# Date 2008-01-16 Time 01:22:25 PST -0800 (1200475345.76 s)
#phil __OFF__

Command line arguments: "../398.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 = 21466
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 398

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.4607, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.971
Completeness in resolution range: 0.977641
Completeness with d_max=infinity: 0.974529

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8236
                             d_min =   1.9710

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.971
Completeness in resolution range: 0.977641
Completeness with d_max=infinity: 0.974529

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8240 -  4.2169 [2101/2125]  1892   209   9.9%
  bin  2:  4.2169 -  3.3599 [2029/2048]  1826   203  10.0%
  bin  3:  3.3599 -  2.9389 [1993/2012]  1790   203  10.2%
  bin  4:  2.9389 -  2.6719 [1969/1999]  1775   194   9.9%
  bin  5:  2.6719 -  2.4814 [1964/1983]  1767   197  10.0%
  bin  6:  2.4814 -  2.3357 [1950/1975]  1755   195  10.0%
  bin  7:  2.3357 -  2.2191 [1970/1998]  1772   198  10.1%
  bin  8:  2.2191 -  2.1228 [1928/1964]  1737   191   9.9%
  bin  9:  2.1228 -  2.0413 [1914/1956]  1725   189   9.9%
  bin 10:  2.0413 -  1.9710 [1771/1977]  1591   180  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_398/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: 0.13 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:
        1.59 -     2.25: 18
        2.25 -     2.91: 1498
        2.91 -     3.58: 4565
        3.58 -     4.24: 9359
        4.24 -     4.90: 13363
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.588 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.842 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.911 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.943 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28798 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_398/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_398/model_refine_001.geo

