# Date 2008-01-16 Time 00:51:35 PST -0800 (1200473495.74 s)
#phil __OFF__

Command line arguments: "../179.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 = 4627
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 179

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 46.93, 85.5261, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7343 1.96062
Completeness in resolution range: 0.958413
Completeness with d_max=infinity: 0.955421

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7343
                             d_min =   1.9606

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7343 1.96062
Completeness in resolution range: 0.958413
Completeness with d_max=infinity: 0.955421

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7347 -  4.1946 [2157/2185]  1941   216  10.0%
  bin  2:  4.1946 -  3.3421 [2045/2064]  1841   204  10.0%
  bin  3:  3.3421 -  2.9234 [2049/2070]  1844   205  10.0%
  bin  4:  2.9234 -  2.6578 [2009/2033]  1809   200  10.0%
  bin  5:  2.6578 -  2.4683 [2007/2028]  1802   205  10.2%
  bin  6:  2.4683 -  2.3234 [1982/2028]  1792   190   9.6%
  bin  7:  2.3234 -  2.2074 [1992/2024]  1789   203  10.2%
  bin  8:  2.2074 -  2.1116 [1971/2006]  1770   201  10.2%
  bin  9:  2.1116 -  2.0305 [1953/1983]  1760   193   9.9%
  bin 10:  2.0305 -  1.9606 [1424/2018]  1282   142  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_179/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.40 -     2.10: 15
        2.10 -     2.80: 782
        2.80 -     3.50: 4528
        3.50 -     4.20: 9509
        4.20 -     4.90: 13937
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.403 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.423 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.460 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 109 " - " O   HOH Z 417 "  1.807 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28766 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_179/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_179/model_refine_001.geo

CPU time processing inputs: 9.26


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.93 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4539   r_free= 0.4465   ksol= 0.00   Bsol= 0.00   scale= 0.821    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.251716                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6781 0.99   1396  156 0.3750 0.3737       6.543       6.573|
|  2:  4.6781 -  3.7330 0.99   1334  149 0.3615 0.3555      6.6968       6.711|
|  3:  3.7330 -  3.2670 0.99   1325  150 0.4032 0.3891      6.6097      6.6601|
|  4:  3.2670 -  2.9710 0.99   1308  135 0.4243 0.4281      6.4716      6.4263|
|  5:  2.9710 -  2.7595 0.99   1294  146 0.4706 0.4798      6.3476      6.3692|
|  6:  2.7595 -  2.5978 0.98   1290  143 0.4844 0.5277      6.2569      6.2086|
|  7:  2.5978 -  2.4683 0.99   1290  151 0.4893 0.4648      6.2377      6.1398|
|  8:  2.4683 -  2.3613 0.98   1299  136 0.4983 0.4844      6.1616       6.167|
|  9:  2.3613 -  2.2707 0.98   1267  145 0.4988 0.5062      6.1003      6.1546|
| 10:  2.2707 -  2.1926 0.97   1251  136 0.5081 0.4887       6.108      6.0308|
| 11:  2.1926 -  2.1243 0.99   1284  150 0.5165 0.4861      6.0283      6.0589|
| 12:  2.1243 -  2.0637 0.98   1278  139 0.5126 0.5067      5.9781      5.9989|
| 13:  2.0637 -  2.0095 0.97   1260  133 0.5392 0.5081      5.8984       5.844|
| 14:  2.0095 -  1.9606 0.60    754   90 0.5077 0.4874      5.8478      5.7669|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7347 -  4.6781  1396   156  0.69  35.52   0.82     0.71      73364.13|
|  2:  4.6781 -  3.7330  1334   149  0.72  33.33   0.91     0.78      94194.33|
|  3:  3.7330 -  3.2670  1325   150  0.65  39.86   0.88     0.76      96313.43|
|  4:  3.2670 -  2.9710  1308   135  0.59  44.87   0.83     0.68      83894.14|
|  5:  2.9710 -  2.7595  1294   146  0.49  52.83   0.76     0.58      72815.09|
|  6:  2.7595 -  2.5978  1290   143  0.45  55.87   0.74     0.52      64436.20|
|  7:  2.5978 -  2.4683  1290   151  0.44  56.42   0.76     0.50      59416.63|
|  8:  2.4683 -  2.3613  1299   136  0.45  56.11   0.76     0.52      51678.15|
|  9:  2.3613 -  2.2707  1267   145  0.45  56.16   0.75     0.54      47132.31|
| 10:  2.2707 -  2.1926  1251   136  0.46  55.12   0.78     0.55      41265.45|
| 11:  2.1926 -  2.1243  1284   150  0.44  57.23   0.76     0.53      40274.94|
| 12:  2.1243 -  2.0637  1278   139  0.41  59.44   0.78     0.51      39462.22|
| 13:  2.0637 -  2.0095  1260   133  0.35  63.96   0.75     0.44      35455.83|
| 14:  2.0095 -  1.9606   754    90  0.35  64.14   0.75     0.36      27088.40|
|alpha:            min =        0.36 max =            0.78 mean =         0.58|
|beta:             min =    27088.40 max =        96313.43 mean =     60415.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.98 mean =        51.63|
|phase err.(test): min =        0.00 max =           89.72 mean =        51.87|
|-----------------------------------------------------------------------------|

============================== 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 = 10.148247             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.726   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.822335              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.028   (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 |  1.130 -  1.507:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.507 -  1.884:       19 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.884 -  2.261:      152 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.261 -  2.638:      660 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.638 -  3.015:     1463 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.015 -  3.392:     2591 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.392 -  3.769:     4032 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.769 -  4.146:     5211 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.146 -  4.523:     6695 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.523 -  4.900:     7968 |
|-----------------------------------------------------------------------------|
|-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 |       53.069 |
| 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  1.130 |       2.484 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.503)------------------------------------------|
|    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 = 11.503)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4607   r_free= 0.4551   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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: 6.255023                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4446   r_free= 0.4393   ksol= 0.37   Bsol= 20.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.33,7.83,8.17,0.00,0.00,0.00); trace/3= 8.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.243012                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.376319              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.032   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.871727              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.273   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4446      final r-factor (work) = 0.3487          |
