# Date 2008-01-16 Time 02:34:46 PST -0800 (1200479686.70 s)
#phil __OFF__

Command line arguments: "../892.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26500
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 892

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.6953, 84.6622, 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: 3.29, 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: (70.9525, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96118
Completeness in resolution range: 0.944549
Completeness with d_max=infinity: 0.941734

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9612

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96118
Completeness in resolution range: 0.944549
Completeness with d_max=infinity: 0.941734

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.1974 [2177/2206]  1962   215   9.9%
  bin  2:  4.1974 -  3.3437 [2090/2106]  1880   210  10.0%
  bin  3:  3.3437 -  2.9245 [2056/2075]  1846   210  10.2%
  bin  4:  2.9245 -  2.6588 [2050/2080]  1855   195   9.5%
  bin  5:  2.6588 -  2.4691 [2045/2064]  1837   208  10.2%
  bin  6:  2.4691 -  2.3241 [2025/2061]  1819   206  10.2%
  bin  7:  2.3241 -  2.2081 [2005/2038]  1805   200  10.0%
  bin  8:  2.2081 -  2.1122 [2009/2043]  1808   201  10.0%
  bin  9:  2.1122 -  2.0311 [1997/2025]  1796   201  10.1%
  bin 10:  2.0311 -  1.9612 [1135/2041]  1022   113  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_892/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:
        1.79 -     2.41: 26
        2.41 -     3.03: 2174
        3.03 -     3.66: 4712
        3.66 -     4.28: 9113
        4.28 -     4.90: 12503
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.791 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.852 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.932 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  2.000 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28523 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_892/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_892/model_refine_001.geo

CPU time processing inputs: 9.90


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.69535 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4612   r_free= 0.4524   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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.260185                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6820 0.99   1412  159 0.3843 0.3865      6.5632      6.5702|
|  2:  4.6820 -  3.7350 0.99   1362  143 0.3712 0.3680      6.7346      6.7265|
|  3:  3.7350 -  3.2684 0.99   1331  155 0.4237 0.3707      6.6329        6.69|
|  4:  3.2684 -  2.9721 0.99   1333  150 0.4350 0.4255      6.4852      6.4575|
|  5:  2.9721 -  2.7605 0.99   1319  145 0.4859 0.4741       6.346      6.3324|
|  6:  2.7605 -  2.5986 0.99   1302  146 0.4856 0.5168      6.2581      6.2577|
|  7:  2.5986 -  2.4691 0.99   1321  140 0.5040 0.4694      6.2488      6.1662|
|  8:  2.4691 -  2.3620 0.98   1285  149 0.5208 0.4887      6.1554      6.1719|
|  9:  2.3620 -  2.2714 0.98   1304  149 0.5002 0.4838      6.1063      6.0721|
| 10:  2.2714 -  2.1933 0.98   1292  138 0.5096 0.5300      6.0824      6.1138|
| 11:  2.1933 -  2.1249 1.00   1276  140 0.5147 0.4941      6.0347      6.0079|
| 12:  2.1249 -  2.0643 0.97   1282  143 0.4966 0.5376      5.9441      5.9948|
| 13:  2.0643 -  2.0101 0.97   1270  142 0.5300 0.5161      5.8772       5.811|
| 14:  2.0101 -  1.9612 0.41    541   60 0.5463 0.5816      5.8516      5.8311|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.6820  1412   159  0.70  34.31   0.81     0.74      69966.02|
|  2:  4.6820 -  3.7350  1362   143  0.73  32.84   0.89     0.80      94855.90|
|  3:  3.7350 -  3.2684  1331   155  0.63  41.29   0.85     0.77     101069.77|
|  4:  3.2684 -  2.9721  1333   150  0.56  47.16   0.83     0.67      91643.08|
|  5:  2.9721 -  2.7605  1319   145  0.46  55.29   0.75     0.55      77710.82|
|  6:  2.7605 -  2.5986  1302   146  0.43  57.15   0.74     0.51      68001.96|
|  7:  2.5986 -  2.4691  1321   140  0.43  57.46   0.75     0.49      58982.70|
|  8:  2.4691 -  2.3620  1285   149  0.43  57.67   0.72     0.52      53425.95|
|  9:  2.3620 -  2.2714  1304   149  0.43  57.55   0.76     0.50      47560.86|
| 10:  2.2714 -  2.1933  1292   138  0.41  59.11   0.76     0.50      45996.95|
| 11:  2.1933 -  2.1249  1276   140  0.37  62.36   0.79     0.45      43866.70|
| 12:  2.1249 -  2.0643  1282   143  0.33  65.60   0.76     0.41      43216.10|
| 13:  2.0643 -  2.0101  1270   142  0.27  69.55   0.75     0.35      38478.06|
| 14:  2.0101 -  1.9612   541    60  0.27  70.06   0.71     0.30      32135.42|
|alpha:            min =        0.30 max =            0.80 mean =         0.55|
|beta:             min =    32135.42 max =       101069.77 mean =     63604.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.87|
|phase err.(test): min =        0.00 max =           89.97 mean =        54.09|
|-----------------------------------------------------------------------------|