CPU time processing inputs: 9.61


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.4607 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4641   r_free= 0.4514   ksol= 0.00   Bsol= 0.00   scale= 0.815    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.262038                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7030 0.99   1372  153 0.3815 0.3847      6.5534       6.569|
|  2:  4.7030 -  3.7528 0.99   1314  145 0.3842 0.3586      6.7404      6.7225|
|  3:  3.7528 -  3.2843 0.99   1287  144 0.4087 0.3960      6.6364      6.6965|
|  4:  3.2843 -  2.9867 0.99   1278  143 0.4432 0.4054      6.5101      6.4481|
|  5:  2.9867 -  2.7741 0.99   1271  141 0.4862 0.5055      6.3603      6.3399|
|  6:  2.7741 -  2.6115 0.99   1277  139 0.4974 0.5630      6.2825      6.2787|
|  7:  2.6115 -  2.4814 0.99   1251  141 0.4935 0.4468      6.2303      6.1563|
|  8:  2.4814 -  2.3738 0.98   1264  139 0.5137 0.4773      6.1918      6.1994|
|  9:  2.3738 -  2.2828 0.98   1258  138 0.5040 0.5282      6.1095      6.1363|
| 10:  2.2828 -  2.2042 0.99   1232  138 0.5176 0.4861      6.1324      6.0715|
| 11:  2.2042 -  2.1355 0.98   1251  143 0.5128 0.4597      6.0537      6.0432|
| 12:  2.1355 -  2.0747 0.97   1239  133 0.5107 0.4893      5.9958      6.0167|
| 13:  2.0747 -  2.0202 1.00   1235  141 0.5276 0.5168      5.8956      5.8839|
| 14:  2.0202 -  1.9710 0.86   1101  121 0.5358 0.5094      5.8486      5.7621|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8240 -  4.7030  1372   153  0.68  36.26   0.81     0.72      76232.96|
|  2:  4.7030 -  3.7528  1314   145  0.72  33.69   0.89     0.80      98807.14|
|  3:  3.7528 -  3.2843  1287   144  0.64  40.40   0.88     0.76     101709.01|
|  4:  3.2843 -  2.9867  1278   143  0.57  46.36   0.83     0.67      89340.36|
|  5:  2.9867 -  2.7741  1271   141  0.47  54.02   0.76     0.56      75250.18|
|  6:  2.7741 -  2.6115  1277   139  0.44  56.78   0.74     0.51      67713.48|
|  7:  2.6115 -  2.4814  1251   141  0.41  59.32   0.75     0.47      63027.74|
|  8:  2.4814 -  2.3738  1264   139  0.41  59.44   0.76     0.48      57062.18|
|  9:  2.3738 -  2.2828  1258   138  0.43  57.90   0.74     0.49      49096.48|
| 10:  2.2828 -  2.2042  1232   138  0.45  55.76   0.77     0.53      42321.29|
| 11:  2.2042 -  2.1355  1251   143  0.45  56.51   0.78     0.54      39544.68|
| 12:  2.1355 -  2.0747  1239   133  0.41  59.30   0.78     0.50      39233.42|
| 13:  2.0747 -  2.0202  1235   141  0.32  66.21   0.76     0.39      36884.38|
| 14:  2.0202 -  1.9710  1101   121  0.23  73.10   0.73     0.26      32895.44|
|alpha:            min =        0.26 max =            0.80 mean =         0.55|
|beta:             min =    32895.44 max =       101709.01 mean =     62753.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.53|
|phase err.(test): min =        0.00 max =           89.99 mean =        53.60|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.772876             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.107   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.036877              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.180   (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 |  1.091 -  1.472:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.472 -  1.853:       10 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.853 -  2.234:      134 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.234 -  2.615:      601 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.615 -  2.996:     1431 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.996 -  3.377:     2591 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.377 -  3.757:     3991 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.757 -  4.138:     5230 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.138 -  4.519:     6807 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.519 -  4.900:     8001 |
|-----------------------------------------------------------------------------|
|-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 |       53.033 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.091 |       2.054 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.502)------------------------------------------|
|    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 = 11.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4710   r_free= 0.4571   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.265021                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4558   r_free= 0.4417   ksol= 0.37   Bsol= 9.39   scale= 1.001    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.56,8.51,8.11,0.00,0.00,0.00); trace/3= 7.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.254408                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.548118              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.232   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.948379              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.660   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4558      final r-factor (work) = 0.3640          |
| start r-factor (free) = 0.4417      final r-factor (free) = 0.3834          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.9384 = 9.55 * 0.50 * 6.2641 + 1.00 * 53.0331                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.5030 = 9.55 * 0.50 * 6.1521 + 1.00 * 0.1325                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3640      final r-factor (work) = 0.3125          |
| start r-factor (free) = 0.3834      final r-factor (free) = 0.3540          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8488 = 0.95 * 1.00 * 6.1521 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7349 = 0.95 * 1.00 * 6.0315 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.82   12.07    None  None   None       |
|    all(noH): 2823   0      0.00    82.82   12.07    None  None   None       |
|    Sol.    : 438    0      0.00    69.53   27.05    None  None   None       |
|    Mac.    : 2385   0      0.00    82.82   9.32     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 -   8.282: 1355   |   5:    41.409 -  49.691:   51        |
|      1:     8.282 -  16.564:  775   |   6:    49.691 -  57.973:   16        |
|      2:    16.564 -  24.846:  330   |   7:    57.973 -  66.255:    7        |
|      3:    24.846 -  33.128:  172   |   8:    66.255 -  74.537:    4        |
|      4:    33.128 -  41.409:  112   |   9:    74.537 -  82.819:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3125 r_free = 0.3540             target_work(ml) = 6.001         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3116 r_free = 0.3542             target_work(ml) = 6.000         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3116   r_free= 0.3542   ksol= 0.37   Bsol= 9.39   scale= 1.092    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.56,8.51,8.11,0.00,0.00,0.00); trace/3= 7.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.999788                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3087   r_free= 0.3497   ksol= 0.34   Bsol= 23.27   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.69,4.72,5.38,0.00,0.00,0.00); trace/3= 4.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.997968                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.378823              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.153   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.380982              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.684  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3087      final r-factor (work) = 0.2199          |
| start r-factor (free) = 0.3497      final r-factor (free) = 0.2696          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3169 = 3.38 * 0.50 * 6.0283 + 1.00 * 0.1325                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9394 = 3.38 * 0.50 * 5.8453 + 1.00 * 0.0642                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2199      final r-factor (work) = 0.2016          |
| start r-factor (free) = 0.2696      final r-factor (free) = 0.2501          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2418 = 0.38 * 1.00 * 5.8453 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1794 = 0.38 * 1.00 * 5.6742 + 1.00 * 0.0176                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.26   11.97    None  None   None       |
|    all(noH): 2823   0      0.00    83.26   11.97    None  None   None       |
|    Sol.    : 438    0      1.23    65.44   31.07    None  None   None       |
|    Mac.    : 2385   0      0.00    83.26   8.46     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 -   8.327: 1567   |   5:    41.632 -  49.959:   57        |
|      1:     8.327 -  16.653:  629   |   6:    49.959 -  58.285:   20        |
|      2:    16.653 -  24.979:  203   |   7:    58.285 -  66.612:    8        |
|      3:    24.979 -  33.306:  176   |   8:    66.612 -  74.938:    3        |
|      4:    33.306 -  41.632:  159   |   9:    74.938 -  83.264:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2016 r_free = 0.2501             target_work(ml) = 5.642         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2013 r_free = 0.2497             target_work(ml) = 5.641         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2013   r_free= 0.2497   ksol= 0.34   Bsol= 23.27   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.69,4.72,5.38,0.00,0.00,0.00); trace/3= 4.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.641041                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2002   r_free= 0.2491   ksol= 0.33   Bsol= 31.87   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,3.00,3.97,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.639892                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.151746              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.815  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.853520              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.172   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2002      final r-factor (work) = 0.1445          |
| start r-factor (free) = 0.2491      final r-factor (free) = 0.1873          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0128 = 3.15 * 0.50 * 5.6785 + 1.00 * 0.0642                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7314 = 3.15 * 0.50 * 5.5011 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1445      final r-factor (work) = 0.1309          |
| start r-factor (free) = 0.1873      final r-factor (free) = 0.1774          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.7084 = 2.85 * 1.00 * 5.5011 + 1.00 * 0.0109                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.1230 = 2.85 * 1.00 * 5.2949 + 1.00 * 0.0138                              |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.94   12.82    None  None   None       |
|    all(noH): 2823   0      0.00    90.94   12.82    None  None   None       |
|    Sol.    : 438    0      0.00    73.68   37.12    None  None   None       |
|    Mac.    : 2385   0      0.00    90.94   8.36     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 -   9.094: 1722   |   5:    45.468 -  54.562:  109        |
|      1:     9.094 -  18.187:  529   |   6:    54.562 -  63.655:   51        |