| start r-factor (free) = 0.4393      final r-factor (free) = 0.3712          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.4115 = 9.38 * 0.50 * 6.2588 + 1.00 * 53.0694                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.8728 = 9.38 * 0.50 * 6.1304 + 1.00 * 0.1325                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3487      final r-factor (work) = 0.2893          |
| start r-factor (free) = 0.3712      final r-factor (free) = 0.3284          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3584 = 0.87 * 1.00 * 6.1304 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2341 = 0.87 * 1.00 * 5.9878 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.503)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.82   11.68    None  None   None       |
|    all(noH): 2823   0      0.00    74.82   11.68    None  None   None       |
|    Sol.    : 438    0      0.00    74.82   27.83    None  None   None       |
|    Mac.    : 2385   0      0.00    70.01   8.71     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.482: 1392   |   5:    37.411 -  44.893:   64        |
|      1:     7.482 -  14.964:  671   |   6:    44.893 -  52.375:   48        |
|      2:    14.964 -  22.447:  329   |   7:    52.375 -  59.857:   23        |
|      3:    22.447 -  29.929:  196   |   8:    59.857 -  67.340:    4        |
|      4:    29.929 -  37.411:   92   |   9:    67.340 -  74.822:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2893 r_free = 0.3284             target_work(ml) = 5.939         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2889 r_free = 0.3278             target_work(ml) = 5.938         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2889   r_free= 0.3278   ksol= 0.37   Bsol= 20.00   scale= 1.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.33,7.83,8.17,0.00,0.00,0.00); trace/3= 8.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.938267                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2850   r_free= 0.3222   ksol= 0.34   Bsol= 31.72   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.78,4.17,5.23,0.00,0.00,0.00); trace/3= 4.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.936592                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.461861              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.088   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.357932              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.182  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2850      final r-factor (work) = 0.2008          |
| start r-factor (free) = 0.3222      final r-factor (free) = 0.2407          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4984 = 3.46 * 0.50 * 5.9886 + 1.00 * 0.1325                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0643 = 3.46 * 0.50 * 5.7781 + 1.00 * 0.0629                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2008      final r-factor (work) = 0.1798          |
| start r-factor (free) = 0.2407      final r-factor (free) = 0.2208          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0835 = 0.36 * 1.00 * 5.7781 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0056 = 0.36 * 1.00 * 5.5733 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.503)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.74   11.98    None  None   None       |
|    all(noH): 2823   0      0.00    77.74   11.98    None  None   None       |
|    Sol.    : 438    0      1.16    74.98   32.26    None  None   None       |
|    Mac.    : 2385   0      0.00    77.74   8.25     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.775: 1521   |   5:    38.872 -  46.647:   92        |
|      1:     7.775 -  15.549:  649   |   6:    46.647 -  54.421:   57        |
|      2:    15.549 -  23.323:  211   |   7:    54.421 -  62.196:   18        |
|      3:    23.323 -  31.098:  131   |   8:    62.196 -  69.970:    8        |
|      4:    31.098 -  38.872:  133   |   9:    69.970 -  77.745:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1798 r_free = 0.2208             target_work(ml) = 5.536         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1795 r_free = 0.2202             target_work(ml) = 5.535         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1795   r_free= 0.2202   ksol= 0.34   Bsol= 31.72   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.78,4.17,5.23,0.00,0.00,0.00); trace/3= 4.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.534880                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1778   r_free= 0.2194   ksol= 0.33   Bsol= 31.72   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,3.15,3.96,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.530927                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.701849              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.507  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.196625              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.546  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1778      final r-factor (work) = 0.1336          |
| start r-factor (free) = 0.2194      final r-factor (free) = 0.1729          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6009 = 2.70 * 0.50 * 5.5798 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3624 = 2.70 * 0.50 * 5.4048 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1336      final r-factor (work) = 0.1268          |
| start r-factor (free) = 0.1729      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0733 = 0.20 * 1.00 * 5.4048 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0416 = 0.20 * 1.00 * 5.2504 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.503)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.85   11.88    None  None   None       |
|    all(noH): 2823   0      0.00    79.85   11.88    None  None   None       |
|    Sol.    : 438    0      1.90    68.88   33.09    None  None   None       |
|    Mac.    : 2385   0      0.00    79.85   7.98     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.985: 1636   |   5:    39.924 -  47.908:   92        |
|      1:     7.985 -  15.969:  605   |   6:    47.908 -  55.893:   56        |
|      2:    15.969 -  23.954:  158   |   7:    55.893 -  63.878:   14        |
|      3:    23.954 -  31.939:  121   |   8:    63.878 -  71.862:    6        |
|      4:    31.939 -  39.924:  133   |   9:    71.862 -  79.847:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1268 r_free = 0.1648             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1266 r_free = 0.1648             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1648   ksol= 0.33   Bsol= 31.72   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,3.15,3.96,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.224824                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1268   r_free= 0.1643   ksol= 0.33   Bsol= 31.72   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.00,2.75,3.50,0.00,0.00,0.00); trace/3= 2.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.225018                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.317452              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.784  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.161550              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.934  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1268      final r-factor (work) = 0.1195          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5212 = 1.32 * 0.50 * 5.2531 + 1.00 * 0.0608                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4759 = 1.32 * 0.50 * 5.1991 + 1.00 * 0.0511                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1195      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8492 = 0.16 * 1.00 * 5.1991 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8476 = 0.16 * 1.00 * 5.1810 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.503)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.86   11.91    None  None   None       |