============================== 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 = 11.449967             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.110   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.032763              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.805   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      706 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1523 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2658 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3941 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5133 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6600 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7756 |
|-----------------------------------------------------------------------------|
|-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 |       53.442 |
| 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 |       1.805 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    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 = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4675   r_free= 0.4584   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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.263806                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4519   r_free= 0.4413   ksol= 0.34   Bsol= 5.05   scale= 1.014    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.92,8.05,9.57,0.00,0.00,0.00); trace/3= 8.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.256613                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.452786              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.068   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.915458              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.840   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4519      final r-factor (work) = 0.3661          |
| start r-factor (free) = 0.4413      final r-factor (free) = 0.3887          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 83.0346 = 9.45 * 0.50 * 6.2612 + 1.00 * 53.4416                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.2195 = 9.45 * 0.50 * 6.1549 + 1.00 * 0.1290                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3661      final r-factor (work) = 0.3188          |
| start r-factor (free) = 0.3887      final r-factor (free) = 0.3721          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6489 = 0.92 * 1.00 * 6.1549 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5507 = 0.92 * 1.00 * 6.0474 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    60.73   11.47    None  None   None       |
|    all(noH): 2823   0      0.00    60.73   11.47    None  None   None       |
|    Sol.    : 438    0      0.00    53.39   23.96    None  None   None       |
|    Mac.    : 2385   0      0.00    60.73   9.17     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 -   6.073:  985   |   5:    30.366 -  36.439:  101        |
|      1:     6.073 -  12.147:  799   |   6:    36.439 -  42.513:   42        |
|      2:    12.147 -  18.220:  453   |   7:    42.513 -  48.586:   14        |
|      3:    18.220 -  24.293:  273   |   8:    48.586 -  54.659:    5        |
|      4:    24.293 -  30.366:  150   |   9:    54.659 -  60.732:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3188 r_free = 0.3721             target_work(ml) = 6.027         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3183 r_free = 0.3726             target_work(ml) = 6.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3183   r_free= 0.3726   ksol= 0.34   Bsol= 5.05   scale= 1.105    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.92,8.05,9.57,0.00,0.00,0.00); trace/3= 8.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.025860                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3136   r_free= 0.3663   ksol= 0.33   Bsol= 28.80   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,3.51,5.71,0.00,0.00,0.00); trace/3= 4.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.024202                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.375069              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.876   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.460730              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.816  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3136      final r-factor (work) = 0.2249          |
| start r-factor (free) = 0.3663      final r-factor (free) = 0.2840          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3876 = 5.38 * 0.50 * 6.0496 + 1.00 * 0.1290                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8878 = 5.38 * 0.50 * 5.8853 + 1.00 * 0.0710                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2249      final r-factor (work) = 0.2013          |
| start r-factor (free) = 0.2840      final r-factor (free) = 0.2581          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7468 = 0.46 * 1.00 * 5.8853 + 1.00 * 0.0353                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6379 = 0.46 * 1.00 * 5.7032 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.63   12.10    None  None   None       |
|    all(noH): 2823   0      0.00    63.63   12.10    None  None   None       |
|    Sol.    : 438    0      0.99    63.63   31.73    None  None   None       |
|    Mac.    : 2385   0      0.00    62.38   8.49     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 -   6.363: 1191   |   5:    31.814 -  38.177:  118        |
|      1:     6.363 -  12.726:  837   |   6:    38.177 -  44.540:   91        |
|      2:    12.726 -  19.089:  261   |   7:    44.540 -  50.903:   57        |
|      3:    19.089 -  25.451:  126   |   8:    50.903 -  57.266:   21        |
|      4:    25.451 -  31.814:  113   |   9:    57.266 -  63.629:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2013 r_free = 0.2581             target_work(ml) = 5.657         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2009 r_free = 0.2576             target_work(ml) = 5.655         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2009   r_free= 0.2576   ksol= 0.33   Bsol= 28.80   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,3.51,5.71,0.00,0.00,0.00); trace/3= 4.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.655281                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2006   r_free= 0.2564   ksol= 0.32   Bsol= 39.70   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,2.38,3.78,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.653970                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.332349              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.437  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.687580              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.441  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2006      final r-factor (work) = 0.1476          |
| start r-factor (free) = 0.2564      final r-factor (free) = 0.1939          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5803 = 3.33 * 0.50 * 5.7073 + 1.00 * 0.0710                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2836 = 3.33 * 0.50 * 5.5342 + 1.00 * 0.0628                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1476      final r-factor (work) = 0.1348          |
| start r-factor (free) = 0.1939      final r-factor (free) = 0.1813          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8154 = 0.69 * 1.00 * 5.5342 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6800 = 0.69 * 1.00 * 5.3345 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.85   12.92    None  None   None       |
|    all(noH): 2823   0      0.00    78.85   12.92    None  None   None       |
|    Sol.    : 438    0      2.46    74.93   36.91    None  None   None       |
|    Mac.    : 2385   0      0.00    78.85   8.52     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.885: 1523   |   5:    39.427 -  47.312:   97        |
|      1:     7.885 -  15.771:  658   |   6:    47.312 -  55.197:   70        |
|      2:    15.771 -  23.656:  189   |   7:    55.197 -  63.082:   47        |
|      3:    23.656 -  31.541:   99   |   8:    63.082 -  70.968:   21        |
|      4:    31.541 -  39.427:  112   |   9:    70.968 -  78.853:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1348 r_free = 0.1813             target_work(ml) = 5.298         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1347 r_free = 0.1809             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1347   r_free= 0.1809   ksol= 0.32   Bsol= 39.70   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,2.38,3.78,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.296685                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1345   r_free= 0.1805   ksol= 0.32   Bsol= 43.80   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,2.12,2.95,0.00,0.00,0.00); trace/3= 2.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.294761                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.458450              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.115  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.334505              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.460  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1345      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1805      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2897 = 3.46 * 0.50 * 5.3359 + 1.00 * 0.0628                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1326 = 3.46 * 0.50 * 5.2393 + 1.00 * 0.0727                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7645 = 0.33 * 1.00 * 5.2393 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7417 = 0.33 * 1.00 * 5.1751 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.10   12.62    None  None   None       |