|      2:    18.187 -  27.281:  161   |   7:    63.655 -  72.749:   17        |
|      3:    27.281 -  36.375:  114   |   8:    72.749 -  81.843:    3        |
|      4:    36.375 -  45.468:  115   |   9:    81.843 -  90.936:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1309 r_free = 0.1774             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1307 r_free = 0.1774             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1307   r_free= 0.1774   ksol= 0.33   Bsol= 31.87   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,3.00,3.97,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.264635                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1777   ksol= 0.32   Bsol= 36.01   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.26,2.59,3.48,0.00,0.00,0.00); trace/3= 2.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.264473                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.110175              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.494  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.250099              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.943  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1311      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1777      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6511 = 2.11 * 0.50 * 5.2969 + 1.00 * 0.0623                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5675 = 2.11 * 0.50 * 5.2221 + 1.00 * 0.0577                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3199 = 0.25 * 1.00 * 5.2221 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3076 = 0.25 * 1.00 * 5.1860 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.77   12.21    None  None   None       |
|    all(noH): 2823   0      0.00    89.77   12.21    None  None   None       |
|    Sol.    : 438    0      1.81    73.56   34.78    None  None   None       |
|    Mac.    : 2385   0      0.00    89.77   8.07     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 -   8.977: 1759   |   5:    44.886 -  53.863:   89        |
|      1:     8.977 -  17.954:  535   |   6:    53.863 -  62.840:   45        |
|      2:    17.954 -  26.931:  141   |   7:    62.840 -  71.817:   14        |
|      3:    26.931 -  35.909:  130   |   8:    71.817 -  80.794:    2        |
|      4:    35.909 -  44.886:  106   |   9:    80.794 -  89.771:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1610             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1168 r_free = 0.1607             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1607   ksol= 0.32   Bsol= 36.01   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.26,2.59,3.48,0.00,0.00,0.00); trace/3= 2.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.167871                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1607   ksol= 0.32   Bsol= 36.01   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.26,2.59,3.48,0.00,0.00,0.00); trace/3= 2.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167997                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.491228              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.343  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.395292              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.184  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9239 = 1.49 * 0.50 * 5.1855 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8979 = 1.49 * 0.50 * 5.1571 + 1.00 * 0.0527                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0492 = 0.40 * 1.00 * 5.1571 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0462 = 0.40 * 1.00 * 5.1454 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.80   12.20    None  None   None       |
|    all(noH): 2823   0      0.00    89.80   12.20    None  None   None       |
|    Sol.    : 438    0      2.04    73.59   34.78    None  None   None       |
|    Mac.    : 2385   0      0.00    89.80   8.05     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 -   8.980: 1757   |   5:    44.899 -  53.878:   89        |
|      1:     8.980 -  17.959:  537   |   6:    53.878 -  62.858:   45        |
|      2:    17.959 -  26.939:  141   |   7:    62.858 -  71.838:   14        |
|      3:    26.939 -  35.919:  129   |   8:    71.838 -  80.817:    2        |
|      4:    35.919 -  44.899:  107   |   9:    80.817 -  89.797:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1137 r_free = 0.1574             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1136 r_free = 0.1574             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1574   ksol= 0.32   Bsol= 36.01   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.26,2.59,3.48,0.00,0.00,0.00); trace/3= 2.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.145415                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7030 0.99   1372  153 0.1027 0.1244      5.4009      5.5127|
|  2:  4.7030 -  3.7528 0.99   1314  145 0.0881 0.1146      5.4547      5.6489|
|  3:  3.7528 -  3.2843 0.99   1287  144 0.1066 0.1483       5.488      5.8255|
|  4:  3.2843 -  2.9867 0.99   1278  143 0.1243 0.1629      5.4665      5.6218|
|  5:  2.9867 -  2.7741 0.99   1271  141 0.1291 0.1655      5.3158      5.4836|
|  6:  2.7741 -  2.6115 0.99   1277  139 0.1187 0.1789      5.1973      5.4288|
|  7:  2.6115 -  2.4814 0.99   1251  141 0.1275 0.1651      5.1623       5.381|
|  8:  2.4814 -  2.3738 0.98   1264  139 0.1183 0.1738      5.0817      5.3675|
|  9:  2.3738 -  2.2828 0.98   1258  138 0.1178 0.1721      5.0316      5.2665|
| 10:  2.2828 -  2.2042 0.99   1232  138 0.1133 0.1777      4.9618      5.2088|
| 11:  2.2042 -  2.1355 0.98   1251  143 0.1184 0.1662      4.9478      5.2471|
| 12:  2.1355 -  2.0747 0.97   1239  133 0.1133 0.1696      4.8936      5.2118|
| 13:  2.0747 -  2.0202 1.00   1235  141 0.1156 0.1651      4.8142      5.0428|
| 14:  2.0202 -  1.9710 0.86   1101  121 0.1105 0.1840      4.6968      4.9784|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8240 -  4.7030  1372   153  0.94   9.01   0.99     0.96       7011.17|
|  2:  4.7030 -  3.7528  1314   145  0.95   7.85   1.03     1.02       8876.20|
|  3:  3.7528 -  3.2843  1287   144  0.93  11.14   1.04     1.03      10437.19|
|  4:  3.2843 -  2.9867  1278   143  0.92  13.24   1.02     1.01      10035.20|
|  5:  2.9867 -  2.7741  1271   141  0.91  15.24   1.00     0.97       7863.56|
|  6:  2.7741 -  2.6115  1277   139  0.91  15.23   0.99     0.96       6690.05|
|  7:  2.6115 -  2.4814  1251   141  0.90  15.90   1.00     0.97       6117.67|
|  8:  2.4814 -  2.3738  1264   139  0.91  14.44   1.00     0.98       5162.45|
|  9:  2.3738 -  2.2828  1258   138  0.91  14.90   1.02     1.01       4899.01|
| 10:  2.2828 -  2.2042  1232   138  0.91  15.16   1.02     0.98       4258.02|
| 11:  2.2042 -  2.1355  1251   143  0.90  15.96   1.01     0.97       4282.33|
| 12:  2.1355 -  2.0747  1239   133  0.91  15.13   1.03     1.02       3966.18|
| 13:  2.0747 -  2.0202  1235   141  0.91  15.57   1.03     1.02       3409.65|
| 14:  2.0202 -  1.9710  1101   121  0.91  14.89   1.01     0.98       2647.36|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2647.36 max =        10437.19 mean =      6186.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.76|
|phase err.(test): min =        0.00 max =           88.71 mean =        13.30|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1574   ksol= 0.32   Bsol= 38.71   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-0.20,0.70,-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: 5.145353                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1574   ksol= 0.32   Bsol= 38.71   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-0.20,0.70,-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: 5.145353                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7030 0.99   1372  153 0.1027 0.1243      5.4004      5.5122|
|  2:  4.7030 -  3.7528 0.99   1314  145 0.0881 0.1147      5.4546      5.6491|
|  3:  3.7528 -  3.2843 0.99   1287  144 0.1066 0.1484      5.4881      5.8256|
|  4:  3.2843 -  2.9867 0.99   1278  143 0.1243 0.1629      5.4665      5.6218|
|  5:  2.9867 -  2.7741 0.99   1271  141 0.1291 0.1655      5.3158      5.4836|
|  6:  2.7741 -  2.6115 0.99   1277  139 0.1187 0.1789      5.1973      5.4287|
|  7:  2.6115 -  2.4814 0.99   1251  141 0.1275 0.1652      5.1622      5.3811|
|  8:  2.4814 -  2.3738 0.98   1264  139 0.1183 0.1738      5.0817      5.3675|
|  9:  2.3738 -  2.2828 0.98   1258  138 0.1178 0.1721      5.0316      5.2666|
| 10:  2.2828 -  2.2042 0.99   1232  138 0.1133 0.1777      4.9617      5.2089|
| 11:  2.2042 -  2.1355 0.98   1251  143 0.1184 0.1662      4.9477      5.2471|
| 12:  2.1355 -  2.0747 0.97   1239  133 0.1133 0.1696      4.8936      5.2117|
| 13:  2.0747 -  2.0202 1.00   1235  141 0.1156 0.1651      4.8141      5.0428|
| 14:  2.0202 -  1.9710 0.86   1101  121 0.1105 0.1839      4.6967      4.9781|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8240 -  4.7030  1372   153  0.94   9.01   0.99     0.96       7002.85|
|  2:  4.7030 -  3.7528  1314   145  0.95   7.85   1.03     1.01       8872.61|
|  3:  3.7528 -  3.2843  1287   144  0.93  11.14   1.04     1.03      10440.31|
|  4:  3.2843 -  2.9867  1278   143  0.92  13.24   1.02     1.01      10035.60|
|  5:  2.9867 -  2.7741  1271   141  0.91  15.24   1.00     0.96       7864.00|
|  6:  2.7741 -  2.6115  1277   139  0.91  15.23   0.99     0.96       6690.26|
|  7:  2.6115 -  2.4814  1251   141  0.90  15.90   0.99     0.97       6118.13|
|  8:  2.4814 -  2.3738  1264   139  0.91  14.44   1.00     0.98       5162.64|
|  9:  2.3738 -  2.2828  1258   138  0.91  14.90   1.02     1.01       4899.52|
| 10:  2.2828 -  2.2042  1232   138  0.91  15.16   1.01     0.98       4257.84|
| 11:  2.2042 -  2.1355  1251   143  0.90  15.96   1.01     0.97       4282.46|
| 12:  2.1355 -  2.0747  1239   133  0.91  15.12   1.02     1.01       3965.72|
| 13:  2.0747 -  2.0202  1235   141  0.91  15.57   1.02     1.02       3408.74|
| 14:  2.0202 -  1.9710  1101   121  0.91  14.89   1.00     0.97       2645.96|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2645.96 max =        10440.31 mean =      6185.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.76|
|phase err.(test): min =        0.00 max =           88.71 mean =        13.30|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.69    92.49   14.89    None  None   None       |
|    all(noH): 2823   0      2.69    92.49   14.89    None  None   None       |
|    Sol.    : 438    0      4.73    76.28   37.47    None  None   None       |
|    Mac.    : 2385   0      2.69    92.49   10.74    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:     2.695 -  11.675: 1757   |   5:    47.593 -  56.573:   89        |
|      1:    11.675 -  20.654:  537   |   6:    56.573 -  65.553:   45        |
|      2:    20.654 -  29.634:  141   |   7:    65.553 -  74.532:   14        |
|      3:    29.634 -  38.614:  129   |   8:    74.532 -  83.512:    2        |
|      4:    38.614 -  47.593:  107   |   9:    83.512 -  92.492:    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)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.405 - 5.716
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 324
   mapped sites are within: 0.748 - 5.716