|    all(noH): 2823   0      0.00    79.86   11.91    None  None   None       |
|    Sol.    : 438    0      1.68    68.84   33.09    None  None   None       |
|    Mac.    : 2385   0      0.00    79.86   8.02     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.986: 1632   |   5:    39.932 -  47.919:   93        |
|      1:     7.986 -  15.973:  610   |   6:    47.919 -  55.905:   55        |
|      2:    15.973 -  23.959:  157   |   7:    55.905 -  63.891:   14        |
|      3:    23.959 -  31.946:  121   |   8:    63.891 -  71.878:    6        |
|      4:    31.946 -  39.932:  133   |   9:    71.878 -  79.864:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1193 r_free = 0.1581             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1192 r_free = 0.1582             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1582   ksol= 0.33   Bsol= 31.72   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.00,2.75,3.50,0.00,0.00,0.00); trace/3= 2.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.179917                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1581   ksol= 0.32   Bsol= 34.80   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.86,2.63,3.39,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.179175                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.289086              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.881  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.970296              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.981  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5703 = 3.29 * 0.50 * 5.1802 + 1.00 * 0.0511                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5338 = 3.29 * 0.50 * 5.1425 + 1.00 * 0.0768                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.2914 = 2.97 * 1.00 * 5.1425 + 1.00 * 0.0168                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.2084 = 2.97 * 1.00 * 5.1160 + 1.00 * 0.0125                              |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.503)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.81   12.23    None  None   None       |
|    all(noH): 2823   0      0.00    85.81   12.23    None  None   None       |
|    Sol.    : 438    0      1.32    70.59   35.05    None  None   None       |
|    Mac.    : 2385   0      0.00    85.81   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 -   8.581: 1711   |   5:    42.903 -  51.484:   98        |
|      1:     8.581 -  17.161:  550   |   6:    51.484 -  60.064:   59        |
|      2:    17.161 -  25.742:  152   |   7:    60.064 -  68.645:   15        |
|      3:    25.742 -  34.322:  117   |   8:    68.645 -  77.225:    7        |
|      4:    34.322 -  42.903:  111   |   9:    77.225 -  85.806:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1076 r_free = 0.1560             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1076 r_free = 0.1559             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1076   r_free= 0.1559   ksol= 0.32   Bsol= 34.80   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.86,2.63,3.39,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120712                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6781 0.99   1396  156 0.0996 0.1286      5.3827      5.5356|
|  2:  4.6781 -  3.7330 0.99   1334  149 0.0819 0.1102      5.4051      5.6195|
|  3:  3.7330 -  3.2670 0.99   1325  150 0.1020 0.1453      5.4363      5.7791|
|  4:  3.2670 -  2.9710 0.99   1308  135 0.1135 0.1578      5.4058      5.5934|
|  5:  2.9710 -  2.7595 0.99   1294  146 0.1239 0.1606      5.2802      5.4756|
|  6:  2.7595 -  2.5978 0.98   1290  143 0.1182 0.1904      5.1864      5.4511|
|  7:  2.5978 -  2.4683 0.99   1290  151 0.1154 0.1656      5.1314      5.3648|
|  8:  2.4683 -  2.3613 0.98   1299  136 0.1128 0.1688      5.0724      5.3376|
|  9:  2.3613 -  2.2707 0.98   1267  145 0.1140 0.1799      5.0043      5.3067|
| 10:  2.2707 -  2.1926 0.97   1251  136 0.1077 0.1591      4.9437      5.1165|
| 11:  2.1926 -  2.1243 0.99   1284  150 0.1081 0.1735      4.8968       5.279|
| 12:  2.1243 -  2.0637 0.98   1278  139 0.1073 0.1738      4.8445      5.1525|
| 13:  2.0637 -  2.0095 0.97   1260  133 0.1064 0.1674      4.7662      4.9938|
| 14:  2.0095 -  1.9606 0.60    754   90 0.1046 0.1742      4.6934      4.9623|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7347 -  4.6781  1396   156  0.94   8.98   0.99     0.96       7036.75|
|  2:  4.6781 -  3.7330  1334   149  0.96   7.59   1.03     1.01       8594.35|
|  3:  3.7330 -  3.2670  1325   150  0.94  10.85   1.04     1.03       9738.11|
|  4:  3.2670 -  2.9710  1308   135  0.93  12.85   1.02     1.01       9585.97|
|  5:  2.9710 -  2.7595  1294   146  0.90  15.39   1.00     0.97       7775.37|
|  6:  2.7595 -  2.5978  1290   143  0.90  15.99   0.98     0.94       6779.26|
|  7:  2.5978 -  2.4683  1290   151  0.91  15.21   0.99     0.95       5974.22|
|  8:  2.4683 -  2.3613  1299   136  0.91  15.10   1.00     0.98       5481.12|
|  9:  2.3613 -  2.2707  1267   145  0.91  15.44   1.01     0.99       4883.36|
| 10:  2.2707 -  2.1926  1251   136  0.90  15.90   1.00     0.97       4437.98|
| 11:  2.1926 -  2.1243  1284   150  0.91  15.46   1.00     0.97       4115.58|
| 12:  2.1243 -  2.0637  1278   139  0.91  14.96   1.02     0.99       3755.38|
| 13:  2.0637 -  2.0095  1260   133  0.90  15.89   1.01     1.00       3295.87|
| 14:  2.0095 -  1.9606   754    90  0.91  15.08   0.99     0.95       2737.78|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2737.78 max =         9738.11 mean =      6148.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.81|
|phase err.(test): min =        0.00 max =           88.04 mean =        13.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1559   ksol= 0.32   Bsol= 39.88   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,0.00,0.78,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120411                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1559   ksol= 0.32   Bsol= 39.88   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,0.00,0.78,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120411                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6781 0.99   1396  156 0.0996 0.1288      5.3815      5.5355|
|  2:  4.6781 -  3.7330 0.99   1334  149 0.0823 0.1105      5.4071      5.6216|
|  3:  3.7330 -  3.2670 0.99   1325  150 0.1020 0.1453      5.4375      5.7798|
|  4:  3.2670 -  2.9710 0.99   1308  135 0.1135 0.1574      5.4054      5.5923|
|  5:  2.9710 -  2.7595 0.99   1294  146 0.1238 0.1605      5.2792      5.4746|
|  6:  2.7595 -  2.5978 0.98   1290  143 0.1181 0.1902      5.1853      5.4499|
|  7:  2.5978 -  2.4683 0.99   1290  151 0.1153 0.1656      5.1304      5.3642|
|  8:  2.4683 -  2.3613 0.98   1299  136 0.1127 0.1685      5.0716      5.3366|
|  9:  2.3613 -  2.2707 0.98   1267  145 0.1140 0.1800      5.0041      5.3073|
| 10:  2.2707 -  2.1926 0.97   1251  136 0.1076 0.1591      4.9435      5.1156|