|    all(noH): 2823   0      0.00    84.10   12.62    None  None   None       |
|    Sol.    : 438    0      2.43    73.43   35.52    None  None   None       |
|    Mac.    : 2385   0      0.00    84.10   8.42     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.410: 1617   |   5:    42.049 -  50.459:   92        |
|      1:     8.410 -  16.820:  627   |   6:    50.459 -  58.868:   53        |
|      2:    16.820 -  25.229:  164   |   7:    58.868 -  67.278:   27        |
|      3:    25.229 -  33.639:  119   |   8:    67.278 -  75.688:   14        |
|      4:    33.639 -  42.049:  108   |   9:    75.688 -  84.098:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1150 r_free = 0.1611             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1149 r_free = 0.1606             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1606   ksol= 0.32   Bsol= 43.80   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,2.12,2.95,0.00,0.00,0.00); trace/3= 2.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.165440                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1604   ksol= 0.33   Bsol= 43.80   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.21,2.09,2.74,0.00,0.00,0.00); trace/3= 2.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.165395                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.042368              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.453  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.177026              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.585  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1604      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3569 = 2.04 * 0.50 * 5.1746 + 1.00 * 0.0727                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3325 = 2.04 * 0.50 * 5.1622 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9244 = 0.18 * 1.00 * 5.1622 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9228 = 0.18 * 1.00 * 5.1624 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.74   12.26    None  None   None       |
|    all(noH): 2823   0      0.00    83.74   12.26    None  None   None       |
|    Sol.    : 438    0      2.26    72.25   33.70    None  None   None       |
|    Mac.    : 2385   0      0.00    83.74   8.32     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.374: 1630   |   5:    41.869 -  50.243:   92        |
|      1:     8.374 -  16.748:  635   |   6:    50.243 -  58.616:   45        |
|      2:    16.748 -  25.121:  158   |   7:    58.616 -  66.990:   18        |
|      3:    25.121 -  33.495:  129   |   8:    66.990 -  75.364:    8        |
|      4:    33.495 -  41.869:  106   |   9:    75.364 -  83.738:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1144 r_free = 0.1584             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1583             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1583   ksol= 0.33   Bsol= 43.80   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.21,2.09,2.74,0.00,0.00,0.00); trace/3= 2.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.160089                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6820 0.99   1412  159 0.1010 0.1341      5.3972      5.5604|
|  2:  4.6820 -  3.7350 0.99   1362  143 0.0897 0.1175      5.4659      5.6711|
|  3:  3.7350 -  3.2684 0.99   1331  155 0.1089 0.1569      5.4925      5.8721|
|  4:  3.2684 -  2.9721 0.99   1333  150 0.1240 0.1510      5.4646      5.5755|
|  5:  2.9721 -  2.7605 0.99   1319  145 0.1332 0.1685      5.3239      5.4948|
|  6:  2.7605 -  2.5986 0.99   1302  146 0.1239 0.1801      5.2083      5.4683|
|  7:  2.5986 -  2.4691 0.99   1321  140 0.1280 0.1615      5.1847      5.3598|
|  8:  2.4691 -  2.3620 0.98   1285  149 0.1171 0.1773      5.0541      5.3652|
|  9:  2.3620 -  2.2714 0.98   1304  149 0.1177 0.1784      5.0359      5.3017|
| 10:  2.2714 -  2.1933 0.98   1292  138 0.1155 0.1741      4.9602      5.2314|
| 11:  2.1933 -  2.1249 1.00   1276  140 0.1185 0.1766      4.9598      5.2816|
| 12:  2.1249 -  2.0643 0.97   1282  143 0.1116 0.1677      4.8739      5.0804|
| 13:  2.0643 -  2.0101 0.97   1270  142 0.1250 0.1762      4.8087      5.0452|
| 14:  2.0101 -  1.9612 0.41    541   60 0.1009 0.1587      4.6315      4.8696|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.6820  1412   159  0.94   8.81   0.98     0.96       7182.69|
|  2:  4.6820 -  3.7350  1362   143  0.95   8.12   1.02     1.00       9255.45|
|  3:  3.7350 -  3.2684  1331   155  0.93  11.81   1.03     1.02      10837.62|
|  4:  3.2684 -  2.9721  1333   150  0.92  13.82   1.00     0.98      10284.58|
|  5:  2.9721 -  2.7605  1319   145  0.90  15.90   0.99     0.96       8054.81|
|  6:  2.7605 -  2.5986  1302   146  0.90  15.87   0.98     0.96       6914.35|
|  7:  2.5986 -  2.4691  1321   140  0.91  15.33   0.99     0.97       6300.49|
|  8:  2.4691 -  2.3620  1285   149  0.91  15.50   0.99     0.96       5122.44|
|  9:  2.3620 -  2.2714  1304   149  0.91  15.32   1.01     1.00       5051.44|
| 10:  2.2714 -  2.1933  1292   138  0.91  15.32   1.01     0.97       4271.27|
| 11:  2.1933 -  2.1249  1276   140  0.90  16.55   1.01     0.98       4495.58|
| 12:  2.1249 -  2.0643  1282   143  0.91  15.19   1.01     1.00       3957.75|
| 13:  2.0643 -  2.0101  1270   142  0.90  16.48   1.01     1.01       3319.73|
| 14:  2.0101 -  1.9612   541    60  0.91  14.70   1.00     0.97       2409.50|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2409.50 max =        10837.62 mean =      6457.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.11|
|phase err.(test): min =        0.00 max =           87.96 mean =        13.58|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1582   ksol= 0.33   Bsol= 46.14   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.14,-0.26,0.40,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.160114                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1582   ksol= 0.33   Bsol= 46.14   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.14,-0.26,0.40,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.160114                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6820 0.99   1412  159 0.1011 0.1340      5.3977      5.5603|
|  2:  4.6820 -  3.7350 0.99   1362  143 0.0897 0.1175      5.4657      5.6708|
|  3:  3.7350 -  3.2684 0.99   1331  155 0.1088 0.1569      5.4923      5.8721|
|  4:  3.2684 -  2.9721 0.99   1333  150 0.1240 0.1510      5.4646      5.5755|
|  5:  2.9721 -  2.7605 0.99   1319  145 0.1332 0.1685      5.3239      5.4949|
|  6:  2.7605 -  2.5986 0.99   1302  146 0.1239 0.1801      5.2084      5.4683|
|  7:  2.5986 -  2.4691 0.99   1321  140 0.1280 0.1615      5.1848      5.3598|
|  8:  2.4691 -  2.3620 0.98   1285  149 0.1171 0.1774      5.0541      5.3652|
|  9:  2.3620 -  2.2714 0.98   1304  149 0.1177 0.1784      5.0359      5.3017|
| 10:  2.2714 -  2.1933 0.98   1292  138 0.1155 0.1741      4.9602      5.2314|
| 11:  2.1933 -  2.1249 1.00   1276  140 0.1185 0.1766      4.9598      5.2816|
| 12:  2.1249 -  2.0643 0.97   1282  143 0.1116 0.1677      4.8739      5.0804|
| 13:  2.0643 -  2.0101 0.97   1270  142 0.1250 0.1762      4.8087      5.0452|
| 14:  2.0101 -  1.9612 0.41    541   60 0.1009 0.1587      4.6315      4.8696|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.6820  1412   159  0.94   8.81   0.98     0.96       7186.95|
|  2:  4.6820 -  3.7350  1362   143  0.95   8.12   1.02     1.00       9254.38|
|  3:  3.7350 -  3.2684  1331   155  0.93  11.81   1.03     1.02      10833.65|
|  4:  3.2684 -  2.9721  1333   150  0.92  13.82   1.00     0.98      10284.41|
|  5:  2.9721 -  2.7605  1319   145  0.90  15.90   0.99     0.96       8055.36|
|  6:  2.7605 -  2.5986  1302   146  0.90  15.88   0.98     0.96       6914.86|
|  7:  2.5986 -  2.4691  1321   140  0.91  15.33   0.99     0.97       6300.95|
|  8:  2.4691 -  2.3620  1285   149  0.91  15.50   0.99     0.96       5122.64|
|  9:  2.3620 -  2.2714  1304   149  0.91  15.32   1.01     1.00       5051.60|
| 10:  2.2714 -  2.1933  1292   138  0.91  15.32   1.01     0.97       4271.35|
| 11:  2.1933 -  2.1249  1276   140  0.90  16.55   1.01     0.98       4495.69|
| 12:  2.1249 -  2.0643  1282   143  0.91  15.19   1.01     1.00       3957.84|
| 13:  2.0643 -  2.0101  1270   142  0.90  16.48   1.01     1.01       3319.82|
| 14:  2.0101 -  1.9612   541    60  0.91  14.70   1.00     0.97       2409.57|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2409.57 max =        10833.65 mean =      6457.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.11|
|phase err.(test): min =        0.00 max =           87.97 mean =        13.58|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.35    86.09   14.60    None  None   None       |
|    all(noH): 2823   0      2.35    86.09   14.60    None  None   None       |
|    Sol.    : 438    0      4.61    74.60   36.05    None  None   None       |
|    Mac.    : 2385   0      2.35    86.09   10.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.348 -  10.721: 1630   |   5:    44.216 -  52.590:   92        |
|      1:    10.721 -  19.095:  635   |   6:    52.590 -  60.964:   45        |
|      2:    19.095 -  27.469:  158   |   7:    60.964 -  69.338:   18        |
|      3:    27.469 -  35.843:  129   |   8:    69.338 -  77.711:    8        |
|      4:    35.843 -  44.216:  106   |   9:    77.711 -  86.085:    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)= 337         
Filter by distance & map next to the model:
   mapped sites are within: 0.425 - 5.556
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 332 from: 337
   mapped sites are within: 0.742 - 5.556