peak=   11.255 closest distance to " CB  VAL A 230 " =    1.437
peak=   10.680 closest distance to " CG2 VAL A 296 " =    1.538
peak=    6.107 closest distance to " CD2 LEU A   5 " =    1.264
peak=    5.906 closest distance to " CG  LEU A   5 " =    1.230
peak=    5.831 closest distance to " NE2 GLN A  11 " =    1.143
peak=    5.411 closest distance to " O   HOH Z 124 " =    1.599
peak=    5.399 closest distance to " O   HOH Z 142 " =    1.938
peak=    5.384 closest distance to " O   HOH Z 193 " =    1.732
peak=    5.286 closest distance to " NH2 ARG A  56 " =    1.985
peak=    5.159 closest distance to " O   HOH Z 126 " =    1.883
peak=    5.128 closest distance to " CG  PRO A 213 " =    1.299
peak=    5.105 closest distance to " CB  ARG A 275 " =    0.936
peak=    5.071 closest distance to " CD1AILE A 234 " =    0.967
peak=    5.007 closest distance to " O   HOH Z 278 " =    1.063
peak=    4.910 closest distance to " O   HOH Z 427 " =    2.611
peak=    4.857 closest distance to " CG  PRO A 198 " =    1.230
peak=    4.838 closest distance to " CG  LEU A 228 " =    1.224
peak=    4.833 closest distance to " O   HOH Z 232 " =    2.381
peak=    4.732 closest distance to " CB  GLN A 183 " =    1.233
peak=    4.729 closest distance to " O   HOH Z 130 " =    0.965
peak=    4.724 closest distance to " CB  GLN A 223 " =    1.477
peak=    4.719 closest distance to " CB  VAL A 230 " =    1.125
peak=    4.671 closest distance to " O   HOH Z 272 " =    1.874
peak=    4.559 closest distance to " O   HOH Z 209 " =    2.253
peak=    4.527 closest distance to " O   SER A  87 " =    2.329
peak=    4.411 closest distance to " CB  SER A   3 " =    1.351
peak=    4.335 closest distance to " CB BVAL A  41 " =    0.952
peak=    4.332 closest distance to " O   HOH Z 316 " =    2.845
peak=    4.299 closest distance to " O   HOH Z 263 " =    1.495
peak=    4.288 closest distance to " O   HOH Z 298 " =    1.811
peak=    4.250 closest distance to " O   HOH Z  44 " =    1.861
peak=    4.233 closest distance to " O   HOH Z 287 " =    1.872
peak=    4.210 closest distance to " C   PRO A 198 " =    1.507
peak=    4.206 closest distance to " CB  VAL A 265 " =    1.252
peak=    4.192 closest distance to " CG1BVAL A  72 " =    1.468
peak=    4.154 closest distance to " O   HOH Z 411 " =    3.729
peak=    4.133 closest distance to " CB  SER A  63 " =    1.201
peak=    4.131 closest distance to " CB  ASN A 148 " =    1.413
peak=    4.126 closest distance to " O   HOH Z 236 " =    1.365
peak=    4.104 closest distance to " N   PHE A 130 " =    1.315
peak=    4.101 closest distance to " O   HOH Z  59 " =    1.783
peak=    4.089 closest distance to " CG  PRO A 243 " =    1.172
peak=    4.086 closest distance to " O   HOH Z  85 " =    1.191
peak=    4.053 closest distance to " CB  GLU A 152 " =    1.222
peak=    4.048 closest distance to " CD2 LEU A 228 " =    1.217
peak=    4.041 closest distance to " O   HOH Z 250 " =    1.366
peak=    4.038 closest distance to " CB  TYR A 169 " =    0.897
peak=    4.034 closest distance to " O   HOH Z  68 " =    2.191
peak=    4.027 closest distance to " NZ  LYS A 117 " =    3.071
peak=    4.011 closest distance to " O   HOH Z 189 " =    2.606
peak=    4.009 closest distance to " O   HOH Z 234 " =    3.510
peak=    3.989 closest distance to " O   HOH Z 117 " =    2.018
peak=    3.987 closest distance to " O   HOH Z  78 " =    1.665
peak=    3.979 closest distance to " O   HOH Z 346 " =    1.588
peak=    3.977 closest distance to " CG2 VAL A 257 " =    0.917
peak=    3.976 closest distance to " O   HOH Z   9 " =    1.945
peak=    3.971 closest distance to " O   HOH Z 203 " =    1.513
peak=    3.962 closest distance to " CB  TRP A 179 " =    1.294
peak=    3.949 closest distance to " O   HOH Z 202 " =    1.094
peak=    3.947 closest distance to " O   HOH Z  93 " =    2.352
peak=    3.935 closest distance to " O   HOH Z   3 " =    1.956
peak=    3.916 closest distance to " CB  ARG A  79 " =    1.369
peak=    3.910 closest distance to " O   HOH Z 322 " =    2.087
peak=    3.884 closest distance to " O   HOH Z 130 " =    2.486
peak=    3.866 closest distance to " N   ARG A 156 " =    1.293
peak=    3.866 closest distance to " ND2 ASN A 187 " =    1.610
peak=    3.866 closest distance to " CB  VAL A 202 " =    1.646
peak=    3.853 closest distance to " O   HOH Z 425 " =    1.394
peak=    3.823 closest distance to " O   HOH Z  61 " =    1.608
peak=    3.819 closest distance to " OD1 ASN A  69 " =    2.663
peak=    3.816 closest distance to " O   HOH Z 402 " =    1.382
peak=    3.815 closest distance to " CB  SER A 216 " =    0.882
peak=    3.815 closest distance to " O   HOH Z 425 " =    2.075
peak=    3.814 closest distance to " CD  GLN A 194 " =    1.444
peak=    3.809 closest distance to " CA  TYR A  30 " =    1.003
peak=    3.808 closest distance to " O   HOH Z 303 " =    2.154
peak=    3.808 closest distance to " O   HOH Z 128 " =    1.958
peak=    3.808 closest distance to " CA  ASN A 127 " =    1.014
peak=    3.803 closest distance to " O   HOH Z 344 " =    2.791
peak=    3.794 closest distance to " CB  GLU A 128 " =    1.021
peak=    3.789 closest distance to " O   HOH Z  43 " =    2.064
peak=    3.789 closest distance to " CB  TRP A 266 " =    1.053
peak=    3.787 closest distance to " OD2 ASP A 286 " =    2.541
peak=    3.784 closest distance to " CB  ARG A 139 " =    0.954
peak=    3.780 closest distance to " CG  PRO A 280 " =    0.854
peak=    3.777 closest distance to " O   HOH Z 403 " =    1.758
peak=    3.765 closest distance to " CG2 ILE A 120 " =    1.296
peak=    3.763 closest distance to " O   HOH Z  22 " =    2.103
peak=    3.758 closest distance to " O   HOH Z 368 " =    2.026
peak=    3.757 closest distance to " O   HOH Z 371 " =    2.886
peak=    3.755 closest distance to " O   HOH Z 227 " =    1.699
peak=    3.749 closest distance to " CB  VAL A 296 " =    0.997
peak=    3.742 closest distance to " O   HOH Z 130 " =    2.129
peak=    3.739 closest distance to " O   HOH Z  55 " =    2.324
peak=    3.739 closest distance to " CA  ASN A 215 " =    1.067
peak=    3.735 closest distance to " O   HOH Z 227 " =    2.180
peak=    3.732 closest distance to " CG AARG A 275 " =    1.088
peak=    3.725 closest distance to " O   HOH Z 261 " =    2.225
peak=    3.715 closest distance to " O   HOH Z 344 " =    1.220
peak=    3.711 closest distance to " O   HOH Z 419 " =    1.902
peak=    3.702 closest distance to " CG  LEU A 167 " =    1.129
peak=    3.682 closest distance to " CG  ARG A 138 " =    0.845
peak=    3.681 closest distance to " O   HOH Z 137 " =    1.571
peak=    3.673 closest distance to " O   HOH Z 369 " =    2.157
peak=    3.666 closest distance to " O   HOH Z  40 " =    1.900
peak=    3.661 closest distance to " CA  LYS A 290 " =    1.254
peak=    3.640 closest distance to " O   HOH Z   7 " =    1.464
