1.561
peak=   -3.362 closest distance to " NE2 GLN A  88 " =    1.905
peak=   -3.354 closest distance to " O   HOH Z 216 " =    1.347
peak=   -3.350 closest distance to " O   HOH Z 131 " =    4.130
peak=   -3.348 closest distance to " O   HOH Z 345 " =    2.010
peak=   -3.347 closest distance to " CB  GLN A  11 " =    1.866
peak=   -3.344 closest distance to " O   PRO A 198 " =    1.295
peak=   -3.343 closest distance to " C   ASP A 231 " =    2.362
peak=   -3.342 closest distance to " O   ALA A  51 " =    1.241
peak=   -3.334 closest distance to " O   HOH Z 198 " =    1.881
peak=   -3.332 closest distance to " ND2 ASN A 252 " =    1.906
peak=   -3.332 closest distance to " CD  PRO A 243 " =    2.076
peak=   -3.328 closest distance to " O   SER A 276 " =    1.690
peak=   -3.326 closest distance to " CG  GLU A 277 " =    1.274
peak=   -3.325 closest distance to " OD2 ASP A 191 " =    1.372
peak=   -3.323 closest distance to " O   PHE A 218 " =    1.603
peak=   -3.320 closest distance to " NE  ARG A 156 " =    1.936
peak=   -3.318 closest distance to " N   THR A  52 " =    1.664
peak=   -3.316 closest distance to " O   HOH Z 140 " =    1.887
peak=   -3.314 closest distance to " OE1 GLN A 183 " =    1.504
peak=   -3.313 closest distance to " O   GLY A  80 " =    2.554
peak=   -3.308 closest distance to " CZ2 TRP A 274 " =    1.013
peak=   -3.305 closest distance to " C   SER A 206 " =    1.556
peak=   -3.304 closest distance to " N   SER A 276 " =    1.377
peak=   -3.300 closest distance to " O   ALA A  10 " =    1.815
peak=   -3.296 closest distance to " OD1 ASN A 301 " =    2.018
peak=   -3.295 closest distance to " OG  SER A  97 " =    2.277
peak=   -3.290 closest distance to " CB  ALA A  10 " =    2.350
peak=   -3.289 closest distance to " OG  SER A  87 " =    1.447
peak=   -3.289 closest distance to " CB  TRP A  85 " =    2.613
peak=   -3.284 closest distance to " O   HOH Z 437 " =    1.674
peak=   -3.281 closest distance to " O   HOH Z 372 " =    2.279
peak=   -3.274 closest distance to " O   HOH Z 389 " =    2.121
peak=   -3.272 closest distance to " OG  SER A   3 " =    1.695
peak=   -3.269 closest distance to " CG1 VAL A 197 " =    2.261
peak=   -3.268 closest distance to " N   ALA A 248 " =    1.867
peak=   -3.267 closest distance to " O   HOH Z 133 " =    3.386
peak=   -3.267 closest distance to " O   MET A  40 " =    2.846
peak=   -3.266 closest distance to " CG1BVAL A  72 " =    2.269
peak=   -3.264 closest distance to " CZ  ARG A 259 " =    0.919
peak=   -3.262 closest distance to " CG  PHE A 283 " =    2.626
peak=   -3.260 closest distance to " O   HOH Z 377 " =    2.119
peak=   -3.258 closest distance to " O   HOH Z 174 " =    3.952
peak=   -3.257 closest distance to " CE1 PHE A  59 " =    2.054
peak=   -3.256 closest distance to " N   ALA A  43 " =    2.604
peak=   -3.254 closest distance to " CA  ASN A 127 " =    1.329
peak=   -3.251 closest distance to " OE2 GLU A 152 " =    1.345
peak=   -3.246 closest distance to " O   GLY A  17 " =    1.131
peak=   -3.242 closest distance to " O   SER A  22 " =    2.303
peak=   -3.238 closest distance to " CD2 LEU A 237 " =    2.833
peak=   -3.232 closest distance to " NH2 ARG A  79 " =    2.025
peak=   -3.227 closest distance to " O   ASN A 301 " =    1.658
peak=   -3.223 closest distance to " CG1 VAL A 230 " =    1.874
peak=   -3.223 closest distance to " CZ  TYR A 169 " =    1.760
peak=   -3.222 closest distance to " O   HOH Z 389 " =    1.415
peak=   -3.219 closest distance to " CB  ALA A 291 " =    2.204