| 11:  2.1926 -  2.1243 0.99   1284  150 0.1080 0.1734      4.8966      5.2791|
| 12:  2.1243 -  2.0637 0.98   1278  139 0.1073 0.1739      4.8443      5.1529|
| 13:  2.0637 -  2.0095 0.97   1260  133 0.1064 0.1674      4.7657      4.9931|
| 14:  2.0095 -  1.9606 0.60    754   90 0.1046 0.1739      4.6921      4.9608|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7347 -  4.6781  1396   156  0.94   8.98   0.99     0.96       7017.57|
|  2:  4.6781 -  3.7330  1334   149  0.96   7.60   1.03     1.02       8605.86|
|  3:  3.7330 -  3.2670  1325   150  0.94  10.87   1.04     1.04       9764.52|
|  4:  3.2670 -  2.9710  1308   135  0.93  12.84   1.02     1.02       9574.33|
|  5:  2.9710 -  2.7595  1294   146  0.90  15.38   1.00     0.97       7760.80|
|  6:  2.7595 -  2.5978  1290   143  0.90  15.98   0.98     0.95       6765.54|
|  7:  2.5978 -  2.4683  1290   151  0.91  15.19   0.99     0.96       5961.50|
|  8:  2.4683 -  2.3613  1299   136  0.91  15.09   1.01     0.98       5471.86|
|  9:  2.3613 -  2.2707  1267   145  0.91  15.42   1.02     0.99       4878.38|
| 10:  2.2707 -  2.1926  1251   136  0.90  15.90   1.01     0.98       4437.72|
| 11:  2.1926 -  2.1243  1284   150  0.91  15.46   1.01     0.98       4114.46|
| 12:  2.1243 -  2.0637  1278   139  0.91  14.96   1.02     1.00       3755.14|
| 13:  2.0637 -  2.0095  1260   133  0.90  15.88   1.02     1.01       3291.00|
| 14:  2.0095 -  1.9606   754    90  0.91  15.05   0.99     0.96       2727.66|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2727.66 max =         9764.52 mean =      6144.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.80|
|phase err.(test): min =        0.00 max =           88.11 mean =        13.35|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.503)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.76    88.56   14.99    None  None   None       |
|    all(noH): 2823   0      2.76    88.56   14.99    None  None   None       |
|    Sol.    : 438    0      4.08    73.35   37.81    None  None   None       |
|    Mac.    : 2385   0      2.76    88.56   10.80    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:     2.759 -  11.339: 1711   |   5:    45.662 -  54.242:   98        |
|      1:    11.339 -  19.920:  550   |   6:    54.242 -  62.823:   59        |
|      2:    19.920 -  28.501:  152   |   7:    62.823 -  71.404:   15        |
|      3:    28.501 -  37.081:  117   |   8:    71.404 -  79.984:    7        |
|      4:    37.081 -  45.662:  111   |   9:    79.984 -  88.565:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.271 - 5.959
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 301
   mapped sites are within: 0.756 - 5.959

peak=   11.231 closest distance to " CB  VAL A 230 " =    1.425
peak=    7.851 closest distance to " CG2 VAL A 296 " =    1.226
peak=    6.346 closest distance to " CG  LEU A   5 " =    1.138
peak=    5.698 closest distance to " NE2 GLN A  11 " =    1.089
peak=    5.546 closest distance to " O   HOH Z 142 " =    1.845
peak=    5.465 closest distance to " O   HOH Z 193 " =    1.766
peak=    5.436 closest distance to " O   HOH Z 126 " =    1.932
peak=    5.355 closest distance to " CG  LEU A 228 " =    1.127
peak=    5.309 closest distance to " CB  GLN A 183 " =    1.330
peak=    5.147 closest distance to " CB  VAL A 296 " =    1.040
peak=    5.135 closest distance to " CD2 LEU A   5 " =    1.118
peak=    5.125 closest distance to " O   HOH Z 209 " =    2.303
peak=    4.940 closest distance to " O   HOH Z 232 " =    2.346
peak=    4.925 closest distance to " CB  ARG A 275 " =    0.966
peak=    4.888 closest distance to " O   HOH Z  85 " =    1.509
peak=    4.868 closest distance to " O   HOH Z 272 " =    1.915
peak=    4.785 closest distance to " NH2 ARG A  56 " =    2.122
peak=    4.739 closest distance to " O   SER A  87 " =    2.289
peak=    4.678 closest distance to " CB  GLN A 223 " =    1.486
peak=    4.651 closest distance to " O   HOH Z 402 " =    1.458
peak=    4.650 closest distance to " CB  VAL A 230 " =    1.123
peak=    4.631 closest distance to " CG  PRO A  54 " =    1.132
peak=    4.626 closest distance to " CB  SER A  63 " =    1.213
peak=    4.588 closest distance to " O   HOH Z 124 " =    1.455
peak=    4.568 closest distance to " CB  ARG A  79 " =    1.491
peak=    4.453 closest distance to " O   HOH Z 298 " =    1.830
peak=    4.404 closest distance to " C   PRO A 198 " =    1.466
peak=    4.391 closest distance to " O   HOH Z 346 " =    1.626
peak=    4.378 closest distance to " O   HOH Z  59 " =    1.996
peak=    4.364 closest distance to " O   HOH Z 427 " =    2.709
peak=    4.350 closest distance to " O   HOH Z 303 " =    2.038
peak=    4.345 closest distance to " O   HOH Z 368 " =    2.136
peak=    4.328 closest distance to " CD2 TRP A 179 " =    1.439
peak=    4.318 closest distance to " CB  GLU A 152 " =    1.129
peak=    4.301 closest distance to " O   HOH Z  97 " =    2.407
peak=    4.300 closest distance to " O   HOH Z  54 " =    1.636
peak=    4.297 closest distance to " CB  ASN A 148 " =    1.426
peak=    4.253 closest distance to " CB  SER A   3 " =    1.239
peak=    4.234 closest distance to " O   HOH Z 250 " =    1.360
peak=    4.223 closest distance to " O   HOH Z  44 " =    1.940
peak=    4.219 closest distance to " O   HOH Z 411 " =    3.733
peak=    4.191 closest distance to " CA  TYR A  30 " =    0.977
peak=    4.185 closest distance to " O   HOH Z 403 " =    1.785
peak=    4.179 closest distance to " OE1 GLU A   2 " =    2.162
peak=    4.162 closest distance to " O   HOH Z 392 " =    2.827
peak=    4.159 closest distance to " O   HOH Z 203 " =    1.519
peak=    4.158 closest distance to " CG  PRO A 213 " =    1.191
peak=    4.149 closest distance to " O   HOH Z  43 " =    2.250
peak=    4.139 closest distance to " O   HOH Z 234 " =    3.454
peak=    4.129 closest distance to " O   HOH Z 423 " =    1.835
peak=    4.117 closest distance to " O   HOH Z 128 " =    2.125
peak=    4.111 closest distance to " O   HOH Z 316 " =    2.867
peak=    4.092 closest distance to " O   HOH Z 287 " =    1.894
peak=    4.086 closest distance to " CB  PRO A  54 " =    0.931
peak=    4.077 closest distance to " O   HOH Z 369 " =    2.393
peak=    4.077 closest distance to " O   HOH Z 327 " =    1.605
peak=    4.038 closest distance to " O   HOH Z  61 " =    1.645
peak=    4.020 closest distance to " O   HOH Z 371 " =    3.155
peak=    4.005 closest distance to " O   HOH Z  97 " =    1.913
peak=    4.005 closest distance to " O   HOH Z 322 " =    2.113
peak=    3.995 closest distance to " CB  TRP A 266 " =    1.102
peak=    3.994 closest distance to " O   HOH Z 245 " =    1.410
peak=    3.994 closest distance to " CB  TYR A 169 " =    0.825
peak=    3.987 closest distance to " CB  SER A  26 " =    1.685
peak=    3.984 closest distance to " O   HOH Z 261 " =    2.065
peak=    3.979 closest distance to " O   HOH Z 189 " =    2.537
peak=    3.965 closest distance to " O   HOH Z 248 " =    1.670
peak=    3.959 closest distance to " O   HOH Z  78 " =    1.628
peak=    3.950 closest distance to " CB  VAL A 265 " =    1.236
peak=    3.945 closest distance to " CB  ARG A 139 " =    0.991
peak=    3.928 closest distance to " O   HOH Z 407 " =    2.578
peak=    3.915 closest distance to " O   HOH Z 284 " =    2.894
peak=    3.914 closest distance to " NZ  LYS A 117 " =    2.873
peak=    3.907 closest distance to " CB  TRP A 179 " =    1.252
peak=    3.894 closest distance to " CB  ALA A   9 " =    1.598