peak=   10.993 closest distance to " CB  VAL A 230 " =    1.465
peak=    7.655 closest distance to " CG2 VAL A 296 " =    1.163
peak=    6.071 closest distance to " CG  LEU A   5 " =    1.265
peak=    5.957 closest distance to " NH2 ARG A  56 " =    2.220
peak=    5.699 closest distance to " O   HOH Z 278 " =    1.194
peak=    5.578 closest distance to " CD2 LEU A   5 " =    1.262
peak=    5.429 closest distance to " NE2 GLN A  11 " =    1.177
peak=    5.139 closest distance to " CG  LEU A 228 " =    1.234
peak=    5.129 closest distance to " CB  SER A  63 " =    1.335
peak=    4.950 closest distance to " CD1AILE A 234 " =    1.014
peak=    4.879 closest distance to " CB  GLN A 223 " =    1.405
peak=    4.877 closest distance to " O   HOH Z 126 " =    1.844
peak=    4.865 closest distance to " O   HOH Z 232 " =    2.293
peak=    4.758 closest distance to " CB  SER A   3 " =    1.424
peak=    4.747 closest distance to " C   PRO A 198 " =    1.571
peak=    4.738 closest distance to " O   HOH Z  37 " =    1.280
peak=    4.713 closest distance to " O   HOH Z 263 " =    1.615
peak=    4.708 closest distance to " CB  GLN A 183 " =    1.216
peak=    4.684 closest distance to " O   HOH Z 193 " =    1.828
peak=    4.659 closest distance to " CG  PRO A 213 " =    1.200
peak=    4.635 closest distance to " CB  GLU A 152 " =    1.201
peak=    4.628 closest distance to " O   HOH Z 202 " =    1.313
peak=    4.613 closest distance to " CG  PRO A 198 " =    1.344
peak=    4.613 closest distance to " OD1 ASN A  69 " =    2.648
peak=    4.589 closest distance to " CD2 LEU A 228 " =    1.230
peak=    4.558 closest distance to " CB  VAL A 296 " =    1.148
peak=    4.553 closest distance to " O   HOH Z 144 " =    1.712
peak=    4.533 closest distance to " CB  ARG A 275 " =    0.856
peak=    4.527 closest distance to " CB  ASN A 148 " =    1.392
peak=    4.516 closest distance to " O   HOH Z 427 " =    2.895
peak=    4.492 closest distance to " O   HOH Z 236 " =    1.838
peak=    4.457 closest distance to " O   HOH Z 316 " =    2.947
peak=    4.377 closest distance to " CB  VAL A 230 " =    1.211
peak=    4.341 closest distance to " O   HOH Z 298 " =    1.779
peak=    4.329 closest distance to " O   HOH Z 132 " =    0.953
peak=    4.328 closest distance to " O   HOH Z 108 " =    1.405
peak=    4.309 closest distance to " CB  TYR A 169 " =    0.906
peak=    4.307 closest distance to " CA  GLY A 241 " =    3.809
peak=    4.269 closest distance to " CB  GLU A 128 " =    1.064
peak=    4.258 closest distance to " O   HOH Z 368 " =    2.047
peak=    4.225 closest distance to " O   HOH Z 126 " =    1.613
peak=    4.202 closest distance to " O   HOH Z 124 " =    1.397
peak=    4.195 closest distance to " O   HOH Z 371 " =    3.074
peak=    4.121 closest distance to " O   SER A  87 " =    2.319
peak=    4.120 closest distance to " O   HOH Z  97 " =    2.068
peak=    4.119 closest distance to " OD2 ASP A 286 " =    2.792
peak=    4.117 closest distance to " O   HOH Z 272 " =    1.890
peak=    4.116 closest distance to " O   HOH Z 303 " =    2.085
peak=    4.099 closest distance to " CB  VAL A 265 " =    1.251
peak=    4.069 closest distance to " ND2 ASN A 187 " =    1.620
peak=    4.067 closest distance to " O   HOH Z  48 " =    1.601
peak=    4.053 closest distance to " O   HOH Z 203 " =    1.678
peak=    4.028 closest distance to " O   HOH Z 260 " =    1.279
peak=    4.026 closest distance to " O   HOH Z   9 " =    2.229
peak=    4.023 closest distance to " O   HOH Z 389 " =    1.858
peak=    4.012 closest distance to " O   HOH Z 193 " =    1.681
peak=    4.009 closest distance to " CG  PRO A 243 " =    1.166
peak=    3.989 closest distance to " O   HOH Z 247 " =    1.315
peak=    3.987 closest distance to " O   HOH Z 234 " =    3.662
peak=    3.927 closest distance to " O   HOH Z  78 " =    1.770
peak=    3.923 closest distance to " CG  GLN A  88 " =    1.077
peak=    3.922 closest distance to " O   HOH Z 193 " =    1.876
peak=    3.922 closest distance to " CA  ALA A  21 " =    1.131
peak=    3.903 closest distance to " O   HOH Z 346 " =    1.567
peak=    3.897 closest distance to " CB  VAL A 202 " =    1.588
peak=    3.892 closest distance to " CB  ARG A  79 " =    1.390
peak=    3.887 closest distance to " CA  ALA A  51 " =    1.016
peak=    3.886 closest distance to " CB  SER A 216 " =    0.803
peak=    3.880 closest distance to " O   HOH Z 128 " =    1.939
peak=    3.879 closest distance to " CG1BVAL A  72 " =    1.557
peak=    3.865 closest distance to " CA  SER A  87 " =    0.913
peak=    3.859 closest distance to " CD1 LEU A 300 " =    1.206
peak=    3.858 closest distance to " O   HOH Z 344 " =    2.801
peak=    3.855 closest distance to " O   HOH Z 158 " =    2.897
peak=    3.854 closest distance to " CA  VAL A  41 " =    0.881
peak=    3.852 closest distance to " CA  THR A 221 " =    0.915
peak=    3.848 closest distance to " O   HOH Z 280 " =    2.992
peak=    3.845 closest distance to " O   HOH Z 295 " =    1.534
peak=    3.824 closest distance to " O   HOH Z  61 " =    1.591
peak=    3.818 closest distance to " O   HOH Z 425 " =    1.366
peak=    3.811 closest distance to " CB  PRO A  54 " =    0.742
peak=    3.809 closest distance to " O   HOH Z 369 " =    1.928
peak=    3.804 closest distance to " O   HOH Z 126 " =    1.546
peak=    3.783 closest distance to " N   PHE A 130 " =    1.366
peak=    3.781 closest distance to " CB  ASN A 148 " =    1.873
peak=    3.776 closest distance to " CG  ARG A  66 " =    2.681
peak=    3.776 closest distance to " O   HOH Z  88 " =    3.247
peak=    3.773 closest distance to " CB  TRP A 266 " =    0.978
peak=    3.772 closest distance to " O   HOH Z 209 " =    2.363
peak=    3.771 closest distance to " O   HOH Z  78 " =    2.411
peak=    3.770 closest distance to " O   HOH Z 227 " =    1.678
peak=    3.767 closest distance to " O   HOH Z   9 " =    1.960
peak=    3.758 closest distance to " CA  ASN A 215 " =    1.156
peak=    3.757 closest distance to " O   HOH Z 189 " =    2.657
peak=    3.752 closest distance to " O   HOH Z  59 " =    1.979
peak=    3.751 closest distance to " O   HOH Z 248 " =    1.823
peak=    3.736 closest distance to " OG BSER A 164 " =    2.232
peak=    3.735 closest distance to " CB  ILE A 234 " =    0.876
peak=    3.728 closest distance to " CG  LEU A 167 " =    1.172
peak=    3.706 closest distance to " CA  LEU A 282 " =    1.031
peak=    3.704 closest distance to " O   HOH Z 345 " =    3.371
peak=    3.695 closest distance to " O   HOH Z 133 " =    1.685
peak=    3.693 closest distance to " O   HOH Z 134 " =    1.432
peak=    3.691 closest distance to " O   HOH Z  21 " =    1.735
peak=    3.688 closest distance to " CB  GLN A  88 " =    1.237
peak=    3.675 closest distance to " O   HOH Z   3 " =    1.784
peak=    3.666 closest distance to " CD  ARG A 159 " =    0.752
peak=    3.659 closest distance to " O   HOH Z 132 " =    2.578
peak=    3.648 closest distance to " CB  ASN A  39 " =    0.871
peak=    3.647 closest distance to " O   HOH Z 112 " =    1.453
peak=    3.647 closest distance to " O   HOH Z 197 " =    3.127