peak=    3.640 closest distance to " O   HOH Z  48 " =    1.552
peak=    3.625 closest distance to " O   HOH Z 273 " =    2.739
peak=    3.625 closest distance to " CB  SER A  26 " =    1.608
peak=    3.624 closest distance to " CG  MET A 185 " =    1.259
peak=    3.624 closest distance to " O   HOH Z 222 " =    2.326
peak=    3.623 closest distance to " N   ASN A  39 " =    1.137
peak=    3.623 closest distance to " OG BSER A 164 " =    2.176
peak=    3.622 closest distance to " O   HOH Z 422 " =    2.480
peak=    3.619 closest distance to " O   HOH Z 371 " =    1.665
peak=    3.618 closest distance to " O   HOH Z  10 " =    1.733
peak=    3.613 closest distance to " OG  SER A  62 " =    2.938
peak=    3.609 closest distance to " CB  LEU A 255 " =    0.821
peak=    3.602 closest distance to " CB  GLN A  88 " =    1.293
peak=    3.597 closest distance to " O   HOH Z  78 " =    2.307
peak=    3.597 closest distance to " CB  PRO A 198 " =    0.950
peak=    3.591 closest distance to " CB  ALA A 248 " =    1.369
peak=    3.573 closest distance to " O   HOH Z  54 " =    1.545
peak=    3.566 closest distance to " O   GLN A 194 " =    1.798
peak=    3.555 closest distance to " CA  THR A 264 " =    0.846
peak=    3.544 closest distance to " CG BARG A 102 " =    1.783
peak=    3.541 closest distance to " CB  SER A 273 " =    0.886
peak=    3.541 closest distance to " ND2 ASN A 110 " =    1.687
peak=    3.533 closest distance to " C   ALA A 299 " =    0.952
peak=    3.533 closest distance to " CD BLYS A 290 " =    1.151
peak=    3.527 closest distance to " O   HOH Z  61 " =    1.549
peak=    3.523 closest distance to " O   HOH Z 345 " =    3.246
peak=    3.517 closest distance to " O   HOH Z 175 " =    2.327
peak=    3.515 closest distance to " O   HOH Z 352 " =    1.315
peak=    3.515 closest distance to " CA  ALA A  21 " =    1.167
peak=    3.513 closest distance to " O   HOH Z 248 " =    1.741
peak=    3.512 closest distance to " O   HOH Z 389 " =    3.086
peak=    3.511 closest distance to " CA  ILE A 234 " =    0.937
peak=    3.510 closest distance to " CB  ASN A  39 " =    0.859
peak=    3.509 closest distance to " O   HOH Z 334 " =    1.457
peak=    3.508 closest distance to " CD  ARG A 269 " =    1.152
peak=    3.506 closest distance to " CE3 TRP A 274 " =    2.423
peak=    3.498 closest distance to " CD  PRO A 243 " =    1.443
peak=    3.495 closest distance to " CD2 TRP A 179 " =    1.438
peak=    3.495 closest distance to " O   HOH Z 426 " =    1.493
peak=    3.488 closest distance to " CA  LYS A 117 " =    1.214
peak=    3.487 closest distance to " O   HOH Z 134 " =    1.411
peak=    3.484 closest distance to " NH1BARG A 145 " =    1.406
peak=    3.483 closest distance to " O   TRP A 274 " =    1.902
peak=    3.483 closest distance to " O   HOH Z 280 " =    2.903
peak=    3.470 closest distance to " O   HOH Z 258 " =    2.357
peak=    3.469 closest distance to " CB  MET A  40 " =    0.826
peak=    3.469 closest distance to " O   HOH Z 303 " =    1.691
peak=    3.468 closest distance to " OG BSER A 134 " =    3.019
peak=    3.461 closest distance to " O   HOH Z 128 " =    2.102
peak=    3.460 closest distance to " CA  SER A  87 " =    0.977
peak=    3.453 closest distance to " CE  MET A  93 " =    1.507
peak=    3.453 closest distance to " O   HOH Z 251 " =    1.582
peak=    3.452 closest distance to " O   HOH Z 366 " =    2.872
peak=    3.451 closest distance to " CB  GLU A 277 " =    3.504
peak=    3.448 closest distance to " O   HOH Z 389 " =    1.674
peak=    3.446 closest distance to " CA  ALA A  51 " =    1.006
peak=    3.445 closest distance to " CG2 THR A 221 " =    1.288
peak=    3.442 closest distance to " O   HOH Z 380 " =    1.611
peak=    3.439 closest distance to " CB  GLN A 278 " =    0.748
peak=    3.436 closest distance to " CB  ALA A 291 " =    1.344
peak=    3.435 closest distance to " O   HOH Z 368 " =    3.606
peak=    3.427 closest distance to " N   SER A 135 " =    1.364
peak=    3.424 closest distance to " O   HOH Z 193 " =    1.769
peak=    3.423 closest distance to " O   HOH Z 143 " =    1.057
peak=    3.421 closest distance to " CE  LYS A  76 " =    0.954
peak=    3.421 closest distance to " O   HOH Z 180 " =    2.113
peak=    3.419 closest distance to " CB  PRO A  54 " =    0.896
peak=    3.417 closest distance to " CA  PHE A 283 " =    1.284
peak=    3.416 closest distance to " O   HOH Z   9 " =    1.093
peak=    3.413 closest distance to " O   HOH Z 151 " =    1.595
peak=    3.405 closest distance to " CA  VAL A 126 " =    0.861
peak=    3.404 closest distance to " CA  GLN A 194 " =    1.168
peak=    3.401 closest distance to " O   HOH Z  80 " =    2.210
peak=    3.400 closest distance to " CB  ALA A 295 " =    1.228
peak=    3.400 closest distance to " CB  HIS A 108 " =    0.876
peak=    3.395 closest distance to " CG AARG A 275 " =    1.089
peak=    3.386 closest distance to " O   HOH Z 423 " =    1.436
peak=    3.384 closest distance to " O   HOH Z 374 " =    2.467
peak=    3.381 closest distance to " O   HOH Z   2 " =    1.727
peak=    3.379 closest distance to " CG  GLN A  88 " =    1.067
peak=    3.377 closest distance to " NH2BARG A 145 " =    2.034
peak=    3.376 closest distance to " CB  ALA A   9 " =    1.529
peak=    3.373 closest distance to " O   HOH Z 132 " =    2.457
peak=    3.370 closest distance to " O   HOH Z 407 " =    2.303
peak=    3.368 closest distance to " O   HOH Z 244 " =    1.585
peak=    3.367 closest distance to " O   HOH Z 233 " =    1.625
peak=    3.364 closest distance to " O   HOH Z  59 " =    2.069
peak=    3.362 closest distance to " O   HOH Z 437 " =    2.175
peak=    3.362 closest distance to " CG1 ILE A  33 " =    1.439
peak=    3.356 closest distance to " CB  THR A  31 " =    1.638
peak=    3.355 closest distance to " CD1 ILE A  33 " =    1.652
peak=    3.350 closest distance to " O   HOH Z 388 " =    1.856
peak=    3.349 closest distance to " NH2 ARG A 156 " =    1.097
peak=    3.342 closest distance to " NH1 ARG A  14 " =    0.949
peak=    3.341 closest distance to " O   PRO A 198 " =    1.211
peak=    3.340 closest distance to " O   HOH Z 247 " =    1.266
peak=    3.337 closest distance to " O   HOH Z 405 " =    1.234
peak=    3.336 closest distance to " O   HOH Z 272 " =    2.221
peak=    3.331 closest distance to " OE1 GLU A   2 " =    2.097
peak=    3.327 closest distance to " O   HOH Z 276 " =    1.248
peak=    3.325 closest distance to " CB  LEU A 143 " =    1.105
peak=    3.320 closest distance to " CA  ARG A  66 " =    0.812
peak=    3.319 closest distance to " O   HOH Z 213 " =    2.016
peak=    3.317 closest distance to " N   VAL A 126 " =    1.152
peak=    3.312 closest distance to " CB  ASN A 142 " =    1.118
peak=    3.311 closest distance to " O   HOH Z  71 " =    1.286