peak=    3.890 closest distance to " O   HOH Z 128 " =    1.902
peak=    3.875 closest distance to " O   HOH Z 425 " =    2.110
peak=    3.873 closest distance to " O   HOH Z  15 " =    2.182
peak=    3.866 closest distance to " O   HOH Z 130 " =    2.363
peak=    3.861 closest distance to " CA  ALA A  21 " =    1.130
peak=    3.856 closest distance to " O   HOH Z 130 " =    2.711
peak=    3.843 closest distance to " O   HOH Z 299 " =    4.172
peak=    3.842 closest distance to " O   HOH Z 345 " =    3.007
peak=    3.818 closest distance to " CB BVAL A  41 " =    1.188
peak=    3.805 closest distance to " O   HOH Z  80 " =    1.625
peak=    3.801 closest distance to " CG2 ILE A  20 " =    1.460
peak=    3.795 closest distance to " O   HOH Z  66 " =    2.211
peak=    3.779 closest distance to " CB  GLU A 128 " =    1.056
peak=    3.753 closest distance to " CB  ASN A 110 " =    1.149
peak=    3.736 closest distance to " N   ASN A  39 " =    1.276
peak=    3.726 closest distance to " O   HOH Z 118 " =    1.686
peak=    3.722 closest distance to " CA  ALA A  51 " =    1.027
peak=    3.721 closest distance to " OG BSER A 164 " =    2.083
peak=    3.710 closest distance to " O   HOH Z 263 " =    1.651
peak=    3.707 closest distance to " O   HOH Z 344 " =    2.641
peak=    3.703 closest distance to " CB  THR A  31 " =    1.667
peak=    3.698 closest distance to " O   HOH Z  61 " =    1.484
peak=    3.694 closest distance to " O   HOH Z 265 " =    2.370
peak=    3.691 closest distance to " CD2 LEU A 228 " =    1.218
peak=    3.680 closest distance to " O   HOH Z 417 " =    3.265
peak=    3.662 closest distance to " O   HOH Z 158 " =    2.975
peak=    3.653 closest distance to " CD  ARG A 269 " =    1.067
peak=    3.651 closest distance to " CB  GLN A  88 " =    1.255
peak=    3.648 closest distance to " O   TRP A 274 " =    1.908
peak=    3.647 closest distance to " O   HOH Z  48 " =    1.706
peak=    3.645 closest distance to " O   HOH Z 134 " =    1.243
peak=    3.644 closest distance to " O   HOH Z 261 " =    1.801
peak=    3.643 closest distance to " O   HOH Z 227 " =    2.202
peak=    3.643 closest distance to " O   LYS A 290 " =    2.342
peak=    3.642 closest distance to " OD1 ASN A  69 " =    2.643
peak=    3.632 closest distance to " O   HOH Z  88 " =    2.735
peak=    3.629 closest distance to " O   HOH Z 172 " =    3.896
peak=    3.626 closest distance to " O   HOH Z 366 " =    2.900
peak=    3.619 closest distance to " O   HOH Z 251 " =    1.622
peak=    3.618 closest distance to " O   HOH Z  47 " =    1.738
peak=    3.615 closest distance to " O   HOH Z 426 " =    1.493
peak=    3.614 closest distance to " ND2 ASN A 187 " =    1.384
peak=    3.614 closest distance to " O   ASP A 124 " =    1.270
peak=    3.608 closest distance to " CA  LYS A 117 " =    1.251
peak=    3.601 closest distance to " CB  VAL A 202 " =    1.533
peak=    3.593 closest distance to " CA  VAL A  41 " =    0.815
peak=    3.592 closest distance to " CG1BVAL A  72 " =    1.548
peak=    3.590 closest distance to " O   HOH Z 425 " =    1.303
peak=    3.590 closest distance to " CB  ASN A  39 " =    0.807
peak=    3.588 closest distance to " CB  GLU A 277 " =    3.489
peak=    3.587 closest distance to " O   HOH Z  10 " =    1.753
peak=    3.585 closest distance to " CZ AARG A 102 " =    1.759
peak=    3.582 closest distance to " CG2 ILE A 120 " =    1.198
peak=    3.580 closest distance to " CG  MET A 185 " =    1.179
peak=    3.576 closest distance to " CB  ALA A 295 " =    1.259
peak=    3.575 closest distance to " CD1 ILE A 106 " =    1.127
peak=    3.563 closest distance to " CG  ARG A  66 " =    1.001
peak=    3.560 closest distance to " CE1 TYR A 186 " =    1.300
peak=    3.560 closest distance to " CA  ASN A 176 " =    1.066
peak=    3.559 closest distance to " O   HOH Z 118 " =    1.295
peak=    3.556 closest distance to " O   HOH Z 193 " =    1.903
peak=    3.553 closest distance to " O   HOH Z 406 " =    1.153
peak=    3.553 closest distance to " CG2 THR A 294 " =    1.536
peak=    3.547 closest distance to " CG2AVAL A 121 " =    2.253
peak=    3.545 closest distance to " O   HOH Z 222 " =    2.348
peak=    3.536 closest distance to " CG  GLN A  58 " =    2.775
peak=    3.533 closest distance to " CG AARG A 275 " =    1.150
peak=    3.520 closest distance to " O   HOH Z 273 " =    2.787
peak=    3.517 closest distance to " O   HOH Z 189 " =    2.571
peak=    3.515 closest distance to " O   HOH Z 329 " =    3.802
peak=    3.512 closest distance to " O   HOH Z   9 " =    2.148
peak=    3.510 closest distance to " CG  GLN A  77 " =    2.161
peak=    3.503 closest distance to " NH2BARG A 145 " =    1.956
peak=    3.501 closest distance to " CG1 ILE A  33 " =    1.277
peak=    3.499 closest distance to " O   HOH Z 187 " =    2.179
peak=    3.499 closest distance to " O   HOH Z 137 " =    1.552
peak=    3.496 closest distance to " CB  ARG A 190 " =    1.661
peak=    3.489 closest distance to " O   HOH Z 422 " =    2.507
peak=    3.468 closest distance to " O   HOH Z 236 " =    1.365
peak=    3.461 closest distance to " O   HOH Z 214 " =    2.467
peak=    3.460 closest distance to " CB  ALA A 248 " =    1.426
peak=    3.458 closest distance to " CD2 TYR A  30 " =    0.915
peak=    3.457 closest distance to " O   HOH Z 374 " =    2.518
peak=    3.451 closest distance to " O   HOH Z 389 " =    1.695
peak=    3.445 closest distance to " CD  GLN A 194 " =    1.404
peak=    3.443 closest distance to " O   HOH Z 412 " =    2.065
peak=    3.438 closest distance to " CA  ASN A 215 " =    1.119
peak=    3.437 closest distance to " CA  ALA A 158 " =    1.365
peak=    3.436 closest distance to " O   HOH Z 145 " =    2.131
peak=    3.432 closest distance to " CB  VAL A 268 " =    0.833
peak=    3.419 closest distance to " O   HOH Z  59 " =    2.066
peak=    3.419 closest distance to " O   HOH Z 175 " =    2.098
peak=    3.419 closest distance to " O   HOH Z   1 " =    4.651
peak=    3.419 closest distance to " CA  ARG A  36 " =    1.053
peak=    3.419 closest distance to " CG  LYS A  76 " =    1.712
peak=    3.413 closest distance to " O   HOH Z 209 " =    2.313
peak=    3.406 closest distance to " O   HOH Z 180 " =    2.196
peak=    3.402 closest distance to " O   HOH Z 102 " =    1.223
peak=    3.397 closest distance to " O   HOH Z 423 " =    2.957
peak=    3.395 closest distance to " CD  LYS A 166 " =    1.327
peak=    3.393 closest distance to " CE  LYS A 119 " =    1.065
peak=    3.390 closest distance to " O   HOH Z 421 " =    1.648
peak=    3.390 closest distance to " CG  PRO A 243 " =    1.193
peak=    3.389 closest distance to " CA  SER A 146 " =    1.899
peak=    3.388 closest distance to " CB  ALA A  10 " =    1.497
peak=    3.387 closest distance to " O   HOH Z 213 " =    1.711
peak=    3.384 closest distance to " ND2 ASN A 110 " =    1.624
peak=    3.381 closest distance to " O   HOH Z  40 " =    1.437
peak=    3.376 closest distance to " CA  ALA A 291 " =    0.868
peak=    3.368 closest distance to " O   HOH Z  39 " =    2.666
peak=    3.368 closest distance to " O   HOH Z 244 " =    1.569
peak=    3.367 closest distance to " CA  VAL A 126 " =    1.037
peak=    3.366 closest distance to " CG2 THR A 221 " =    1.158
peak=    3.362 closest distance to " CB  HIS A 108 " =    0.850
peak=    3.359 closest distance to " O   HOH Z   3 " =    1.689
peak=    3.352 closest distance to " OH  TYR A 116 " =    1.154
peak=    3.351 closest distance to " O   HOH Z 357 " =    1.812
peak=    3.351 closest distance to " CB  ASP A 140 " =    1.049