peak=   -3.217 closest distance to " CZ  PHE A  38 " =    2.109
peak=   -3.216 closest distance to " O   HOH Z  73 " =    2.312
peak=   -3.211 closest distance to " OG  SER A  63 " =    1.130
peak=   -3.208 closest distance to " CD  LYS A 289 " =    2.441
peak=   -3.208 closest distance to " O   ASN A 187 " =    1.600
peak=   -3.208 closest distance to " CB  ALA A 114 " =    2.465
peak=   -3.201 closest distance to " CB  GLN A  55 " =    1.253
peak=   -3.199 closest distance to " CG  GLU A 152 " =    1.517
peak=   -3.199 closest distance to " O   HOH Z 166 " =    1.494
peak=   -3.198 closest distance to " CB  ASP A 132 " =    2.250
peak=   -3.196 closest distance to " C   LEU A 222 " =    0.871
peak=   -3.195 closest distance to " CB  ALA A  51 " =    1.941
peak=   -3.195 closest distance to " O   HOH Z 313 " =    1.649
peak=   -3.194 closest distance to " CB  ASN A  69 " =    1.315
peak=   -3.193 closest distance to " OD2 ASP A  50 " =    2.096
peak=   -3.188 closest distance to " O   HOH Z 111 " =    1.734
peak=   -3.184 closest distance to " CG1 VAL A 125 " =    1.870
peak=   -3.183 closest distance to " O   ARG A 145 " =    1.656
peak=   -3.182 closest distance to " O   HOH Z 154 " =    1.752
peak=   -3.182 closest distance to " CD2 HIS A 207 " =    2.430
peak=   -3.182 closest distance to " NE2 GLN A 194 " =    1.828
peak=   -3.178 closest distance to " ND2 ASN A  39 " =    1.162
peak=   -3.175 closest distance to " O   HOH Z  71 " =    2.293
peak=   -3.169 closest distance to " O   HOH Z 252 " =    3.948
peak=   -3.167 closest distance to " CB  ALA A 291 " =    2.174
peak=   -3.160 closest distance to " CA  GLY A 203 " =    2.442
peak=   -3.157 closest distance to " CA  GLY A 133 " =    2.239
peak=   -3.157 closest distance to " ND2 ASN A  69 " =    1.897
peak=   -3.157 closest distance to " O   HOH Z   9 " =    1.457
peak=   -3.154 closest distance to " CA  GLY A 241 " =    3.122
peak=   -3.154 closest distance to " O   ALA A 248 " =    1.647
peak=   -3.150 closest distance to " CD2 PHE A 225 " =    1.124
peak=   -3.144 closest distance to " CD1 ILE A 239 " =    2.231
peak=   -3.141 closest distance to " SG BCYS A 201 " =    2.095
peak=   -3.141 closest distance to " OG BSER A 134 " =    1.795
peak=   -3.136 closest distance to " CG  PRO A 163 " =    2.674
peak=   -3.136 closest distance to " CB  ASN A  39 " =    2.265
peak=   -3.133 closest distance to " O   HOH Z 256 " =    1.389
peak=   -3.130 closest distance to " CD2 PHE A  61 " =    2.063
peak=   -3.125 closest distance to " NE2 GLN A 240 " =    1.640
peak=   -3.122 closest distance to " O   HOH Z 174 " =    2.262
peak=   -3.118 closest distance to " O   HOH Z 431 " =    1.947
peak=   -3.117 closest distance to " CG  LEU A 228 " =    0.962
peak=   -3.100 closest distance to " O   HOH Z 346 " =    1.790
peak=   -3.098 closest distance to " CB  ALA A   9 " =    2.475
peak=   -3.098 closest distance to " O   HOH Z 200 " =    4.383
peak=   -3.097 closest distance to " CG  ARG A 269 " =    2.220
peak=   -3.089 closest distance to " N   ALA A 248 " =    2.401
peak=   -3.082 closest distance to " C   ALA A 158 " =    1.376
peak=   -3.072 closest distance to " O   HOH Z 281 " =    2.924
peak=   -3.057 closest distance to " CG2 THR A  42 " =    1.765
peak=   -3.056 closest distance to " O   HOH Z 111 " =    4.448
peak=   -3.045 closest distance to " CA  PRO A 243 " =    2.218
peak=   -3.039 closest distance to " CE  LYS A  76 " =    2.738
peak=   -2.983 closest distance to " O   HOH Z 357 " =    2.130