peak=    3.311 closest distance to " O   HOH Z 158 " =    3.100
peak=    3.307 closest distance to " O   HOH Z 108 " =    2.146
peak=    3.305 closest distance to " O   HOH Z 245 " =    1.354
peak=    3.300 closest distance to " CB  ILE A  20 " =    1.456
peak=    3.295 closest distance to " NH2AARG A 190 " =    1.811
peak=    3.294 closest distance to " O   HOH Z 151 " =    1.589
peak=    3.293 closest distance to " O   HOH Z   1 " =    1.656
peak=    3.292 closest distance to " CB  VAL A 268 " =    0.822
peak=    3.292 closest distance to " CE1 TYR A 186 " =    1.327
peak=    3.289 closest distance to " CA  VAL A  41 " =    0.832
peak=    3.289 closest distance to " O   HOH Z 261 " =    1.554
peak=    3.285 closest distance to " O   HOH Z 148 " =    3.364
peak=    3.285 closest distance to " O   HOH Z 209 " =    2.330
peak=    3.281 closest distance to " O   HOH Z  47 " =    1.749
peak=    3.280 closest distance to " CB  ASN A 110 " =    1.043
peak=    3.277 closest distance to " O   HOH Z 118 " =    1.370
peak=    3.268 closest distance to " OG ASER A 134 " =    1.406
peak=    3.264 closest distance to " O   HOH Z   9 " =    1.817
peak=    3.263 closest distance to " O   HOH Z 192 " =    1.326
peak=    3.259 closest distance to " O   HOH Z 438 " =    2.204
peak=    3.258 closest distance to " OG1 THR A 294 " =    2.377
peak=    3.257 closest distance to " CA  ASN A 176 " =    1.040
peak=    3.256 closest distance to " O   HOH Z 423 " =    1.679
peak=    3.254 closest distance to " CG2 ILE A  20 " =    1.619
peak=    3.250 closest distance to " O   HOH Z 145 " =    1.922
peak=    3.249 closest distance to " O   HOH Z 193 " =    1.857
peak=    3.248 closest distance to " CA  ALA A 158 " =    1.158
peak=    3.246 closest distance to " CG1 VAL A 153 " =    0.903
peak=    3.240 closest distance to " O   HOH Z  89 " =    1.583
peak=    3.239 closest distance to " O   HOH Z 260 " =    1.410
peak=    3.238 closest distance to " CA  LEU A 101 " =    1.403
peak=    3.237 closest distance to " O   HOH Z 181 " =    2.041
peak=    3.236 closest distance to " O   HOH Z 172 " =    5.716
peak=    3.235 closest distance to " CZ  PHE A 218 " =    1.161
peak=    3.234 closest distance to " CG  GLN A  77 " =    2.214
peak=    3.232 closest distance to " CB  ALA A 248 " =    1.043
peak=    3.229 closest distance to " O   HOH Z 281 " =    1.472
peak=    3.227 closest distance to " O   GLN A  58 " =    1.435
peak=    3.226 closest distance to " NZ  LYS A  76 " =    1.476
peak=    3.226 closest distance to " CD2 TYR A 186 " =    0.945
peak=    3.225 closest distance to " N   GLN A 278 " =    1.049
peak=    3.214 closest distance to " CG1 ILE A 120 " =    1.277
peak=    3.208 closest distance to " NE AARG A 275 " =    1.599
peak=    3.208 closest distance to " CG  MET A 185 " =    1.006
peak=    3.208 closest distance to " O   HOH Z 329 " =    3.700
peak=    3.205 closest distance to " CA  LEU A 282 " =    1.152
peak=    3.204 closest distance to " CG  GLU A 277 " =    2.129
peak=    3.203 closest distance to " O   GLY A 147 " =    1.484
peak=    3.202 closest distance to " O   HOH Z 145 " =    1.321
peak=    3.201 closest distance to " CE1 HIS A 108 " =    1.172
peak=    3.201 closest distance to " O   HOH Z 128 " =    2.030
peak=    3.201 closest distance to " CB  ARG A 190 " =    1.790
peak=    3.200 closest distance to " O   ALA A   1 " =    1.704
peak=    3.197 closest distance to " CZ2 TRP A 274 " =    1.796
peak=    3.197 closest distance to " O   HOH Z 383 " =    1.808
peak=    3.195 closest distance to " O   HOH Z 412 " =    2.000
peak=    3.194 closest distance to " CD1 ILE A 106 " =    1.121
peak=    3.193 closest distance to " O   HOH Z 106 " =    2.478
peak=    3.191 closest distance to " O   HOH Z 424 " =    2.619
peak=    3.190 closest distance to " O   HOH Z 217 " =    2.246
peak=    3.189 closest distance to " CG  LEU A 281 " =    0.961
peak=    3.189 closest distance to " O   HOH Z 146 " =    1.617
peak=    3.187 closest distance to " O   HOH Z 135 " =    1.995
peak=    3.181 closest distance to " CB  ALA A   1 " =    1.153
peak=    3.179 closest distance to " O   HOH Z 250 " =    1.803
peak=    3.177 closest distance to " O   HOH Z 123 " =    1.035
peak=    3.174 closest distance to " O   HOH Z 172 " =    3.598
peak=    3.172 closest distance to " O   HOH Z 173 " =    2.205
peak=    3.171 closest distance to " O   HOH Z 114 " =    4.048
peak=    3.170 closest distance to " O   HOH Z 423 " =    2.468
peak=    3.170 closest distance to " CG  GLN A  89 " =    1.473
peak=    3.165 closest distance to " O   HOH Z 148 " =    1.524
peak=    3.164 closest distance to " O   HOH Z 305 " =    3.398
peak=    3.164 closest distance to " OE2 GLU A  53 " =    2.050
peak=    3.162 closest distance to " C   GLU A 277 " =    1.364
peak=    3.159 closest distance to " CD2 LEU A 297 " =    0.975
peak=    3.155 closest distance to " CB  ASP A 140 " =    0.755
peak=    3.155 closest distance to " CB  LYS A 290 " =    1.183
peak=    3.154 closest distance to " O   HOH Z  88 " =    2.570
peak=    3.146 closest distance to " CD  LYS A 166 " =    1.281
peak=    3.146 closest distance to " O   HOH Z  43 " =    2.705
peak=    3.142 closest distance to " O   HOH Z 365 " =    1.686
peak=    3.142 closest distance to " ND2 ASN A 249 " =    0.889
peak=    3.140 closest distance to " O   PHE A  38 " =    1.950
peak=    3.138 closest distance to " CG  MET A 188 " =    1.153
peak=    3.134 closest distance to " CB  TYR A  30 " =    1.705
peak=    3.131 closest distance to " CA  GLY A 267 " =    1.081
peak=    3.129 closest distance to " CD  LYS A 119 " =    1.445
peak=    3.128 closest distance to " O   HOH Z 194 " =    2.048
peak=    3.123 closest distance to " NE1 TRP A 274 " =    0.962
peak=    3.122 closest distance to " CD1 LEU A 261 " =    1.169
peak=    3.122 closest distance to " OD1 ASN A 148 " =    1.714
peak=    3.103 closest distance to " O   HOH Z 327 " =    1.783
peak=    3.099 closest distance to " O   HOH Z  30 " =    1.387
peak=    3.094 closest distance to " CA  ILE A  20 " =    0.797
peak=    3.089 closest distance to " CB  ASN A 215 " =    1.032
peak=    3.089 closest distance to " CD1 LEU A   5 " =    1.727
peak=    3.088 closest distance to " OG  SER A  22 " =    2.690
peak=    3.083 closest distance to " CB  LYS A 117 " =    1.175
peak=    3.080 closest distance to " CA  ASP A 140 " =    1.213
peak=    3.080 closest distance to " O   HOH Z 153 " =    3.681
peak=    3.075 closest distance to " O   HOH Z 396 " =    1.359
peak=    3.071 closest distance to " CD2 TYR A  30 " =    0.954
peak=    3.064 closest distance to " N   ASP A 162 " =    1.280
peak=    3.057 closest distance to " O   HOH Z 406 " =    1.570
peak=    3.037 closest distance to " O   HOH Z 371 " =    3.216
peak=    3.032 closest distance to " O   HOH Z 218 " =    2.207