peak=    3.350 closest distance to " O   HOH Z 435 " =    1.950
peak=    3.350 closest distance to " CG  LYS A  76 " =    1.029
peak=    3.348 closest distance to " O   HOH Z 147 " =    1.647
peak=    3.347 closest distance to " CB  GLN A 278 " =    0.944
peak=    3.344 closest distance to " O   HOH Z 303 " =    1.553
peak=    3.340 closest distance to " N   ASP A 162 " =    1.233
peak=    3.331 closest distance to " O   HOH Z 337 " =    1.449
peak=    3.331 closest distance to " O   HOH Z 250 " =    1.473
peak=    3.331 closest distance to " CB  LEU A 255 " =    0.756
peak=    3.328 closest distance to " CG  ARG A  66 " =    3.132
peak=    3.324 closest distance to " O   HOH Z 433 " =    1.833
peak=    3.323 closest distance to " OG  SER A  62 " =    2.826
peak=    3.320 closest distance to " O   HOH Z 414 " =    1.381
peak=    3.316 closest distance to " CG2 ILE A 234 " =    1.008
peak=    3.314 closest distance to " O   HOH Z 438 " =    1.996
peak=    3.313 closest distance to " O   HOH Z 148 " =    3.323
peak=    3.313 closest distance to " O   HOH Z 392 " =    1.565
peak=    3.304 closest distance to " CG1 ILE A  49 " =    1.323
peak=    3.304 closest distance to " CD BLYS A 290 " =    1.220
peak=    3.303 closest distance to " O   HOH Z  71 " =    1.905
peak=    3.293 closest distance to " CA  LYS A 290 " =    1.271
peak=    3.291 closest distance to " CD  LYS A 119 " =    1.875
peak=    3.291 closest distance to " O   HOH Z 109 " =    2.294
peak=    3.287 closest distance to " O   HOH Z 352 " =    1.284
peak=    3.286 closest distance to " CD1 LEU A 228 " =    1.848
peak=    3.283 closest distance to " O   HOH Z 197 " =    2.157
peak=    3.282 closest distance to " O   HOH Z  49 " =    2.180
peak=    3.279 closest distance to " O   HOH Z 437 " =    1.887
peak=    3.277 closest distance to " CZ2 TRP A 179 " =    1.755
peak=    3.271 closest distance to " O   HOH Z 271 " =    1.565
peak=    3.270 closest distance to " O   HOH Z 112 " =    1.708
peak=    3.264 closest distance to " C   ALA A   1 " =    1.670
peak=    3.261 closest distance to " O   HOH Z  89 " =    1.607
peak=    3.260 closest distance to " CD2 LEU A 297 " =    1.002
peak=    3.259 closest distance to " O   HOH Z 408 " =    1.521
peak=    3.259 closest distance to " O   HOH Z 132 " =    2.351
peak=    3.258 closest distance to " CA  ASP A 140 " =    1.197
peak=    3.255 closest distance to " N   PHE A 130 " =    1.317
peak=    3.250 closest distance to " OG BSER A 258 " =    2.885
peak=    3.249 closest distance to " O   HOH Z  94 " =    1.879
peak=    3.249 closest distance to " O   HOH Z 280 " =    2.497
peak=    3.242 closest distance to " CB  ALA A 114 " =    1.459
peak=    3.241 closest distance to " NH1 ARG A 138 " =    1.231
peak=    3.235 closest distance to " O   HOH Z 227 " =    1.511
peak=    3.227 closest distance to " CA  ASP A 162 " =    1.084
peak=    3.225 closest distance to " O   HOH Z  35 " =    2.337
peak=    3.224 closest distance to " CD2 TYR A 186 " =    0.999
peak=    3.223 closest distance to " O   GLN A  58 " =    1.434
peak=    3.223 closest distance to " O   HOH Z 337 " =    3.406
peak=    3.216 closest distance to " C   ILE A 106 " =    1.917
peak=    3.215 closest distance to " O   HOH Z  21 " =    1.720
peak=    3.213 closest distance to " O   GLY A  91 " =    1.639
peak=    3.213 closest distance to " CG  GLN A  88 " =    1.023
peak=    3.213 closest distance to " O   HOH Z 255 " =    1.587
peak=    3.211 closest distance to " CG  LEU A 167 " =    1.207
peak=    3.210 closest distance to " O   HOH Z 388 " =    2.016
peak=    3.204 closest distance to " OD1 ASP A 231 " =    1.934
peak=    3.202 closest distance to " OD1 ASP A 286 " =    1.666
peak=    3.201 closest distance to " O   HOH Z 409 " =    3.591
peak=    3.200 closest distance to " O   HOH Z  59 " =    2.362
peak=    3.199 closest distance to " CG  GLN A  89 " =    1.511
peak=    3.196 closest distance to " O   HOH Z 367 " =    3.452
peak=    3.196 closest distance to " O   HOH Z 313 " =    1.875
peak=    3.189 closest distance to " O   HOH Z 128 " =    2.248
peak=    3.187 closest distance to " CB  SER A 216 " =    0.804
peak=    3.182 closest distance to " CB  LYS A 290 " =    1.168
peak=    3.180 closest distance to " O   HOH Z 326 " =    1.402
peak=    3.180 closest distance to " CB  ASN A 142 " =    1.129
peak=    3.178 closest distance to " O   GLN A 278 " =    1.111
peak=    3.178 closest distance to " O   HOH Z 380 " =    1.831
peak=    3.176 closest distance to " O   HOH Z 151 " =    1.714
peak=    3.174 closest distance to " CB  GLN A 205 " =    1.257
peak=    3.166 closest distance to " NH1 ARG A  66 " =    1.712
peak=    3.165 closest distance to " O   HOH Z 302 " =    1.837
peak=    3.154 closest distance to " NE2 GLN A  58 " =    5.959
peak=    3.153 closest distance to " O   HOH Z  80 " =    2.178
peak=    3.152 closest distance to " CB  ASN A 215 " =    1.062
peak=    3.151 closest distance to " CA  LEU A 101 " =    1.487
peak=    3.143 closest distance to " O   HOH Z  88 " =    2.440
peak=    3.140 closest distance to " N   VAL A 126 " =    1.186
peak=    3.139 closest distance to " O   HOH Z 344 " =    1.463
peak=    3.137 closest distance to " O   ASP A 124 " =    1.740
peak=    3.129 closest distance to " O   HOH Z 172 " =    3.552
peak=    3.128 closest distance to " O   HOH Z   1 " =    1.970
peak=    3.123 closest distance to " O   HOH Z 380 " =    2.007
peak=    3.115 closest distance to " O   HOH Z 365 " =    3.441
peak=    3.112 closest distance to " OD1 ASN A 148 " =    1.687
peak=    3.106 closest distance to " NE  ARG A  24 " =    0.936
peak=    3.103 closest distance to " CZ  PHE A 218 " =    1.072
peak=    3.103 closest distance to " CB  THR A  52 " =    1.046
peak=    3.102 closest distance to " CG  MET A 188 " =    1.320
peak=    3.097 closest distance to " N   TYR A 116 " =    1.662
peak=    3.096 closest distance to " CZ3 TRP A  85 " =    0.953
peak=    3.092 closest distance to " ND1 HIS A  81 " =    1.548
peak=    3.089 closest distance to " O   HOH Z 233 " =    1.576
peak=    3.089 closest distance to " O   HOH Z 188 " =    2.406
peak=    3.085 closest distance to " OE2 GLU A  53 " =    2.065
peak=    3.080 closest distance to " CB  SER A  62 " =    1.353
peak=    3.072 closest distance to " O   SER A 164 " =    1.201
peak=    3.071 closest distance to " O   HOH Z 361 " =    3.048
peak=    3.062 closest distance to " OD2 ASP A 286 " =    2.508
peak=    3.061 closest distance to " CB  ILE A  20 " =    1.523
peak=    3.055 closest distance to " O   HOH Z  28 " =    2.112
peak=    3.049 closest distance to " O   HOH Z 342 " =    0.842
peak=    3.046 closest distance to " N   SER A 135 " =    1.268
peak=    3.033 closest distance to " CB  TYR A  30 " =    1.065

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.773 - 5.823
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 197
   mapped sites are within: 0.773 - 5.823

peak=   -4.644 closest distance to " CD  ARG A 156 " =    2.082
peak=   -4.624 closest distance to " SG  CYS A 254 " =    3.191
peak=   -4.524 closest distance to " CG2 VAL A 230 " =    0.799
peak=   -4.436 closest distance to " O   HOH Z 266 " =    4.799
peak=   -4.413 closest distance to " OXT GLY A 302 " =    2.732
peak=   -4.372 closest distance to " CA  VAL A  67 " =    2.832
peak=   -4.287 closest distance to " CD1 LEU A 101 " =    2.352
peak=   -4.274 closest distance to " OG BSER A 134 " =    1.225
peak=   -4.201 closest distance to " C   HIS A 108 " =    1.229