peak=    3.639 closest distance to " OE1 GLU A   2 " =    2.158
peak=    3.633 closest distance to " O   HOH Z  55 " =    2.237
peak=    3.633 closest distance to " NH1AARG A 145 " =    1.026
peak=    3.633 closest distance to " CA  TYR A  30 " =    0.963
peak=    3.631 closest distance to " CB  LEU A 143 " =    1.129
peak=    3.629 closest distance to " O   TRP A 274 " =    1.898
peak=    3.628 closest distance to " O   HOH Z 273 " =    2.629
peak=    3.627 closest distance to " CA  THR A 264 " =    0.814
peak=    3.621 closest distance to " N   ASN A  39 " =    1.142
peak=    3.615 closest distance to " O   HOH Z  61 " =    1.627
peak=    3.614 closest distance to " CD BLYS A 290 " =    1.124
peak=    3.613 closest distance to " NH2 ARG A 156 " =    1.129
peak=    3.612 closest distance to " CG2 THR A 221 " =    1.057
peak=    3.609 closest distance to " N   ARG A 156 " =    1.286
peak=    3.608 closest distance to " CG2 VAL A 257 " =    0.947
peak=    3.605 closest distance to " O   HOH Z 271 " =    1.964
peak=    3.602 closest distance to " O   HOH Z 357 " =    1.844
peak=    3.597 closest distance to " CB  PRO A 198 " =    0.893
peak=    3.586 closest distance to " CA  ALA A 154 " =    1.095
peak=    3.585 closest distance to " C   ALA A 299 " =    0.978
peak=    3.584 closest distance to " O   HOH Z 133 " =    2.345
peak=    3.583 closest distance to " CD2 LEU A 255 " =    1.407
peak=    3.582 closest distance to " O   HOH Z 171 " =    2.268
peak=    3.578 closest distance to " O   MET A 105 " =    1.729
peak=    3.569 closest distance to " NZ  LYS A 117 " =    3.231
peak=    3.564 closest distance to " O   HOH Z 425 " =    2.081
peak=    3.563 closest distance to " CB  ASN A 187 " =    0.965
peak=    3.563 closest distance to " CB  TRP A 179 " =    1.343
peak=    3.563 closest distance to " CB  ARG A 139 " =    0.926
peak=    3.560 closest distance to " O   HOH Z 135 " =    1.815
peak=    3.560 closest distance to " CB  ALA A 291 " =    1.406
peak=    3.558 closest distance to " O   HOH Z 227 " =    2.082
peak=    3.549 closest distance to " CA  VAL A 126 " =    0.937
peak=    3.540 closest distance to " CA  ALA A 248 " =    1.380
peak=    3.538 closest distance to " O   HOH Z 130 " =    2.283
peak=    3.534 closest distance to " O   HOH Z  43 " =    2.052
peak=    3.534 closest distance to " CB  GLU A 277 " =    3.503
peak=    3.525 closest distance to " O   HOH Z  54 " =    1.515
peak=    3.522 closest distance to " O   HOH Z  68 " =    2.087
peak=    3.513 closest distance to " CB  LEU A 228 " =    1.327
peak=    3.504 closest distance to " ND1 HIS A  86 " =    1.598
peak=    3.500 closest distance to " O   HOH Z 255 " =    1.727
peak=    3.499 closest distance to " O   HOH Z  93 " =    2.530
peak=    3.495 closest distance to " C   LYS A 290 " =    1.306
peak=    3.490 closest distance to " O   HOH Z 355 " =    1.779
peak=    3.487 closest distance to " O   HOH Z 426 " =    1.508
peak=    3.485 closest distance to " O   HOH Z 423 " =    1.809
peak=    3.482 closest distance to " CG BARG A 102 " =    1.849
peak=    3.481 closest distance to " OG  SER A  22 " =    2.884
peak=    3.478 closest distance to " O   HOH Z 329 " =    3.732
peak=    3.469 closest distance to " O   HOH Z 116 " =    1.705
peak=    3.467 closest distance to " O   HOH Z 303 " =    1.760
peak=    3.465 closest distance to " O   HOH Z 145 " =    1.757
peak=    3.463 closest distance to " O   HOH Z 250 " =    1.349
peak=    3.462 closest distance to " O   HOH Z  10 " =    1.816
peak=    3.461 closest distance to " O   HOH Z  58 " =    1.523
peak=    3.453 closest distance to " O   HOH Z 280 " =    1.694
peak=    3.450 closest distance to " NH1 ARG A  14 " =    0.940
peak=    3.447 closest distance to " NE2 GLN A  58 " =    5.556
peak=    3.447 closest distance to " O   HOH Z 281 " =    4.484
peak=    3.446 closest distance to " CB  MET A  40 " =    0.859
peak=    3.445 closest distance to " CB  ALA A 248 " =    0.990
peak=    3.432 closest distance to " O   HOH Z 276 " =    1.263
peak=    3.424 closest distance to " O   HOH Z 403 " =    1.652
peak=    3.422 closest distance to " CB  ASN A 142 " =    1.000
peak=    3.412 closest distance to " O   HOH Z 284 " =    1.694
peak=    3.409 closest distance to " O   HOH Z 109 " =    2.683
peak=    3.406 closest distance to " CE1 TYR A 186 " =    1.290
peak=    3.404 closest distance to " O   HOH Z 374 " =    2.461
peak=    3.403 closest distance to " O   HOH Z 222 " =    2.431
peak=    3.387 closest distance to " O   GLN A  58 " =    1.563
peak=    3.386 closest distance to " O   HOH Z 350 " =    1.507
peak=    3.379 closest distance to " O   HOH Z 108 " =    1.943
peak=    3.378 closest distance to " CD  ARG A 269 " =    0.998
peak=    3.378 closest distance to " O   HOH Z 412 " =    2.035
peak=    3.376 closest distance to " O   HOH Z 411 " =    1.865
peak=    3.373 closest distance to " O   ALA A 158 " =    1.314
peak=    3.372 closest distance to " CD2 TYR A 186 " =    0.980
peak=    3.370 closest distance to " O   HOH Z 407 " =    2.310
peak=    3.370 closest distance to " O   HOH Z 119 " =    2.250
peak=    3.369 closest distance to " CG1 ILE A  33 " =    1.353
peak=    3.368 closest distance to " O   HOH Z 313 " =    1.767
peak=    3.368 closest distance to " O   HOH Z 344 " =    1.262
peak=    3.361 closest distance to " CB BVAL A  41 " =    1.260
peak=    3.360 closest distance to " CG1 VAL A 153 " =    0.940
peak=    3.356 closest distance to " O   HOH Z 216 " =    2.356
peak=    3.353 closest distance to " CG BARG A 275 " =    1.473
peak=    3.346 closest distance to " O   HOH Z 236 " =    1.551
peak=    3.344 closest distance to " CA  ALA A 158 " =    1.140
peak=    3.342 closest distance to " O   HOH Z 214 " =    1.951
peak=    3.339 closest distance to " O   HOH Z  44 " =    1.747
peak=    3.339 closest distance to " CE  LYS A  76 " =    0.911
peak=    3.337 closest distance to " CA  ALA A 295 " =    0.998
peak=    3.331 closest distance to " CG2 ILE A 120 " =    1.305
peak=    3.329 closest distance to " N   TRP A 177 " =    1.708
peak=    3.325 closest distance to " CB  LYS A 117 " =    1.202
peak=    3.325 closest distance to " O   HOH Z 172 " =    3.657
peak=    3.324 closest distance to " O   HOH Z 175 " =    2.086
peak=    3.324 closest distance to " O   HOH Z 180 " =    2.101
peak=    3.323 closest distance to " CG  MET A 185 " =    1.056
peak=    3.319 closest distance to " O   HOH Z 419 " =    1.767
peak=    3.316 closest distance to " O   HOH Z 209 " =    2.381
peak=    3.312 closest distance to " N   VAL A 126 " =    1.205
peak=    3.311 closest distance to " O   HOH Z 171 " =    3.871
peak=    3.310 closest distance to " CD1 ILE A  33 " =    1.654
peak=    3.310 closest distance to " CG2 VAL A 174 " =    1.385
peak=    3.308 closest distance to " O   ALA A   1 " =    1.532
peak=    3.308 closest distance to " CB  TYR A  30 " =    1.479
peak=    3.307 closest distance to " CA  GLY A 211 " =    1.178
peak=    3.303 closest distance to " CB  LEU A 255 " =    0.930