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 183         
Filter by distance & map next to the model:
   mapped sites are within: 0.653 - 5.227
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 181 from: 183
   mapped sites are within: 0.722 - 5.227

peak=   -5.034 closest distance to " CG2 VAL A 230 " =    0.722
peak=   -4.829 closest distance to " CD  ARG A 156 " =    2.006
peak=   -4.326 closest distance to " O   PRO A 198 " =    1.220
peak=   -4.273 closest distance to " SG  CYS A 254 " =    3.219
peak=   -4.229 closest distance to " O   ALA A 161 " =    1.601
peak=   -4.211 closest distance to " N   GLN A  58 " =    1.965
peak=   -4.159 closest distance to " C   HIS A 108 " =    1.173
peak=   -4.146 closest distance to " O   HOH Z 290 " =    1.042
peak=   -4.145 closest distance to " OG BSER A 134 " =    1.168
peak=   -4.141 closest distance to " CD1 LEU A 255 " =    2.750
peak=   -4.064 closest distance to " CA  VAL A  67 " =    2.818
peak=   -4.059 closest distance to " CG2 THR A   4 " =    1.960
peak=   -4.054 closest distance to " O   VAL A  67 " =    2.715
peak=   -4.043 closest distance to " CB  ALA A 248 " =    2.084
peak=   -4.031 closest distance to " O   HOH Z 351 " =    1.462
peak=   -4.028 closest distance to " CE2 TYR A  30 " =    2.884
peak=   -4.022 closest distance to " CG2 VAL A 296 " =    1.921
peak=   -4.014 closest distance to " CB  PRO A 243 " =    2.616
peak=   -4.014 closest distance to " CA  GLY A  23 " =    1.987
peak=   -3.951 closest distance to " O   HOH Z 231 " =    1.816
peak=   -3.895 closest distance to " O   HOH Z 389 " =    1.930
peak=   -3.886 closest distance to " N   HIS A 115 " =    2.079
peak=   -3.849 closest distance to " CG  PHE A 283 " =    2.623
peak=   -3.842 closest distance to " CB  TYR A  15 " =    2.161
peak=   -3.831 closest distance to " O   HOH Z 266 " =    4.649
peak=   -3.821 closest distance to " CB  ALA A 100 " =    2.532
peak=   -3.819 closest distance to " CZ  PHE A  59 " =    1.373
peak=   -3.804 closest distance to " O   HOH Z 377 " =    0.749
peak=   -3.770 closest distance to " O   HOH Z 407 " =    3.037
peak=   -3.751 closest distance to " NH2 ARG A  79 " =    1.925
peak=   -3.743 closest distance to " O   HOH Z 388 " =    2.178
peak=   -3.730 closest distance to " O   ALA A  51 " =    1.313
peak=   -3.724 closest distance to " CG  ASP A 231 " =    0.798
peak=   -3.715 closest distance to " CD1 LEU A 101 " =    2.303
peak=   -3.706 closest distance to " O   PRO A 163 " =    1.948
peak=   -3.700 closest distance to " OG  SER A   3 " =    1.307
peak=   -3.679 closest distance to " C   ASN A 285 " =    2.147
peak=   -3.676 closest distance to " N   THR A 157 " =    1.343
peak=   -3.668 closest distance to " O   HOH Z 423 " =    2.215
peak=   -3.664 closest distance to " O   HOH Z  47 " =    1.530
peak=   -3.657 closest distance to " C   ASP A 231 " =    2.444
peak=   -3.648 closest distance to " OXT GLY A 302 " =    2.816
peak=   -3.626 closest distance to " CB  ALA A  43 " =    2.274
peak=   -3.624 closest distance to " CA  GLY A  98 " =    1.911
peak=   -3.624 closest distance to " CA  GLY A 133 " =    1.946
peak=   -3.617 closest distance to " CG  GLN A 223 " =    1.957
peak=   -3.612 closest distance to " O   HOH Z 102 " =    1.640
peak=   -3.606 closest distance to " O   HOH Z 140 " =    1.516
peak=   -3.603 closest distance to " O   HOH Z  11 " =    2.042
peak=   -3.599 closest distance to " CG1 VAL A 112 " =    2.809
peak=   -3.593 closest distance to " O   HOH Z 166 " =    1.592
peak=   -3.590 closest distance to " CB  ALA A 244 " =    2.061
peak=   -3.585 closest distance to " O   HOH Z 111 " =    4.316
peak=   -3.579 closest distance to " O   HOH Z 191 " =    5.227
peak=   -3.569 closest distance to " O   HOH Z 211 " =    1.565
peak=   -3.565 closest distance to " CB  PRO A 163 " =    2.581
peak=   -3.539 closest distance to " CB  ALA A 161 " =    2.506
peak=   -3.528 closest distance to " CE2 PHE A 218 " =    2.519
peak=   -3.524 closest distance to " N   ALA A 248 " =    1.683
peak=   -3.515 closest distance to " OD2 ASP A 191 " =    1.364
peak=   -3.503 closest distance to " O   ASP A 270 " =    1.810
peak=   -3.499 closest distance to " OE1 GLN A  73 " =    2.440
peak=   -3.497 closest distance to " O   HOH Z 126 " =    1.891
peak=   -3.496 closest distance to " CB  ASN A  39 " =    2.172
peak=   -3.491 closest distance to " O   HOH Z 298 " =    1.261
peak=   -3.485 closest distance to " C   ALA A 158 " =    1.259
peak=   -3.483 closest distance to " O   HOH Z 185 " =    2.170
peak=   -3.482 closest distance to " O   HOH Z 198 " =    2.024
peak=   -3.472 closest distance to " O   HOH Z 313 " =    1.638
peak=   -3.466 closest distance to " CG2 THR A 178 " =    2.181
peak=   -3.464 closest distance to " OG  SER A 206 " =    1.551
peak=   -3.462 closest distance to " OG ASER A 134 " =    1.259
peak=   -3.461 closest distance to " O   HOH Z 103 " =    1.789
peak=   -3.460 closest distance to " O   ALA A 256 " =    2.627
peak=   -3.459 closest distance to " CD  GLN A  88 " =    1.082
peak=   -3.442 closest distance to " CE1 PHE A  59 " =    1.993
peak=   -3.441 closest distance to " CG  GLN A  58 " =    1.168
peak=   -3.439 closest distance to " O   HOH Z 134 " =    2.734
peak=   -3.438 closest distance to " N   VAL A 230 " =    1.263
peak=   -3.434 closest distance to " C   ILE A 239 " =    2.196
peak=   -3.433 closest distance to " ND2 ASN A 209 " =    1.855
peak=   -3.421 closest distance to " CE  MET A 105 " =    1.961
peak=   -3.421 closest distance to " O   ALA A   8 " =    1.915
peak=   -3.421 closest distance to " CB  ASP A 132 " =    2.318
peak=   -3.416 closest distance to " O   HOH Z 426 " =    1.633
peak=   -3.416 closest distance to " OD1 ASN A 249 " =    1.331
peak=   -3.414 closest distance to " CB  PHE A 192 " =    1.756
peak=   -3.413 closest distance to " O   SER A 146 " =    1.040
peak=   -3.411 closest distance to " O   SER A  22 " =    2.355
peak=   -3.408 closest distance to " CZ  TYR A 169 " =    1.706
peak=   -3.406 closest distance to " N   GLN A  77 " =    1.561
peak=   -3.403 closest distance to " O   HOH Z 312 " =    1.451
peak=   -3.403 closest distance to " ND2 ASN A  45 " =    0.968
peak=   -3.400 closest distance to " CD  GLU A 152 " =    2.576
peak=   -3.400 closest distance to " CD  LYS A 289 " =    2.539
peak=   -3.396 closest distance to " O   HOH Z 148 " =    1.989
peak=   -3.392 closest distance to " CD1 ILE A 239 " =    2.521
peak=   -3.388 closest distance to " N   SER A 276 " =    1.180
peak=   -3.384 closest distance to " CB  ALA A 291 " =    2.263
peak=   -3.378 closest distance to " CG  MET A 105 " =    0.862
peak=   -3.376 closest distance to " O   HOH Z 250 " =    1.401
peak=   -3.376 closest distance to " O   MET A  40 " =    2.617
peak=   -3.367 closest distance to " OG  SER A  97 " =    2.072
peak=   -3.365 closest distance to " OD2 ASP A 171 " =    2.171
peak=   -3.364 closest distance to " OE1 GLN A  88 " =    1.158
peak=   -3.361 closest distance to " O   HOH Z  13 " =    1.329
peak=   -3.358 closest distance to " CD1 LEU A 228 " =    2.042
peak=   -3.355 closest distance to " O   HOH Z 114 " =    2.891
peak=   -3.350 closest distance to " O   HOH Z  93 " =    1.455
peak=   -3.347 closest distance to " ND2 ASN A 187 " =    1.599
peak=   -3.341 closest distance to " O   HOH Z 368 " =    2.275
peak=   -3.341 closest distance to " OG BSER A 134 " =    1.644
peak=   -3.339 closest distance to " O   HOH Z 309 " =    2.405
peak=   -3.335 closest distance to " CD1 ILE A 199 " =    2.384
peak=   -3.329 closest distance to " N   VAL A 189 " =    1.601
peak=   -3.323 closest distance to " OD1 ASN A 301 " =    1.981
peak=   -3.313 closest distance to " CD2 TYR A 293 " =    2.091
peak=   -3.307 closest distance to " O   SER A 210 " =    1.872
peak=   -3.306 closest distance to " O   PRO A 198 " =    1.263
peak=   -3.301 closest distance to " CG  TRP A 266 " =    1.834
peak=   -3.293 closest distance to " O   HOH Z 231 " =    1.542
peak=   -3.286 closest distance to " O   HOH Z 175 " =    4.212
peak=   -3.281 closest distance to " C   GLN A 205 " =    1.979
peak=   -3.273 closest distance to " O   HOH Z 410 " =    2.056
peak=   -3.268 closest distance to " CB  ASP A 132 " =    2.268
peak=   -3.266 closest distance to " CD2 LEU A 237 " =    2.767
peak=   -3.265 closest distance to " CG2AVAL A  41 " =    2.934
peak=   -3.256 closest distance to " O   HOH Z 165 " =    2.098
peak=   -3.255 closest distance to " CB  ALA A 248 " =    2.363
peak=   -3.255 closest distance to " N   ALA A 226 " =    1.932
peak=   -3.254 closest distance to " O   HOH Z  71 " =    1.048
peak=   -3.254 closest distance to " O   HOH Z 427 " =    1.538
peak=   -3.253 closest distance to " O   HOH Z 192 " =    2.507
peak=   -3.247 closest distance to " O   HOH Z 407 " =    3.336
peak=   -3.246 closest distance to " O   ILE A  49 " =    1.763
peak=   -3.244 closest distance to " O   HOH Z 131 " =    3.992
peak=   -3.241 closest distance to " O   HOH Z 374 " =    2.853
peak=   -3.236 closest distance to " O   HOH Z 222 " =    3.220
peak=   -3.236 closest distance to " CG  LEU A 228 " =    1.013
peak=   -3.233 closest distance to " CD1 ILE A 239 " =    2.178
peak=   -3.229 closest distance to " CD1 TYR A 247 " =    2.618
peak=   -3.228 closest distance to " O   HOH Z 417 " =    2.535
peak=   -3.220 closest distance to " CG  ASP A  50 " =    2.178
peak=   -3.218 closest distance to " CG  LYS A 193 " =    2.095
peak=   -3.207 closest distance to " O   HOH Z 437 " =    1.851
peak=   -3.204 closest distance to " O   HOH Z 193 " =    1.621
peak=   -3.199 closest distance to " O   HOH Z 210 " =    0.974
peak=   -3.198 closest distance to " CG1 VAL A 230 " =    1.837
peak=   -3.196 closest distance to " OG1 THR A 178 " =    1.113
peak=   -3.194 closest distance to " O   SER A 135 " =    1.433
peak=   -3.193 closest distance to " CE3 TRP A 274 " =    2.275
peak=   -3.188 closest distance to " CB  ALA A  64 " =    2.550
peak=   -3.188 closest distance to " NE2 GLN A  88 " =    2.113
peak=   -3.187 closest distance to " OG ASER A 216 " =    0.990
peak=   -3.186 closest distance to " O   GLN A 240 " =    2.048
peak=   -3.173 closest distance to " CZ  PHE A 130 " =    0.794
peak=   -3.172 closest distance to " O   HOH Z 359 " =    3.280
peak=   -3.172 closest distance to " CE3 TRP A 123 " =    1.285
peak=   -3.162 closest distance to " CZ  ARG A 259 " =    0.890
peak=   -3.157 closest distance to " CG  PRO A 213 " =    0.911
peak=   -3.152 closest distance to " OD2 ASP A 270 " =    1.438
peak=   -3.151 closest distance to " CG1 VAL A 268 " =    2.875
peak=   -3.150 closest distance to " OG BSER A 212 " =    1.953
peak=   -3.145 closest distance to " CB  PRO A  90 " =    1.456
peak=   -3.142 closest distance to " ND2 ASN A 142 " =    1.968
peak=   -3.139 closest distance to " CB  ASP A  27 " =    2.370
peak=   -3.134 closest distance to " N   VAL A  72 " =    1.639
peak=   -3.131 closest distance to " O   HOH Z 435 " =    1.887
peak=   -3.128 closest distance to " CG  GLN A 278 " =    2.028
peak=   -3.127 closest distance to " CG1 VAL A 197 " =    2.249
peak=   -3.127 closest distance to " C   LEU A 143 " =    1.047
peak=   -3.127 closest distance to " O   HOH Z 281 " =    3.010
peak=   -3.123 closest distance to " O   HOH Z 350 " =    1.940
peak=   -3.110 closest distance to " O   HOH Z 393 " =    3.444
peak=   -3.093 closest distance to " O   HOH Z 143 " =    1.245
peak=   -3.072 closest distance to " O   TRP A  70 " =    1.474
peak=   -3.071 closest distance to " O   HOH Z 364 " =    1.977
peak=   -3.044 closest distance to " CA  GLY A 133 " =    2.140
peak=   -3.041 closest distance to " O   HOH Z  28 " =    2.217
peak=   -3.024 closest distance to " OG  SER A   3 " =    1.064
peak=   -3.018 closest distance to " CE1 PHE A  59 " =    2.032