peak=   -4.163 closest distance to " O   HOH Z 166 " =    1.444
peak=   -4.162 closest distance to " CG  GLN A 223 " =    2.009
peak=   -4.142 closest distance to " O   PRO A 163 " =    2.058
peak=   -4.088 closest distance to " CE2 TYR A  30 " =    2.746
peak=   -4.066 closest distance to " CB  ALA A 291 " =    2.410
peak=   -4.040 closest distance to " O   PHE A 218 " =    1.664
peak=   -3.988 closest distance to " CG2 VAL A 296 " =    1.424
peak=   -3.949 closest distance to " O   VAL A  67 " =    2.581
peak=   -3.898 closest distance to " CB  PRO A 163 " =    2.575
peak=   -3.897 closest distance to " CG  GLN A  58 " =    1.231
peak=   -3.884 closest distance to " C   GLN A 205 " =    1.881
peak=   -3.866 closest distance to " CB  PHE A 192 " =    1.926
peak=   -3.853 closest distance to " N   ALA A 248 " =    1.661
peak=   -3.852 closest distance to " O   HOH Z 290 " =    1.187
peak=   -3.851 closest distance to " CB  ALA A 161 " =    2.460
peak=   -3.850 closest distance to " OG  SER A  97 " =    2.243
peak=   -3.838 closest distance to " NE2 GLN A  88 " =    1.917
peak=   -3.826 closest distance to " O   HOH Z  37 " =    1.786
peak=   -3.818 closest distance to " CB  ASP A 132 " =    2.323
peak=   -3.818 closest distance to " O   HOH Z 429 " =    1.973
peak=   -3.807 closest distance to " N   GLN A  58 " =    1.728
peak=   -3.807 closest distance to " O   HOH Z 114 " =    3.066
peak=   -3.803 closest distance to " N   HIS A 115 " =    1.951
peak=   -3.784 closest distance to " O   ASN A  45 " =    1.882
peak=   -3.777 closest distance to " CD1 LEU A 255 " =    2.666
peak=   -3.765 closest distance to " O   ALA A   8 " =    1.823
peak=   -3.743 closest distance to " CE  MET A 105 " =    2.208
peak=   -3.728 closest distance to " O   HOH Z 362 " =    5.823
peak=   -3.723 closest distance to " CB  ALA A  43 " =    2.328
peak=   -3.715 closest distance to " OG  SER A   3 " =    1.451
peak=   -3.705 closest distance to " CG  PHE A 283 " =    2.679
peak=   -3.691 closest distance to " CD  ARG A 139 " =    1.584
peak=   -3.682 closest distance to " ND2 ASN A 187 " =    1.552
peak=   -3.675 closest distance to " O   HOH Z 423 " =    2.077
peak=   -3.674 closest distance to " OD1 ASN A  39 " =    2.098
peak=   -3.660 closest distance to " O   HOH Z 166 " =    1.972
peak=   -3.655 closest distance to " O   HOH Z 126 " =    1.868
peak=   -3.647 closest distance to " O   HOH Z 407 " =    2.855
peak=   -3.629 closest distance to " CA  GLY A  23 " =    1.780
peak=   -3.622 closest distance to " O   ASN A 187 " =    1.508
peak=   -3.614 closest distance to " CG  ASP A 231 " =    0.820
peak=   -3.611 closest distance to " O   ALA A 161 " =    1.650
peak=   -3.611 closest distance to " O   HOH Z 102 " =    1.721
peak=   -3.605 closest distance to " OG ASER A 134 " =    1.218
peak=   -3.599 closest distance to " ND2 ASN A  39 " =    1.152
peak=   -3.598 closest distance to " CA  ASP A 298 " =    1.060
peak=   -3.596 closest distance to " CG  GLU A   2 " =    1.969
peak=   -3.588 closest distance to " NH2 ARG A  79 " =    1.930
peak=   -3.585 closest distance to " N   ALA A 226 " =    1.948
peak=   -3.584 closest distance to " OD1 ASP A 191 " =    1.425
peak=   -3.576 closest distance to " CZ  TYR A 169 " =    1.783
peak=   -3.574 closest distance to " O   HOH Z 231 " =    2.213
peak=   -3.566 closest distance to " NE2 GLN A  88 " =    1.179
peak=   -3.565 closest distance to " O   HOH Z 165 " =    1.963
peak=   -3.553 closest distance to " O   HOH Z 351 " =    1.517
peak=   -3.547 closest distance to " CB  ASP A 132 " =    2.242
peak=   -3.545 closest distance to " O   HOH Z 193 " =    1.570
peak=   -3.545 closest distance to " O   HOH Z 131 " =    4.032
peak=   -3.544 closest distance to " O   ALA A  51 " =    1.171
peak=   -3.534 closest distance to " CD2 LEU A 300 " =    2.892
peak=   -3.533 closest distance to " O   HOH Z 191 " =    5.278
peak=   -3.532 closest distance to " O   HOH Z  56 " =    2.351
peak=   -3.531 closest distance to " CD  LYS A 289 " =    2.429
peak=   -3.529 closest distance to " O   ALA A 256 " =    1.537
peak=   -3.528 closest distance to " O   HOH Z  13 " =    1.693
peak=   -3.528 closest distance to " OG BSER A 134 " =    1.603
peak=   -3.525 closest distance to " O   HOH Z 389 " =    1.809
peak=   -3.521 closest distance to " O   HOH Z 211 " =    1.516
peak=   -3.521 closest distance to " ND2 ASN A  45 " =    1.099
peak=   -3.519 closest distance to " CE2 PHE A 218 " =    2.582
peak=   -3.515 closest distance to " O   HOH Z  11 " =    1.785
peak=   -3.511 closest distance to " O   PRO A 198 " =    1.262
peak=   -3.510 closest distance to " OD2 ASP A  50 " =    1.311
peak=   -3.493 closest distance to " CD1 PHE A  59 " =    2.087
peak=   -3.490 closest distance to " CB  PRO A 280 " =    2.128
peak=   -3.487 closest distance to " CD1 ILE A 263 " =    2.720
peak=   -3.476 closest distance to " CG  LEU A 228 " =    1.144
peak=   -3.469 closest distance to " O   HOH Z 427 " =    1.519
peak=   -3.467 closest distance to " CA  GLY A 133 " =    1.883
peak=   -3.458 closest distance to " O   HOH Z 372 " =    2.352
peak=   -3.457 closest distance to " O   GLY A  80 " =    2.446
peak=   -3.456 closest distance to " O   MET A  40 " =    2.719
peak=   -3.454 closest distance to " CE BMET A  47 " =    1.351
peak=   -3.444 closest distance to " N   SER A 276 " =    1.290
peak=   -3.443 closest distance to " CG1 VAL A 112 " =    2.660
peak=   -3.437 closest distance to " CB  ALA A 248 " =    2.285
peak=   -3.430 closest distance to " OD1 ASN A 301 " =    1.896
peak=   -3.417 closest distance to " CG2 THR A 178 " =    2.196
peak=   -3.415 closest distance to " OXT GLY A 302 " =    3.486
peak=   -3.411 closest distance to " C   SER A 206 " =    1.615
peak=   -3.395 closest distance to " CG2 VAL A 230 " =    1.105
peak=   -3.394 closest distance to " O   HOH Z 385 " =    2.021
peak=   -3.394 closest distance to " O   HOH Z 295 " =    1.522
peak=   -3.390 closest distance to " O   HOH Z  15 " =    1.499
peak=   -3.389 closest distance to " O   HOH Z 185 " =    2.326
peak=   -3.380 closest distance to " NH2AARG A 275 " =    4.887
peak=   -3.378 closest distance to " O   HOH Z 353 " =    2.181
peak=   -3.377 closest distance to " O   HOH Z 426 " =    1.655
peak=   -3.377 closest distance to " O   HOH Z  97 " =    1.221
peak=   -3.376 closest distance to " CD1 PHE A  59 " =    1.955
peak=   -3.372 closest distance to " C   ALA A 158 " =    1.263
peak=   -3.368 closest distance to " CD1 TYR A 247 " =    2.410
peak=   -3.365 closest distance to " CB  ASN A  39 " =    2.143
peak=   -3.362 closest distance to " O   VAL A 174 " =    2.036
peak=   -3.359 closest distance to " OD2 ASP A 191 " =    1.457
peak=   -3.354 closest distance to " CB  ALA A 131 " =    2.009
peak=   -3.347 closest distance to " O   HOH Z 389 " =    4.834
peak=   -3.343 closest distance to " O   HOH Z 139 " =    5.084
peak=   -3.341 closest distance to " N   THR A 157 " =    1.448
peak=   -3.340 closest distance to " CG  GLU A 152 " =    1.416
peak=   -3.337 closest distance to " O   TRP A  92 " =    1.712
peak=   -3.333 closest distance to " CD2 TYR A 293 " =    2.032
peak=   -3.332 closest distance to " O   SER A 210 " =    1.837
peak=   -3.330 closest distance to " O   HOH Z 198 " =    2.068
peak=   -3.328 closest distance to " O   HOH Z 234 " =    3.881
peak=   -3.327 closest distance to " CG1 VAL A 125 " =    2.344
peak=   -3.325 closest distance to " O   HOH Z  17 " =    1.542