peak=    3.300 closest distance to " CD1 ILE A 106 " =    1.121
peak=    3.300 closest distance to " CB  SER A 212 " =    1.160
peak=    3.295 closest distance to " O   HOH Z  40 " =    1.905
peak=    3.294 closest distance to " NH2 ARG A 219 " =    1.796
peak=    3.293 closest distance to " CB  ALA A 161 " =    0.896
peak=    3.289 closest distance to " O   HOH Z  68 " =    1.622
peak=    3.288 closest distance to " CZ  PHE A 192 " =    1.013
peak=    3.287 closest distance to " O   HOH Z   2 " =    1.727
peak=    3.281 closest distance to " CA  PHE A 283 " =    1.228
peak=    3.280 closest distance to " CB  THR A 157 " =    1.065
peak=    3.279 closest distance to " NE AARG A 275 " =    1.409
peak=    3.273 closest distance to " CG  GLU A 277 " =    2.258
peak=    3.270 closest distance to " O   HOH Z 388 " =    1.958
peak=    3.269 closest distance to " O   HOH Z 367 " =    3.533
peak=    3.269 closest distance to " CA  GLN A 194 " =    1.189
peak=    3.268 closest distance to " O   HOH Z 285 " =    3.016
peak=    3.268 closest distance to " CB  ALA A   1 " =    1.211
peak=    3.266 closest distance to " N   SER A 135 " =    1.339
peak=    3.265 closest distance to " CA  ASP A 191 " =    0.783
peak=    3.264 closest distance to " CA  TYR A 186 " =    1.411
peak=    3.259 closest distance to " OG  SER A 206 " =    1.229
peak=    3.256 closest distance to " O   HOH Z 261 " =    1.933
peak=    3.255 closest distance to " O   HOH Z   7 " =    1.280
peak=    3.250 closest distance to " O   THR A  31 " =    1.516
peak=    3.249 closest distance to " O   HOH Z  68 " =    2.707
peak=    3.248 closest distance to " O   HOH Z   1 " =    1.726
peak=    3.247 closest distance to " O   HOH Z 151 " =    1.662
peak=    3.246 closest distance to " CB  ALA A   9 " =    1.567
peak=    3.245 closest distance to " O   HOH Z 188 " =    2.004
peak=    3.245 closest distance to " CA  GLY A 267 " =    1.018
peak=    3.239 closest distance to " CA  LYS A 117 " =    1.246
peak=    3.238 closest distance to " O   HOH Z   1 " =    1.753
peak=    3.233 closest distance to " CB  THR A  31 " =    1.643
peak=    3.233 closest distance to " NZ  LYS A  76 " =    1.213
peak=    3.232 closest distance to " O   HOH Z 410 " =    1.590
peak=    3.231 closest distance to " ND1 HIS A  81 " =    1.599
peak=    3.230 closest distance to " CB  ALA A 295 " =    1.300
peak=    3.230 closest distance to " CG2 THR A 220 " =    0.982
peak=    3.229 closest distance to " OE1 GLN A  11 " =    1.778
peak=    3.228 closest distance to " OD1BASN A 224 " =    2.231
peak=    3.225 closest distance to " CB  TRP A 150 " =    1.483
peak=    3.223 closest distance to " CE  MET A  93 " =    1.527
peak=    3.217 closest distance to " O   HOH Z  20 " =    1.551
peak=    3.210 closest distance to " O   HOH Z 423 " =    2.832
peak=    3.210 closest distance to " CA  ASN A  74 " =    1.136
peak=    3.209 closest distance to " CZ  PHE A 218 " =    1.069
peak=    3.208 closest distance to " O  BHOH Z 338 " =    2.606
peak=    3.207 closest distance to " NH1 ARG A  56 " =    0.936
peak=    3.205 closest distance to " CA  ILE A 106 " =    0.821
peak=    3.204 closest distance to " CA  ASP A 140 " =    1.203
peak=    3.201 closest distance to " O   HOH Z 332 " =    1.497
peak=    3.200 closest distance to " CB  GLN A 278 " =    0.838
peak=    3.199 closest distance to " O   HOH Z 189 " =    3.040
peak=    3.195 closest distance to " O   HOH Z 163 " =    1.906
peak=    3.190 closest distance to " CA  ALA A 233 " =    1.460
peak=    3.189 closest distance to " CD  LYS A 166 " =    1.287
peak=    3.188 closest distance to " CD2 LEU A 167 " =    0.763
peak=    3.181 closest distance to " O   HOH Z  49 " =    2.535
peak=    3.177 closest distance to " OD1 ASP A 286 " =    1.566
peak=    3.175 closest distance to " NH2AARG A 190 " =    1.434
peak=    3.174 closest distance to " CG2 THR A 294 " =    1.694
peak=    3.170 closest distance to " CD2 HIS A  81 " =    1.199
peak=    3.169 closest distance to " CB  SER A  62 " =    1.275
peak=    3.167 closest distance to " NH2BARG A 102 " =    0.901
peak=    3.165 closest distance to " O   HOH Z 420 " =    4.348
peak=    3.161 closest distance to " CG  MET A 188 " =    1.357
peak=    3.160 closest distance to " O   HOH Z 334 " =    1.399
peak=    3.156 closest distance to " O   HOH Z 422 " =    2.644
peak=    3.149 closest distance to " NH2AARG A 190 " =    1.039
peak=    3.148 closest distance to " CB  ILE A  20 " =    1.415
peak=    3.148 closest distance to " CB  VAL A 268 " =    0.806
peak=    3.148 closest distance to " CB  THR A  82 " =    1.267
peak=    3.146 closest distance to " CD  LYS A 119 " =    1.472
peak=    3.146 closest distance to " O   HOH Z 287 " =    1.768
peak=    3.146 closest distance to " CB  HIS A 108 " =    0.854
peak=    3.144 closest distance to " CB  MET A  47 " =    1.083
peak=    3.141 closest distance to " O   HOH Z 383 " =    2.054
peak=    3.141 closest distance to " CD  ARG A 219 " =    1.022
peak=    3.140 closest distance to " O   HOH Z 409 " =    3.727
peak=    3.139 closest distance to " O   HOH Z 417 " =    1.993
peak=    3.138 closest distance to " O   PHE A  38 " =    1.956
peak=    3.136 closest distance to " NZ ALYS A 290 " =    1.115
peak=    3.133 closest distance to " O   HOH Z 128 " =    1.726
peak=    3.132 closest distance to " O   HOH Z  48 " =    1.523
peak=    3.127 closest distance to " O   HOH Z 302 " =    1.934
peak=    3.121 closest distance to " N   GLN A 278 " =    0.928
peak=    3.118 closest distance to " CA  LYS A  48 " =    1.327
peak=    3.118 closest distance to " O   HOH Z 217 " =    1.387
peak=    3.117 closest distance to " NH2BARG A 145 " =    2.041
peak=    3.115 closest distance to " CB  ARG A 190 " =    1.803
peak=    3.115 closest distance to " O   HOH Z 280 " =    2.532
peak=    3.112 closest distance to " O   HOH Z 409 " =    3.146
peak=    3.112 closest distance to " C   VAL A 265 " =    1.409
peak=    3.098 closest distance to " O   HOH Z 245 " =    1.443
peak=    3.090 closest distance to " O   HOH Z 322 " =    1.966
peak=    3.088 closest distance to " O   HOH Z 213 " =    2.329
peak=    3.087 closest distance to " O   HOH Z   4 " =    1.885
peak=    3.085 closest distance to " O   HOH Z 272 " =    2.462
peak=    3.081 closest distance to " NH2BARG A 190 " =    1.700
peak=    3.080 closest distance to " CG  GLN A  55 " =    2.124
peak=    3.080 closest distance to " C   GLU A 277 " =    1.398
peak=    3.075 closest distance to " O   HOH Z  88 " =    2.511
peak=    3.071 closest distance to " O   HOH Z 368 " =    3.536
peak=    3.056 closest distance to " O   HOH Z 427 " =    3.805
peak=    3.055 closest distance to " CA  ARG A  56 " =    1.986
peak=    3.047 closest distance to " CB  LEU A 237 " =    0.909
peak=    3.045 closest distance to " CB  GLU A 236 " =    0.831
peak=    3.033 closest distance to " CA  THR A 246 " =    1.347
peak=    3.019 closest distance to " O   HOH Z 353 " =    2.657
peak=    3.017 closest distance to " O   GLN A 278 " =    1.523
peak=    3.012 closest distance to " O   HOH Z 213 " =    1.719