================= 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    :  0.4597 0.4435   6.259570e+00   6.239549e+00
   1_bss:  0.4513 0.4355   6.250089e+00   6.228532e+00
   1_xyz:  0.3544 0.3719   6.093566e+00   6.124293e+00
   1_adp:  0.3004 0.3451   5.969933e+00   6.065259e+00
   1_occ:  0.3001 0.3458   5.968952e+00   6.067048e+00
   2_bss:  0.2970 0.3419   5.968671e+00   6.066253e+00
   2_xyz:  0.2073 0.2532   5.661512e+00   5.824110e+00
   2_adp:  0.1877 0.2391   5.578828e+00   5.759360e+00
   2_occ:  0.1875 0.2389   5.578693e+00   5.759725e+00
   3_bss:  0.1859 0.2390   5.579542e+00   5.759223e+00
   3_xyz:  0.1437 0.1895   5.344972e+00   5.549760e+00
   3_adp:  0.1339 0.1845   5.297378e+00   5.521173e+00
   3_occ:  0.1338 0.1844   5.296944e+00   5.520884e+00
   4_bss:  0.1339 0.1841   5.296022e+00   5.518600e+00
   4_xyz:  0.1170 0.1682   5.199897e+00   5.448273e+00
   4_adp:  0.1151 0.1615   5.174801e+00   5.413975e+00
   4_occ:  0.1149 0.1615   5.174272e+00   5.413756e+00
   5_bss:  0.1149 0.1615   5.173977e+00   5.413540e+00
   5_xyz:  0.1140 0.1578   5.160719e+00   5.397310e+00
   5_adp:  0.1139 0.1570   5.158598e+00   5.391971e+00
   5_occ:  0.1139 0.1570   5.158405e+00   5.392024e+00
   5_bss:  0.1139 0.1570   5.158387e+00   5.392036e+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:  0.357  20.000   7.044   7.429   9.756   0.000   0.000   0.000
   1_xyz:  0.357  20.000   7.044   7.429   9.756   0.000   0.000   0.000
   1_adp:  0.357  20.000   7.044   7.429   9.756   0.000   0.000   0.000
   1_occ:  0.357  20.000   7.044   7.429   9.756   0.000   0.000   0.000
   2_bss:  0.336  40.067   3.998   3.921   6.560   0.000   0.000   0.000
   2_xyz:  0.336  40.067   3.998   3.921   6.560   0.000   0.000   0.000
   2_adp:  0.336  40.067   3.998   3.921   6.560   0.000   0.000   0.000
   2_occ:  0.336  40.067   3.998   3.921   6.560   0.000   0.000   0.000
   3_bss:  0.329  40.067   2.001   2.634   4.687   0.000   0.000   0.000
   3_xyz:  0.329  40.067   2.001   2.634   4.687   0.000   0.000   0.000
   3_adp:  0.329  40.067   2.001   2.634   4.687   0.000   0.000   0.000
   3_occ:  0.329  40.067   2.001   2.634   4.687   0.000   0.000   0.000
   4_bss:  0.312  40.067   1.986   2.645   4.438   0.000   0.000   0.000
   4_xyz:  0.312  40.067   1.986   2.645   4.438   0.000   0.000   0.000
   4_adp:  0.312  40.067   1.986   2.645   4.438   0.000   0.000   0.000
   4_occ:  0.312  40.067   1.986   2.645   4.438   0.000   0.000   0.000
   5_bss:  0.323  45.836   2.040   2.636   4.344   0.000   0.000   0.000
   5_xyz:  0.323  45.836   2.040   2.636   4.344   0.000   0.000   0.000
   5_adp:  0.323  45.836   2.040   2.636   4.344   0.000   0.000   0.000
   5_occ:  0.323  45.836   2.040   2.636   4.344   0.000   0.000   0.000
   5_bss:  0.321  48.843  -0.967  -0.371   1.337   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.326 0.5054  0.5828    60890.132
   1_bss:  51.177 0.5056  0.7434    58420.443
   1_xyz:  40.490 0.6365  0.8982    38219.422
   1_adp:  36.092 0.6889  0.9854    31931.357
   1_occ:  36.164 0.6880  0.9830    32012.928
   2_bss:  35.910 0.6909  0.8792    31708.077
   2_xyz:  25.197 0.8092  0.9943    16487.883
   2_adp:  22.955 0.8329  1.0129    14292.441
   2_occ:  22.988 0.8325  1.0123    14298.587
   3_bss:  22.961 0.8329  0.9507    14314.330
   3_xyz:  17.587 0.8843  0.9817     8956.942
   3_adp:  16.937 0.8903  0.9776     8491.829
   3_occ:  16.927 0.8904  0.9777     8485.967
   4_bss:  16.865 0.8909  0.9745     8424.622
   4_xyz:  15.392 0.9033  0.9820     7232.378