================= 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    :  0.4641 0.4514   6.262038e+00   6.247328e+00
   1_bss:  0.4558 0.4417   6.254408e+00   6.234828e+00
   1_xyz:  0.3640 0.3834   6.114949e+00   6.141886e+00
   1_adp:  0.3125 0.3540   6.000642e+00   6.089801e+00
   1_occ:  0.3116 0.3542   5.999788e+00   6.091005e+00
   2_bss:  0.3087 0.3497   5.997968e+00   6.084782e+00
   2_xyz:  0.2199 0.2696   5.716206e+00   5.877746e+00
   2_adp:  0.2016 0.2501   5.641742e+00   5.811883e+00
   2_occ:  0.2013 0.2497   5.641041e+00   5.811052e+00
   3_bss:  0.2002 0.2491   5.639892e+00   5.810086e+00
   3_xyz:  0.1445 0.1873   5.342213e+00   5.550767e+00
   3_adp:  0.1309 0.1774   5.265012e+00   5.491795e+00
   3_occ:  0.1307 0.1774   5.264635e+00   5.491348e+00
   4_bss:  0.1311 0.1777   5.264473e+00   5.489354e+00
   4_xyz:  0.1181 0.1650   5.188373e+00   5.430553e+00
   4_adp:  0.1169 0.1610   5.168953e+00   5.400435e+00
   4_occ:  0.1168 0.1607   5.167871e+00   5.398982e+00
   5_bss:  0.1168 0.1607   5.167997e+00   5.399122e+00
   5_xyz:  0.1139 0.1574   5.146729e+00   5.380352e+00
   5_adp:  0.1137 0.1574   5.145818e+00   5.380812e+00
   5_occ:  0.1136 0.1574   5.145415e+00   5.380507e+00
   5_bss:  0.1136 0.1574   5.145353e+00   5.380486e+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:  0.372   9.388   6.564   8.514   8.109   0.000   0.000   0.000
   1_xyz:  0.372   9.388   6.564   8.514   8.109   0.000   0.000   0.000
   1_adp:  0.372   9.388   6.564   8.514   8.109   0.000   0.000   0.000
   1_occ:  0.372   9.388   6.564   8.514   8.109   0.000   0.000   0.000
   2_bss:  0.336  23.265   3.690   4.723   5.383   0.000   0.000   0.000
   2_xyz:  0.336  23.265   3.690   4.723   5.383   0.000   0.000   0.000
   2_adp:  0.336  23.265   3.690   4.723   5.383   0.000   0.000   0.000
   2_occ:  0.336  23.265   3.690   4.723   5.383   0.000   0.000   0.000
   3_bss:  0.329  31.870   2.523   2.996   3.968   0.000   0.000   0.000
   3_xyz:  0.329  31.870   2.523   2.996   3.968   0.000   0.000   0.000
   3_adp:  0.329  31.870   2.523   2.996   3.968   0.000   0.000   0.000
   3_occ:  0.329  31.870   2.523   2.996   3.968   0.000   0.000   0.000
   4_bss:  0.320  36.012   2.263   2.588   3.483   0.000   0.000   0.000
   4_xyz:  0.320  36.012   2.263   2.588   3.483   0.000   0.000   0.000
   4_adp:  0.320  36.012   2.263   2.588   3.483   0.000   0.000   0.000
   4_occ:  0.320  36.012   2.263   2.588   3.483   0.000   0.000   0.000
   5_bss:  0.324  36.012   2.263   2.588   3.483   0.000   0.000   0.000
   5_xyz:  0.324  36.012   2.263   2.588   3.483   0.000   0.000   0.000
   5_adp:  0.324  36.012   2.263   2.588   3.483   0.000   0.000   0.000
   5_occ:  0.324  36.012   2.263   2.588   3.483   0.000   0.000   0.000
   5_bss:  0.324  38.707  -0.505  -0.198   0.703  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.538 0.4770  0.5529    62752.822
   1_bss:  53.649 0.4734  0.6825    59736.683
   1_xyz:  42.342 0.6141  0.8698    41416.963
   1_adp:  37.041 0.6785  0.9774    34414.182
   1_occ:  37.116 0.6776  0.9751    34435.650
   2_bss:  36.718 0.6819  0.8766    33626.143
   2_xyz:  27.122 0.7885  0.9843    18594.517
   2_adp:  24.337 0.8189  1.0114    15952.631
   2_occ:  24.303 0.8193  1.0114    15913.792
   3_bss:  24.218 0.8201  0.9608    15834.119
   3_xyz:  17.469 0.8851  0.9996     8782.470
   3_adp:  16.130 0.8973  0.9988     7878.179
   3_occ:  16.123 0.8973  0.9986     7863.261
   4_bss:  16.093 0.8975  0.9846     7823.340
   4_xyz:  14.780 0.9085  0.9913     6813.346
   4_adp:  14.120 0.9141  0.9936     6455.796
   4_occ:  14.096 0.9143  0.9936     6433.219
   5_bss:  14.098 0.9142  0.9936     6436.969
   5_xyz:  13.729 0.9173  0.9935     6183.178
   5_adp:  13.723 0.9174  0.9920     6190.954
   5_occ:  13.718 0.9174  0.9920     6186.312
   5_bss:  13.716 0.9174  0.9889     6185.597
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3033e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3033e+01
   1_xyz:   1.638  0.013  0.105 18.221  0.006  4.107   1.3251e-01
   1_adp:   1.638  0.013  0.105 18.221  0.006  4.107   1.3251e-01
   1_occ:   1.638  0.013  0.105 18.221  0.006  4.107   1.3251e-01
   2_bss:   1.638  0.013  0.105 18.221  0.006  4.107   1.3251e-01
   2_xyz:   0.993  0.006  0.070 15.983  0.004  4.114   6.4250e-02
   2_adp:   0.993  0.006  0.070 15.983  0.004  4.114   6.4250e-02
   2_occ:   0.993  0.006  0.070 15.983  0.004  4.114   6.4250e-02
   3_bss:   0.993  0.006  0.070 15.983  0.004  4.114   6.4250e-02
   3_xyz:   1.020  0.006  0.076 15.827  0.003  4.107   6.2317e-02
   3_adp:   1.020  0.006  0.076 15.827  0.003  4.107   6.2317e-02
   3_occ:   1.020  0.006  0.076 15.827  0.003  4.107   6.2317e-02
   4_bss:   1.020  0.006  0.076 15.827  0.003  4.107   6.2317e-02
   4_xyz:   0.954  0.005  0.073 15.865  0.003  4.108   5.7732e-02
   4_adp:   0.954  0.005  0.073 15.865  0.003  4.108   5.7732e-02
   4_occ:   0.954  0.005  0.073 15.865  0.003  4.108   5.7732e-02
   5_bss:   0.954  0.005  0.073 15.865  0.003  4.108   5.7732e-02
   5_xyz:   0.901  0.005  0.069 15.489  0.003  4.109   5.2685e-02
   5_adp:   0.901  0.005  0.069 15.489  0.003  4.109   5.2685e-02
   5_occ:   0.901  0.005  0.069 15.489  0.003  4.109   5.2685e-02
   5_bss:   0.901  0.005  0.069 15.489  0.003  4.109   5.2685e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.091   6.8734e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.091   6.8734e+00
   1_xyz:  14.156  0.161  0.471 86.159  0.036  2.294   9.5059e-02
   1_adp:  14.156  0.161  0.471 86.159  0.036  2.294   9.5059e-02
   1_occ:  14.156  0.161  0.471 86.159  0.036  2.294   9.5059e-02
   2_bss:  14.156  0.161  0.471 86.159  0.036  2.294   9.5059e-02
   2_xyz:   6.033  0.061  0.290 84.299  0.037  2.346   5.3720e-02
   2_adp:   6.033  0.061  0.290 84.299  0.037  2.346   5.3720e-02
   2_occ:   6.033  0.061  0.290 84.299  0.037  2.346   5.3720e-02
   3_bss:   6.033  0.061  0.290 84.299  0.037  2.346   5.3720e-02
   3_xyz:   6.997  0.052  0.433 84.634  0.023  2.304   5.2848e-02
   3_adp:   6.997  0.052  0.433 84.634  0.023  2.304   5.2848e-02
   3_occ:   6.997  0.052  0.433 84.634  0.023  2.304   5.2848e-02
   4_bss:   6.997  0.052  0.433 84.634  0.023  2.304   5.2848e-02
   4_xyz:   7.096  0.041  0.364 84.395  0.025  2.327   3.6251e-02
   4_adp:   7.096  0.041  0.364 84.395  0.025  2.327   3.6251e-02
   4_occ:   7.096  0.041  0.364 84.395  0.025  2.327   3.6251e-02
   5_bss:   7.096  0.041  0.364 84.395  0.025  2.327   3.6251e-02
   5_xyz:   6.000  0.036  0.356 84.194  0.023  2.327   3.0927e-02
   5_adp:   6.000  0.036  0.356 84.194  0.023  2.327   3.0927e-02
   5_occ:   6.000  0.036  0.356 84.194  0.023  2.327   3.0927e-02
   5_bss:   6.000  0.036  0.356 84.194  0.023  2.327   3.0927e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  82.82   0.00  12.07  82.82   0.00   9.32  69.53   0.00  27.05
   1_occ:  82.82   0.00  12.07  82.82   0.00   9.32  69.53   0.00  27.05
   2_bss:  82.82   0.00  12.07  82.82   0.00   9.32  69.53   0.00  27.05
   2_xyz:  82.82   0.00  12.07  82.82   0.00   9.32  69.53   0.00  27.05
   2_adp:  83.26   0.00  11.97  83.26   0.00   8.46  65.44   1.23  31.07
   2_occ:  83.26   0.00  11.97  83.26   0.00   8.46  65.44   1.23  31.07
   3_bss:  83.26   0.00  11.97  83.26   0.00   8.46  65.44   1.23  31.07
   3_xyz:  83.26   0.00  11.97  83.26   0.00   8.46  65.44   1.23  31.07
   3_adp:  90.94   0.00  12.82  90.94   0.00   8.36  73.68   0.00  37.12
   3_occ:  90.94   0.00  12.82  90.94   0.00   8.36  73.68   0.00  37.12
   4_bss:  90.94   0.00  12.82  90.94   0.00   8.36  73.68   0.00  37.12
   4_xyz:  90.94   0.00  12.82  90.94   0.00   8.36  73.68   0.00  37.12
   4_adp:  89.77   0.00  12.21  89.77   0.00   8.07  73.56   1.81  34.78
   4_occ:  89.77   0.00  12.21  89.77   0.00   8.07  73.56   1.81  34.78
   5_bss:  89.77   0.00  12.21  89.77   0.00   8.07  73.56   1.81  34.78
   5_xyz:  89.77   0.00  12.21  89.77   0.00   8.07  73.56   1.81  34.78
   5_adp:  89.80   0.00  12.20  89.80   0.00   8.05  73.59   2.04  34.78
   5_occ:  89.80   0.00  12.20  89.80   0.00   8.05  73.59   2.04  34.78
   5_bss:  92.49   2.69  14.89  92.49   2.69  10.74  76.28   4.73  37.47
------------------------------------------------------------------------
 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:    1.226    0.013    0.409
   1_adp:    1.226    0.013    0.409
   1_occ:    1.226    0.013    0.409
   2_bss:    1.226    0.013    0.409
   2_xyz:    1.491    0.033    0.531
   2_adp:    1.491    0.033    0.531
   2_occ:    1.491    0.033    0.531
   3_bss:    1.491    0.033    0.531
   3_xyz:    1.431    0.043    0.615
   3_adp:    1.431    0.043    0.615
   3_occ:    1.431    0.043    0.615
   4_bss:    1.431    0.043    0.615
   4_xyz:    1.585    0.042    0.639
   4_adp:    1.585    0.042    0.639
   4_occ:    1.585    0.042    0.639
   5_bss:    1.585    0.042    0.639
   5_xyz:    1.619    0.036    0.650
   5_adp:    1.619    0.036    0.650
   5_occ:    1.619    0.036    0.650
   5_bss:    1.619    0.036    0.650
------------------------------------------------------------------------

CPU time actual refinement: 336.09


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_398/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_398/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_398/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_398/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_398/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.93 
  Macro-tasks:
    bulk solvent and scale       = 46.90  
    individual site refinement   = 133.81 
    weights calculation          = 32.62  
    collect and process          = 6.46   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 219.90 
  Micro-tasks:
    mask                            = 1.92   
    f_calc                          = 101.32 
    alpha_beta                      = 8.31   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 111.15 
    fmodel                         = 7.99   
    r_factors                      = 0.25   
    phase_errors                   = 10.33  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 242.70 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.759 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    635 calls, 100.93 s
gradients_fft:          579 calls,  97.95 s

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

# Date 2008-01-16 Time 01:28:14 PST -0800 (1200475694.13 s)
Start R-work = 0.4641, R-free = 0.4514 (no bulk solvent and anisotropic scale)
Final R-work = 0.1309, R-free = 0.1741 (no bulk solvent and anisotropic scale)

Start R-work = 0.4558, R-free = 0.4417
Final R-work = 0.1136, R-free = 0.1574