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.426 - 5.390
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 185 from: 190
   mapped sites are within: 0.716 - 5.390

peak=   -5.879 closest distance to " CG2 VAL A 230 " =    0.765
peak=   -4.588 closest distance to " O   HOH Z 290 " =    1.020
peak=   -4.388 closest distance to " CG  LEU A 101 " =    2.570
peak=   -4.318 closest distance to " CD  ARG A 156 " =    1.976
peak=   -4.233 closest distance to " O   HOH Z 231 " =    1.472
peak=   -4.192 closest distance to " SG  CYS A 254 " =    3.250
peak=   -4.107 closest distance to " CG  GLN A 223 " =    1.706
peak=   -4.105 closest distance to " O   ILE A 109 " =    2.638
peak=   -4.016 closest distance to " O   HOH Z 266 " =    4.550
peak=   -3.991 closest distance to " N   GLN A  58 " =    1.807
peak=   -3.939 closest distance to " O   PRO A 163 " =    1.927
peak=   -3.916 closest distance to " CB  PRO A 163 " =    2.624
peak=   -3.883 closest distance to " CG  ASP A 231 " =    0.769
peak=   -3.850 closest distance to " CG2 VAL A 296 " =    1.337
peak=   -3.821 closest distance to " CE2 TYR A  30 " =    2.916
peak=   -3.819 closest distance to " CG2 THR A   4 " =    1.958
peak=   -3.814 closest distance to " CB  PRO A 243 " =    2.613
peak=   -3.787 closest distance to " CD1 LEU A 101 " =    2.515
peak=   -3.780 closest distance to " N   THR A 157 " =    1.496
peak=   -3.779 closest distance to " O   HOH Z 166 " =    1.485
peak=   -3.767 closest distance to " O   HOH Z 388 " =    1.991
peak=   -3.765 closest distance to " C   ALA A 158 " =    1.283
peak=   -3.765 closest distance to " CD1 LEU A 228 " =    2.268
peak=   -3.726 closest distance to " O   HOH Z 377 " =    1.954
peak=   -3.724 closest distance to " OXT GLY A 302 " =    2.865
peak=   -3.704 closest distance to " C   ASP A 231 " =    2.537
peak=   -3.694 closest distance to " O   HOH Z  92 " =    1.409
peak=   -3.694 closest distance to " O   HOH Z 389 " =    1.803
peak=   -3.688 closest distance to " N   HIS A 115 " =    2.207
peak=   -3.677 closest distance to " O   HOH Z 435 " =    2.792
peak=   -3.666 closest distance to " O   HOH Z  43 " =    1.790
peak=   -3.658 closest distance to " CG1 VAL A 296 " =    1.413
peak=   -3.646 closest distance to " CG  PHE A 283 " =    2.654
peak=   -3.636 closest distance to " CG  MET A 105 " =    0.951
peak=   -3.633 closest distance to " C   GLN A  58 " =    2.206
peak=   -3.612 closest distance to " O   HOH Z 351 " =    1.379
peak=   -3.608 closest distance to " O   PRO A 198 " =    1.238
peak=   -3.604 closest distance to " O   HOH Z 103 " =    1.922
peak=   -3.602 closest distance to " O   HOH Z  52 " =    1.510
peak=   -3.602 closest distance to " OG BSER A 134 " =    1.684
peak=   -3.594 closest distance to " CB  TYR A  15 " =    2.149
peak=   -3.593 closest distance to " O   GLY A 196 " =    1.169
peak=   -3.587 closest distance to " NH2 ARG A  79 " =    1.831
peak=   -3.580 closest distance to " CZ3 TRP A 179 " =    1.254
peak=   -3.578 closest distance to " CE2 PHE A 218 " =    2.641
peak=   -3.561 closest distance to " C   HIS A 108 " =    1.213
peak=   -3.558 closest distance to " CD2 TYR A 293 " =    2.168
peak=   -3.556 closest distance to " O   HOH Z  98 " =    1.858
peak=   -3.546 closest distance to " O   HOH Z 148 " =    1.799
peak=   -3.546 closest distance to " N   SER A 276 " =    1.280
peak=   -3.542 closest distance to " CD2 LEU A 237 " =    2.755
peak=   -3.541 closest distance to " C   MET A 188 " =    1.603
peak=   -3.540 closest distance to " O   HOH Z  60 " =    2.096
peak=   -3.540 closest distance to " O   ALA A 161 " =    1.539
peak=   -3.539 closest distance to " CG  TRP A 266 " =    1.651
peak=   -3.533 closest distance to " N   ALA A 226 " =    2.079
peak=   -3.524 closest distance to " CD  GLN A  88 " =    2.234
peak=   -3.522 closest distance to " CB  ALA A 248 " =    1.968
peak=   -3.518 closest distance to " ND2 ASN A  45 " =    0.988
peak=   -3.516 closest distance to " CB  ASN A  39 " =    2.032
peak=   -3.508 closest distance to " NH2AARG A 275 " =    5.258
peak=   -3.507 closest distance to " O   HOH Z 166 " =    1.992
peak=   -3.507 closest distance to " CG  LEU A 228 " =    0.919
peak=   -3.501 closest distance to " O   HOH Z  97 " =    1.556
peak=   -3.499 closest distance to " C   ASN A 285 " =    2.448
peak=   -3.496 closest distance to " C   ASN A 187 " =    1.787
peak=   -3.494 closest distance to " O   HOH Z 185 " =    2.251
peak=   -3.494 closest distance to " OG  SER A  87 " =    1.373
peak=   -3.489 closest distance to " O   GLY A 211 " =    1.337
peak=   -3.489 closest distance to " O   HOH Z 211 " =    1.632
peak=   -3.472 closest distance to " OG BSER A 134 " =    1.223
peak=   -3.468 closest distance to " CD  LYS A 289 " =    2.612
peak=   -3.463 closest distance to " O   HOH Z 417 " =    2.813
peak=   -3.461 closest distance to " CG  PRO A 163 " =    2.544
peak=   -3.449 closest distance to " O   VAL A  67 " =    2.504
peak=   -3.447 closest distance to " CD  ARG A 139 " =    1.638
peak=   -3.442 closest distance to " CZ  PHE A  59 " =    1.518
peak=   -3.439 closest distance to " CB  ALA A  43 " =    2.440
peak=   -3.438 closest distance to " CG  LYS A 193 " =    2.299
peak=   -3.434 closest distance to " O   HOH Z  63 " =    1.063
peak=   -3.434 closest distance to " CG  ASP A  50 " =    2.324
peak=   -3.433 closest distance to " O   HOH Z 436 " =    1.450
peak=   -3.429 closest distance to " CB  VAL A 296 " =    1.152
peak=   -3.427 closest distance to " CG2 ILE A 151 " =    2.570
peak=   -3.420 closest distance to " CB  ALA A 291 " =    2.306
peak=   -3.418 closest distance to " CD2 LEU A 300 " =    2.766
peak=   -3.418 closest distance to " OD1 ASN A 148 " =    1.558
peak=   -3.404 closest distance to " CD  GLN A  88 " =    0.798
peak=   -3.377 closest distance to " CB  ASP A 132 " =    2.264
peak=   -3.376 closest distance to " CE  LYS A  76 " =    2.767
peak=   -3.375 closest distance to " OG ASER A 134 " =    1.643
peak=   -3.375 closest distance to " CG2 VAL A 112 " =    2.596
peak=   -3.368 closest distance to " O   HOH Z 377 " =    0.857
peak=   -3.368 closest distance to " CE  MET A 105 " =    2.041
peak=   -3.366 closest distance to " ND2 ASN A  60 " =    1.445
peak=   -3.364 closest distance to " CG1 VAL A 197 " =    2.249
peak=   -3.364 closest distance to " OD1 ASP A 191 " =    1.565
peak=   -3.360 closest distance to " O   HOH Z 184 " =    1.713
peak=   -3.358 closest distance to " O   HOH Z 281 " =    2.808
peak=   -3.356 closest distance to " CA  ASP A  27 " =    2.386
peak=   -3.350 closest distance to " O   HOH Z  71 " =    0.980
peak=   -3.350 closest distance to " O   HOH Z  38 " =    1.968
peak=   -3.348 closest distance to " O   HOH Z 191 " =    5.390
peak=   -3.347 closest distance to " N   ALA A  43 " =    2.365
peak=   -3.345 closest distance to " CD1 PHE A  59 " =    1.878
peak=   -3.335 closest distance to " O   HOH Z 241 " =    1.295
peak=   -3.334 closest distance to " CZ  TYR A 169 " =    1.690
peak=   -3.326 closest distance to " C   GLN A 240 " =    2.297
peak=   -3.323 closest distance to " O   GLY A 203 " =    2.458
peak=   -3.322 closest distance to " O   HOH Z 210 " =    0.884
peak=   -3.315 closest distance to " O   HOH Z 407 " =    3.106
peak=   -3.314 closest distance to " O   HOH Z  13 " =    1.340
peak=   -3.314 closest distance to " NH2 ARG A  66 " =    2.149
peak=   -3.310 closest distance to " CG  GLU A 277 " =    1.140
peak=   -3.310 closest distance to " CE BMET A  47 " =    1.735
peak=   -3.309 closest distance to " O   ASP A 231 " =    2.504
peak=   -3.301 closest distance to " O   HOH Z 426 " =    1.591
peak=   -3.298 closest distance to " O   HOH Z 222 " =    1.324
peak=   -3.295 closest distance to " CD1 ILE A 199 " =    2.495
peak=   -3.292 closest distance to " O   HOH Z 132 " =    0.841
peak=   -3.290 closest distance to " O   HOH Z 275 " =    1.463
peak=   -3.289 closest distance to " OE1 GLN A  88 " =    1.077
peak=   -3.288 closest distance to " N   GLN A  77 " =    1.658
peak=   -3.287 closest distance to " OXT GLY A 302 " =    3.522
peak=   -3.275 closest distance to " C   LEU A 222 " =    0.716
peak=   -3.269 closest distance to " O   HOH Z 298 " =    1.266
peak=   -3.265 closest distance to " O   VAL A  67 " =    2.718
peak=   -3.264 closest distance to " N   ALA A 248 " =    1.635
peak=   -3.258 closest distance to " C   LEU A 143 " =    1.222
peak=   -3.258 closest distance to " CG1 VAL A 112 " =    2.625
peak=   -3.257 closest distance to " O   VAL A 197 " =    1.305
peak=   -3.253 closest distance to " O   HOH Z 309 " =    2.452
peak=   -3.250 closest distance to " CB  PHE A 192 " =    1.863
peak=   -3.246 closest distance to " NH1 ARG A  56 " =    2.495
peak=   -3.238 closest distance to " O   HOH Z  19 " =    2.350
peak=   -3.230 closest distance to " O   HOH Z 385 " =    2.005
peak=   -3.227 closest distance to " O   MET A  40 " =    2.676
peak=   -3.226 closest distance to " O   HOH Z  97 " =    2.058
peak=   -3.224 closest distance to " CA  SER A 146 " =    2.323
peak=   -3.223 closest distance to " O   HOH Z 292 " =    4.436
peak=   -3.219 closest distance to " O   HOH Z 234 " =    4.219
peak=   -3.217 closest distance to " O   TYR A 247 " =    2.806
peak=   -3.208 closest distance to " O   HOH Z 143 " =    2.494
peak=   -3.207 closest distance to " O   HOH Z 118 " =    2.673
peak=   -3.202 closest distance to " O   HOH Z 174 " =    2.413
peak=   -3.199 closest distance to " O   HOH Z 252 " =    4.123
peak=   -3.199 closest distance to " O   PRO A 198 " =    1.263
peak=   -3.195 closest distance to " SG BCYS A 201 " =    2.250
peak=   -3.194 closest distance to " O   HOH Z 353 " =    2.116
peak=   -3.181 closest distance to " CD1 ILE A 239 " =    2.033
peak=   -3.180 closest distance to " C   VAL A 174 " =    1.841
peak=   -3.174 closest distance to " O   HOH Z 423 " =    2.164
peak=   -3.173 closest distance to " CG  GLU A 152 " =    2.338
peak=   -3.167 closest distance to " CD  GLN A  58 " =    1.028
peak=   -3.165 closest distance to " OG  SER A 245 " =    0.871
peak=   -3.163 closest distance to " O   HOH Z  93 " =    1.740
peak=   -3.159 closest distance to " O   HOH Z  90 " =    2.899
peak=   -3.153 closest distance to " CA  GLY A 133 " =    1.924
peak=   -3.151 closest distance to " O   HOH Z 228 " =    1.574
peak=   -3.150 closest distance to " O   HOH Z 165 " =    2.024
peak=   -3.149 closest distance to " O   HOH Z 198 " =    1.450
peak=   -3.146 closest distance to " CA  ASP A 298 " =    1.067
peak=   -3.142 closest distance to " O   VAL A 153 " =    2.241
peak=   -3.138 closest distance to " O   HOH Z 322 " =    0.916
peak=   -3.135 closest distance to " CB  GLN A  55 " =    1.487
peak=   -3.128 closest distance to " NH1AARG A 275 " =    1.870
peak=   -3.125 closest distance to " CG1 VAL A 296 " =    1.241
peak=   -3.122 closest distance to " N   THR A 235 " =    1.242
peak=   -3.122 closest distance to " CZ  ARG A 259 " =    0.802
peak=   -3.114 closest distance to " O   HOH Z 292 " =    2.842
peak=   -3.105 closest distance to " CD1 TRP A 179 " =    0.943
peak=   -3.104 closest distance to " O   HOH Z  47 " =    1.542
peak=   -3.099 closest distance to " CD1 ILE A 263 " =    2.465
peak=   -3.096 closest distance to " NH2BARG A 275 " =    1.811
peak=   -3.087 closest distance to " OD1 ASN A 249 " =    1.233
peak=   -3.087 closest distance to " CE3 TRP A 274 " =    1.098
peak=   -3.086 closest distance to " O   HOH Z 175 " =    4.280
peak=   -3.084 closest distance to " CD  LYS A 166 " =    2.546
peak=   -3.071 closest distance to " CB  ASP A 132 " =    2.186
peak=   -3.067 closest distance to " O   SER A  22 " =    2.280
peak=   -3.064 closest distance to " SG ACYS A 201 " =    2.182
peak=   -3.063 closest distance to " O   HOH Z  10 " =    1.514
peak=   -3.061 closest distance to " CB  TYR A 172 " =    2.216
peak=   -3.058 closest distance to " OD1 ASN A 187 " =    1.690
peak=   -3.047 closest distance to " CG  GLN A 278 " =    2.209