   4_adp:  14.644 0.9097  0.9813     6789.151
   4_occ:  14.650 0.9097  0.9811     6786.797
   5_bss:  14.639 0.9098  0.9810     6786.807
   5_xyz:  14.252 0.9130  0.9813     6535.684
   5_adp:  14.125 0.9142  0.9783     6484.598
   5_occ:  14.126 0.9142  0.9783     6481.970
   5_bss:  14.126 0.9142  0.9783     6482.259
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3595e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3595e+01
   1_xyz:   1.614  0.012  0.104 17.915  0.006  4.108   1.2818e-01
   1_adp:   1.614  0.012  0.104 17.915  0.006  4.108   1.2818e-01
   1_occ:   1.614  0.012  0.104 17.915  0.006  4.108   1.2818e-01
   2_bss:   1.614  0.012  0.104 17.915  0.006  4.108   1.2818e-01
   2_xyz:   1.034  0.007  0.075 15.802  0.004  4.120   6.4621e-02
   2_adp:   1.034  0.007  0.075 15.802  0.004  4.120   6.4621e-02
   2_occ:   1.034  0.007  0.075 15.802  0.004  4.120   6.4621e-02
   3_bss:   1.034  0.007  0.075 15.802  0.004  4.120   6.4621e-02
   3_xyz:   0.966  0.006  0.074 15.466  0.003  4.128   5.7604e-02
   3_adp:   0.966  0.006  0.074 15.466  0.003  4.128   5.7604e-02
   3_occ:   0.966  0.006  0.074 15.466  0.003  4.128   5.7604e-02
   4_bss:   0.966  0.006  0.074 15.466  0.003  4.128   5.7604e-02
   4_xyz:   1.097  0.009  0.083 15.664  0.004  4.110   7.2063e-02
   4_adp:   1.097  0.009  0.083 15.664  0.004  4.110   7.2063e-02
   4_occ:   1.097  0.009  0.083 15.664  0.004  4.110   7.2063e-02
   5_bss:   1.097  0.009  0.083 15.664  0.004  4.110   7.2063e-02
   5_xyz:   1.008  0.007  0.079 15.203  0.004  4.111   6.1005e-02
   5_adp:   1.008  0.007  0.079 15.203  0.004  4.111   6.1005e-02
   5_occ:   1.008  0.007  0.079 15.203  0.004  4.111   6.1005e-02
   5_bss:   1.008  0.007  0.079 15.203  0.004  4.111   6.1005e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9464e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9464e+00
   1_xyz:  13.133  0.160  0.395 88.170  0.044  2.203   9.3727e-02
   1_adp:  13.133  0.160  0.395 88.170  0.044  2.203   9.3727e-02
   1_occ:  13.133  0.160  0.395 88.170  0.044  2.203   9.3727e-02
   2_bss:  13.133  0.160  0.395 88.170  0.044  2.203   9.3727e-02
   2_xyz:   5.979  0.055  0.256 84.218  0.030  2.368   5.0699e-02
   2_adp:   5.979  0.055  0.256 84.218  0.030  2.368   5.0699e-02
   2_occ:   5.979  0.055  0.256 84.218  0.030  2.368   5.0699e-02
   3_bss:   5.979  0.055  0.256 84.218  0.030  2.368   5.0699e-02
   3_xyz:   6.973  0.060  0.395 89.869  0.032  2.347   4.4758e-02
   3_adp:   6.973  0.060  0.395 89.869  0.032  2.347   4.4758e-02
   3_occ:   6.973  0.060  0.395 89.869  0.032  2.347   4.4758e-02
   4_bss:   6.973  0.060  0.395 89.869  0.032  2.347   4.4758e-02
   4_xyz:   7.309  0.049  0.408 83.044  0.033  2.315   5.6951e-02
   4_adp:   7.309  0.049  0.408 83.044  0.033  2.315   5.6951e-02
   4_occ:   7.309  0.049  0.408 83.044  0.033  2.315   5.6951e-02
   5_bss:   7.309  0.049  0.408 83.044  0.033  2.315   5.6951e-02
   5_xyz:   6.483  0.035  0.370 83.757  0.032  2.341   4.0628e-02
   5_adp:   6.483  0.035  0.370 83.757  0.032  2.341   4.0628e-02
   5_occ:   6.483  0.035  0.370 83.757  0.032  2.341   4.0628e-02
   5_bss:   6.483  0.035  0.370 83.757  0.032  2.341   4.0628e-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:  60.71   0.00  11.82  52.86   0.00   9.11  60.71   0.00  26.59
   1_occ:  60.71   0.00  11.82  52.86   0.00   9.11  60.71   0.00  26.59
   2_bss:  60.71   0.00  11.82  52.86   0.00   9.11  60.71   0.00  26.59
   2_xyz:  60.71   0.00  11.82  52.86   0.00   9.11  60.71   0.00  26.59
   2_adp: 102.56   0.00  12.05 102.56   0.00   8.41  62.76   0.00  31.82
   2_occ: 102.56   0.00  12.05 102.56   0.00   8.41  62.76   0.00  31.82
   3_bss: 102.56   0.00  12.05 102.56   0.00   8.41  62.76   0.00  31.82
   3_xyz: 102.56   0.00  12.05 102.56   0.00   8.41  62.76   0.00  31.82
   3_adp:  87.39   0.00  13.23  85.86   0.00   8.55  87.39   0.85  38.72
   3_occ:  87.39   0.00  13.23  85.86   0.00   8.55  87.39   0.85  38.72
   4_bss:  87.39   0.00  13.23  85.86   0.00   8.55  87.39   0.85  38.72
   4_xyz:  87.39   0.00  13.23  85.86   0.00   8.55  87.39   0.85  38.72
   4_adp:  87.92   0.00  12.36  87.92   0.00   8.10  79.94   1.09  35.55
   4_occ:  87.92   0.00  12.36  87.92   0.00   8.10  79.94   1.09  35.55
   5_bss:  87.92   0.00  12.36  87.92   0.00   8.10  79.94   1.09  35.55
   5_xyz:  87.92   0.00  12.36  87.92   0.00   8.10  79.94   1.09  35.55
   5_adp:  88.52   0.00  11.99  88.52   0.00   7.91  75.32   1.50  34.21
   5_occ:  88.52   0.00  11.99  88.52   0.00   7.91  75.32   1.50  34.21
   5_bss:  91.53   3.01  15.00  91.53   3.01  10.92  78.32   4.51  37.22
------------------------------------------------------------------------
 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:    1.271    0.014    0.406
   1_adp:    1.271    0.014    0.406
   1_occ:    1.271    0.014    0.406
   2_bss:    1.271    0.014    0.406
   2_xyz:    1.666    0.043    0.528
   2_adp:    1.666    0.043    0.528
   2_occ:    1.666    0.043    0.528
   3_bss:    1.666    0.043    0.528
   3_xyz:    1.645    0.010    0.580
   3_adp:    1.645    0.010    0.580
   3_occ:    1.645    0.010    0.580
   4_bss:    1.645    0.010    0.580
   4_xyz:    1.724    0.045    0.616
   4_adp:    1.724    0.045    0.616
   4_occ:    1.724    0.045    0.616
   5_bss:    1.724    0.045    0.616
   5_xyz:    1.774    0.019    0.625
   5_adp:    1.774    0.019    0.625
   5_occ:    1.774    0.019    0.625
   5_bss:    1.774    0.019    0.625
------------------------------------------------------------------------

CPU time actual refinement: 341.39


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_294/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_294/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_294/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_294/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_294/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.24 
  Macro-tasks:
    bulk solvent and scale       = 41.61  
    individual site refinement   = 139.22 
    weights calculation          = 32.76  
    collect and process          = 6.74   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 220.48 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 104.01 
    alpha_beta                      = 8.55   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 115.89 
    fmodel                         = 7.76   
    r_factors                      = 0.27   
    phase_errors                   = 10.87  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 250.51 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.758 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    679 calls, 103.61 s
gradients_fft:          625 calls, 101.95 s

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

# Date 2008-01-16 Time 01:15:10 PST -0800 (1200474910.57 s)
Start R-work = 0.4597, R-free = 0.4435 (no bulk solvent and anisotropic scale)
Final R-work = 0.1318, R-free = 0.1744 (no bulk solvent and anisotropic scale)

Start R-work = 0.4513, R-free = 0.4355
Final R-work = 0.1139, R-free = 0.1570