================= 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    :  0.4612 0.4524   6.260185e+00   6.252510e+00
   1_bss:  0.4519 0.4413   6.256613e+00   6.244599e+00
   1_xyz:  0.3661 0.3887   6.121993e+00   6.163103e+00
   1_adp:  0.3188 0.3721   6.026523e+00   6.127736e+00
   1_occ:  0.3183 0.3726   6.025860e+00   6.128194e+00
   2_bss:  0.3136 0.3663   6.024202e+00   6.124555e+00
   2_xyz:  0.2249 0.2840   5.751319e+00   5.926047e+00
   2_adp:  0.2013 0.2581   5.656865e+00   5.844257e+00
   2_occ:  0.2009 0.2576   5.655281e+00   5.843147e+00
   3_bss:  0.2006 0.2564   5.653970e+00   5.840695e+00
   3_xyz:  0.1476 0.1939   5.375655e+00   5.591127e+00
   3_adp:  0.1348 0.1813   5.297916e+00   5.524051e+00
   3_occ:  0.1347 0.1809   5.296685e+00   5.522494e+00
   4_bss:  0.1345 0.1805   5.294761e+00   5.519180e+00
   4_xyz:  0.1174 0.1634   5.182554e+00   5.423181e+00
   4_adp:  0.1150 0.1611   5.166735e+00   5.408878e+00
   4_occ:  0.1149 0.1606   5.165440e+00   5.407441e+00
   5_bss:  0.1148 0.1604   5.165395e+00   5.407296e+00
   5_xyz:  0.1134 0.1587   5.157571e+00   5.399553e+00
   5_adp:  0.1144 0.1584   5.160889e+00   5.398005e+00
   5_occ:  0.1143 0.1583   5.160089e+00   5.397076e+00
   5_bss:  0.1143 0.1582   5.160114e+00   5.397062e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.345   5.051   7.925   8.046   9.567   0.000   0.000   0.000
   1_xyz:  0.345   5.051   7.925   8.046   9.567   0.000   0.000   0.000
   1_adp:  0.345   5.051   7.925   8.046   9.567   0.000   0.000   0.000
   1_occ:  0.345   5.051   7.925   8.046   9.567   0.000   0.000   0.000
   2_bss:  0.328  28.804   3.650   3.505   5.712   0.000   0.000   0.000
   2_xyz:  0.328  28.804   3.650   3.505   5.712   0.000   0.000   0.000
   2_adp:  0.328  28.804   3.650   3.505   5.712   0.000   0.000   0.000
   2_occ:  0.328  28.804   3.650   3.505   5.712   0.000   0.000   0.000
   3_bss:  0.316  39.701   2.652   2.381   3.779   0.000   0.000   0.000
   3_xyz:  0.316  39.701   2.652   2.381   3.779   0.000   0.000   0.000
   3_adp:  0.316  39.701   2.652   2.381   3.779   0.000   0.000   0.000
   3_occ:  0.316  39.701   2.652   2.381   3.779   0.000   0.000   0.000
   4_bss:  0.323  43.797   2.330   2.123   2.947   0.000   0.000   0.000
   4_xyz:  0.323  43.797   2.330   2.123   2.947   0.000   0.000   0.000
   4_adp:  0.323  43.797   2.330   2.123   2.947   0.000   0.000   0.000
   4_occ:  0.323  43.797   2.330   2.123   2.947   0.000   0.000   0.000
   5_bss:  0.327  43.797   2.208   2.090   2.745   0.000   0.000   0.000
   5_xyz:  0.327  43.797   2.208   2.090   2.745   0.000   0.000   0.000
   5_adp:  0.327  43.797   2.208   2.090   2.745   0.000   0.000   0.000
   5_occ:  0.327  43.797   2.208   2.090   2.745   0.000   0.000   0.000
   5_bss:  0.328  46.144  -0.140  -0.257   0.397   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.888 0.4721  0.5538    63608.010
   1_bss:  54.355 0.4634  0.6870    60512.114
   1_xyz:  43.863 0.5946  0.8710    43579.713
   1_adp:  40.071 0.6410  0.9688    38255.324
   1_occ:  40.193 0.6395  0.9660    38389.333
   2_bss:  39.817 0.6438  0.8404    37826.927
   2_xyz:  29.414 0.7631  0.9621    21313.038
   2_adp:  25.883 0.8022  0.9909    17529.538
   2_occ:  25.820 0.8028  0.9912    17448.194
   3_bss:  25.663 0.8043  0.9454    17272.650
   3_xyz:  18.556 0.8752  0.9885     9721.809
   3_adp:  16.897 0.8907  0.9934     8521.390
   3_occ:  16.855 0.8910  0.9935     8482.503
   4_bss:  16.757 0.8919  0.9767     8408.996
   4_xyz:  14.733 0.9088  0.9861     6814.055
   4_adp:  14.380 0.9120  0.9867     6643.631
   4_occ:  14.347 0.9123  0.9867     6621.872
   5_bss:  14.344 0.9123  0.9825     6621.498
   5_xyz:  14.140 0.9141  0.9817     6488.244
   5_adp:  14.069 0.9149  0.9817     6469.440
   5_occ:  14.053 0.9150  0.9817     6458.409
   5_bss:  14.053 0.9150  0.9817     6458.522
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3442e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3442e+01
   1_xyz:   1.597  0.012  0.103 18.316  0.006  4.110   1.2904e-01
   1_adp:   1.597  0.012  0.103 18.316  0.006  4.110   1.2904e-01
   1_occ:   1.597  0.012  0.103 18.316  0.006  4.110   1.2904e-01
   2_bss:   1.597  0.012  0.103 18.316  0.006  4.110   1.2904e-01
   2_xyz:   1.041  0.007  0.074 16.411  0.005  4.113   7.0991e-02
   2_adp:   1.041  0.007  0.074 16.411  0.005  4.113   7.0991e-02
   2_occ:   1.041  0.007  0.074 16.411  0.005  4.113   7.0991e-02
   3_bss:   1.041  0.007  0.074 16.411  0.005  4.113   7.0991e-02
   3_xyz:   1.023  0.007  0.077 15.997  0.003  4.123   6.2771e-02
   3_adp:   1.023  0.007  0.077 15.997  0.003  4.123   6.2771e-02
   3_occ:   1.023  0.007  0.077 15.997  0.003  4.123   6.2771e-02
   4_bss:   1.023  0.007  0.077 15.997  0.003  4.123   6.2771e-02
   4_xyz:   1.106  0.008  0.087 16.245  0.004  4.110   7.2689e-02
   4_adp:   1.106  0.008  0.087 16.245  0.004  4.110   7.2689e-02
   4_occ:   1.106  0.008  0.087 16.245  0.004  4.110   7.2689e-02
   5_bss:   1.106  0.008  0.087 16.245  0.004  4.110   7.2689e-02
   5_xyz:   0.987  0.006  0.078 15.829  0.004  4.110   6.0948e-02
   5_adp:   0.987  0.006  0.078 15.829  0.004  4.110   6.0948e-02
   5_occ:   0.987  0.006  0.078 15.829  0.004  4.110   6.0948e-02
   5_bss:   0.987  0.006  0.078 15.829  0.004  4.110   6.0948e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9283e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9283e+00
   1_xyz:  12.858  0.161  0.422 84.666  0.042  2.250   9.0840e-02
   1_adp:  12.858  0.161  0.422 84.666  0.042  2.250   9.0840e-02
   1_occ:  12.858  0.161  0.422 84.666  0.042  2.250   9.0840e-02
   2_bss:  12.858  0.161  0.422 84.666  0.042  2.250   9.0840e-02
   2_xyz:   6.724  0.061  0.263 83.855  0.037  2.281   5.4609e-02
   2_adp:   6.724  0.061  0.263 83.855  0.037  2.281   5.4609e-02
   2_occ:   6.724  0.061  0.263 83.855  0.037  2.281   5.4609e-02
   3_bss:   6.724  0.061  0.263 83.855  0.037  2.281   5.4609e-02
   3_xyz:   7.825  0.052  0.406 89.655  0.030  2.325   4.6171e-02
   3_adp:   7.825  0.052  0.406 89.655  0.030  2.325   4.6171e-02
   3_occ:   7.825  0.052  0.406 89.655  0.030  2.325   4.6171e-02
   4_bss:   7.825  0.052  0.406 89.655  0.030  2.325   4.6171e-02
   4_xyz:   8.111  0.056  0.594 83.128  0.040  2.282   5.5543e-02
   4_adp:   8.111  0.056  0.594 83.128  0.040  2.282   5.5543e-02
   4_occ:   8.111  0.056  0.594 83.128  0.040  2.282   5.5543e-02
   5_bss:   8.111  0.056  0.594 83.128  0.040  2.282   5.5543e-02
   5_xyz:   7.276  0.038  0.517 83.882  0.036  2.318   3.8347e-02
   5_adp:   7.276  0.038  0.517 83.882  0.036  2.318   3.8347e-02
   5_occ:   7.276  0.038  0.517 83.882  0.036  2.318   3.8347e-02
   5_bss:   7.276  0.038  0.517 83.882  0.036  2.318   3.8347e-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:  60.73   0.00  11.47  60.73   0.00   9.17  53.39   0.00  23.96
   1_occ:  60.73   0.00  11.47  60.73   0.00   9.17  53.39   0.00  23.96
   2_bss:  60.73   0.00  11.47  60.73   0.00   9.17  53.39   0.00  23.96
   2_xyz:  60.73   0.00  11.47  60.73   0.00   9.17  53.39   0.00  23.96
   2_adp:  63.63   0.00  12.10  62.38   0.00   8.49  63.63   0.99  31.73
   2_occ:  63.63   0.00  12.10  62.38   0.00   8.49  63.63   0.99  31.73
   3_bss:  63.63   0.00  12.10  62.38   0.00   8.49  63.63   0.99  31.73
   3_xyz:  63.63   0.00  12.10  62.38   0.00   8.49  63.63   0.99  31.73
   3_adp:  78.85   0.00  12.92  78.85   0.00   8.52  74.93   2.46  36.91
   3_occ:  78.85   0.00  12.92  78.85   0.00   8.52  74.93   2.46  36.91
   4_bss:  78.85   0.00  12.92  78.85   0.00   8.52  74.93   2.46  36.91
   4_xyz:  78.85   0.00  12.92  78.85   0.00   8.52  74.93   2.46  36.91
   4_adp:  84.10   0.00  12.62  84.10   0.00   8.42  73.43   2.43  35.52
   4_occ:  84.10   0.00  12.62  84.10   0.00   8.42  73.43   2.43  35.52
   5_bss:  84.10   0.00  12.62  84.10   0.00   8.42  73.43   2.43  35.52
   5_xyz:  84.10   0.00  12.62  84.10   0.00   8.42  73.43   2.43  35.52
   5_adp:  83.74   0.00  12.26  83.74   0.00   8.32  72.25   2.26  33.70
   5_occ:  83.74   0.00  12.26  83.74   0.00   8.32  72.25   2.26  33.70
   5_bss:  86.09   2.35  14.60  86.09   2.35  10.66  74.60   4.61  36.05
------------------------------------------------------------------------
 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:    1.214    0.014    0.404
   1_adp:    1.214    0.014    0.404
   1_occ:    1.214    0.014    0.404
   2_bss:    1.214    0.014    0.404
   2_xyz:    1.485    0.042    0.554
   2_adp:    1.485    0.042    0.554
   2_occ:    1.485    0.042    0.554
   3_bss:    1.485    0.042    0.554
   3_xyz:    1.502    0.035    0.620
   3_adp:    1.502    0.035    0.620
   3_occ:    1.502    0.035    0.620
   4_bss:    1.502    0.035    0.620
   4_xyz:    1.718    0.031    0.651
   4_adp:    1.718    0.031    0.651
   4_occ:    1.718    0.031    0.651
   5_bss:    1.718    0.031    0.651
   5_xyz:    1.807    0.025    0.657
   5_adp:    1.807    0.025    0.657
   5_occ:    1.807    0.025    0.657
   5_bss:    1.807    0.025    0.657
------------------------------------------------------------------------

CPU time actual refinement: 348.80


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_892/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_892/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_892/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_892/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_892/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.64 
  Macro-tasks:
    bulk solvent and scale       = 43.82  
    individual site refinement   = 142.32 
    weights calculation          = 32.84  
    collect and process          = 6.53   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 225.64 
  Micro-tasks:
    mask                            = 1.85   
    f_calc                          = 109.24 
    alpha_beta                      = 8.15   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 118.47 
    fmodel                         = 7.10   
    r_factors                      = 0.26   
    phase_errors                   = 10.40  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 256.87 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.947 micro seconds
Total CPU time: 6.05 minutes
from_scatterers_fft:    640 calls, 108.80 s
gradients_fft:          586 calls, 105.40 s

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

# Date 2008-01-16 Time 02:40:48 PST -0800 (1200480048.15 s)
Start R-work = 0.4612, R-free = 0.4524 (no bulk solvent and anisotropic scale)
Final R-work = 0.1311, R-free = 0.1751 (no bulk solvent and anisotropic scale)

Start R-work = 0.4519, R-free = 0.4413
Final R-work = 0.1143, R-free = 0.1582