peak=   -3.324 closest distance to " C   LEU A 143 " =    1.014
peak=   -3.319 closest distance to " OG  SER A  62 " =    1.378
peak=   -3.315 closest distance to " CZ3 TRP A 179 " =    1.353
peak=   -3.312 closest distance to " NE2 GLN A 194 " =    1.751
peak=   -3.311 closest distance to " NH1 ARG A 195 " =    2.564
peak=   -3.310 closest distance to " O   HOH Z  11 " =    2.011
peak=   -3.309 closest distance to " C   GLY A  91 " =    1.350
peak=   -3.307 closest distance to " O   HOH Z 166 " =    2.200
peak=   -3.306 closest distance to " O   HOH Z 137 " =    1.466
peak=   -3.300 closest distance to " O   HOH Z  60 " =    1.991
peak=   -3.295 closest distance to " O   HOH Z 174 " =    4.263
peak=   -3.294 closest distance to " N   LYS A 289 " =    1.594
peak=   -3.286 closest distance to " CB  PRO A 243 " =    2.613
peak=   -3.282 closest distance to " O   HOH Z 431 " =    1.769
peak=   -3.278 closest distance to " O   HOH Z 250 " =    1.393
peak=   -3.277 closest distance to " O   HOH Z 339 " =    1.765
peak=   -3.276 closest distance to " O   HOH Z 193 " =    1.817
peak=   -3.275 closest distance to " O   HOH Z 139 " =    3.280
peak=   -3.273 closest distance to " OD2 ASP A 171 " =    2.314
peak=   -3.273 closest distance to " OG  SER A  87 " =    1.338
peak=   -3.271 closest distance to " CG2 ILE A 263 " =    2.232
peak=   -3.261 closest distance to " O   HOH Z 134 " =    2.774
peak=   -3.261 closest distance to " CD1 LEU A 228 " =    1.929
peak=   -3.260 closest distance to " O   HOH Z 313 " =    1.788
peak=   -3.258 closest distance to " CG  GLU A  53 " =    1.712
peak=   -3.254 closest distance to " N   GLN A 122 " =    1.368
peak=   -3.253 closest distance to " O   SER A  22 " =    2.244
peak=   -3.253 closest distance to " O   PRO A 198 " =    1.327
peak=   -3.251 closest distance to " C   ASP A 231 " =    2.547
peak=   -3.249 closest distance to " CB  ALA A 291 " =    2.101
peak=   -3.249 closest distance to " O   HOH Z 407 " =    3.295
peak=   -3.248 closest distance to " O   HOH Z  47 " =    1.599
peak=   -3.244 closest distance to " CA  GLY A 203 " =    2.411
peak=   -3.242 closest distance to " CA  GLY A 241 " =    2.342
peak=   -3.227 closest distance to " CG1 VAL A  78 " =    2.684
peak=   -3.227 closest distance to " O   HOH Z  90 " =    2.603
peak=   -3.225 closest distance to " SG ACYS A 201 " =    2.085
peak=   -3.221 closest distance to " CB  ASP A 286 " =    2.333
peak=   -3.215 closest distance to " CG  ASP A  50 " =    2.256
peak=   -3.215 closest distance to " OG1 THR A 178 " =    1.265
peak=   -3.212 closest distance to " CG  TRP A 266 " =    2.035
peak=   -3.210 closest distance to " OD1 ASN A 249 " =    1.752
peak=   -3.206 closest distance to " CD2 LEU A 237 " =    2.696
peak=   -3.205 closest distance to " C   MET A 188 " =    1.479
peak=   -3.200 closest distance to " CE3 TRP A 150 " =    1.953
peak=   -3.191 closest distance to " O   VAL A 197 " =    1.332
peak=   -3.190 closest distance to " O   SER A 273 " =    1.354
peak=   -3.181 closest distance to " CB  ALA A  64 " =    2.597
peak=   -3.176 closest distance to " CB  SER A 210 " =    1.307
peak=   -3.170 closest distance to " OD1 ASP A 200 " =    1.396
peak=   -3.170 closest distance to " O   ALA A 100 " =    2.438
peak=   -3.158 closest distance to " O   HOH Z 113 " =    1.931
peak=   -3.151 closest distance to " O   HOH Z 411 " =    3.830
peak=   -3.150 closest distance to " CG1 VAL A 112 " =    2.820
peak=   -3.144 closest distance to " O   HOH Z 281 " =    2.946
peak=   -3.139 closest distance to " OD1 ASN A 176 " =    1.274
peak=   -3.135 closest distance to " CZ  ARG A 259 " =    0.895
peak=   -3.132 closest distance to " NH2 ARG A  66 " =    1.848
peak=   -3.128 closest distance to " CG  ARG A 219 " =    2.729
peak=   -3.115 closest distance to " O   HOH Z 407 " =    2.969
peak=   -3.113 closest distance to " O   HOH Z   6 " =    1.701
peak=   -3.111 closest distance to " CD  GLN A 223 " =    0.773
peak=   -3.101 closest distance to " O   HOH Z 307 " =    1.880
peak=   -3.087 closest distance to " O   ASN A 301 " =    1.431
peak=   -3.080 closest distance to " O   HOH Z 197 " =    5.009
peak=   -3.077 closest distance to " NE2 GLN A  58 " =    2.546
peak=   -3.070 closest distance to " O   GLY A  75 " =    1.707
peak=   -3.069 closest distance to " O   HOH Z 301 " =    2.306
peak=   -3.054 closest distance to " CD1 ILE A 239 " =    2.585
peak=   -3.027 closest distance to " CG1 VAL A 268 " =    2.457
peak=   -3.027 closest distance to " CA  ASP A  27 " =    2.306

================= 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    :  0.4539 0.4465   6.251716e+00   6.241447e+00
   1_bss:  0.4446 0.4393   6.243012e+00   6.230323e+00
   1_xyz:  0.3487 0.3712   6.081823e+00   6.128286e+00
   1_adp:  0.2893 0.3284   5.939494e+00   6.043439e+00
   1_occ:  0.2889 0.3278   5.938267e+00   6.042963e+00
   2_bss:  0.2850 0.3222   5.936592e+00   6.039039e+00
   2_xyz:  0.2008 0.2407   5.629215e+00   5.788226e+00
   2_adp:  0.1798 0.2208   5.536121e+00   5.709260e+00
   2_occ:  0.1795 0.2202   5.534880e+00   5.707637e+00
   3_bss:  0.1778 0.2194   5.530927e+00   5.704075e+00
   3_xyz:  0.1336 0.1729   5.275875e+00   5.479569e+00
   3_adp:  0.1268 0.1648   5.225419e+00   5.428527e+00
   3_occ:  0.1266 0.1648   5.224824e+00   5.428169e+00
   4_bss:  0.1268 0.1643   5.225018e+00   5.426079e+00
   4_xyz:  0.1195 0.1584   5.181660e+00   5.391049e+00
   4_adp:  0.1193 0.1581   5.180146e+00   5.389687e+00
   4_occ:  0.1192 0.1582   5.179917e+00   5.389705e+00
   5_bss:  0.1192 0.1581   5.179175e+00   5.389018e+00
   5_xyz:  0.1105 0.1550   5.128974e+00   5.366086e+00
   5_adp:  0.1076 0.1560   5.120892e+00   5.371344e+00
   5_occ:  0.1076 0.1559   5.120712e+00   5.371069e+00
   5_bss:  0.1075 0.1559   5.120411e+00   5.370814e+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:  0.374  20.001   8.330   7.825   8.171   0.000   0.000   0.000
   1_xyz:  0.374  20.001   8.330   7.825   8.171   0.000   0.000   0.000
   1_adp:  0.374  20.001   8.330   7.825   8.171   0.000   0.000   0.000
   1_occ:  0.374  20.001   8.330   7.825   8.171   0.000   0.000   0.000
   2_bss:  0.342  31.719   4.784   4.172   5.233   0.000   0.000   0.000
   2_xyz:  0.342  31.719   4.784   4.172   5.233   0.000   0.000   0.000
   2_adp:  0.342  31.719   4.784   4.172   5.233   0.000   0.000   0.000
   2_occ:  0.342  31.719   4.784   4.172   5.233   0.000   0.000   0.000
   3_bss:  0.327  31.719   2.677   3.148   3.962   0.000   0.000   0.000
   3_xyz:  0.327  31.719   2.677   3.148   3.962   0.000   0.000   0.000
   3_adp:  0.327  31.719   2.677   3.148   3.962   0.000   0.000   0.000
   3_occ:  0.327  31.719   2.677   3.148   3.962   0.000   0.000   0.000
   4_bss:  0.327  31.719   1.995   2.749   3.500   0.000   0.000   0.000
   4_xyz:  0.327  31.719   1.995   2.749   3.500   0.000   0.000   0.000
   4_adp:  0.327  31.719   1.995   2.749   3.500   0.000   0.000   0.000
   4_occ:  0.327  31.719   1.995   2.749   3.500   0.000   0.000   0.000
   5_bss:  0.325  34.802   1.858   2.633   3.391   0.000   0.000   0.000
   5_xyz:  0.325  34.802   1.858   2.633   3.391   0.000   0.000   0.000
   5_adp:  0.325  34.802   1.858   2.633   3.391   0.000   0.000   0.000
   5_occ:  0.325  34.802   1.858   2.633   3.391   0.000   0.000   0.000
   5_bss:  0.322  39.879  -0.779   0.003   0.776   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.650 0.5015  0.5792    60409.006
   1_bss:  52.162 0.4926  0.7259    57930.510
   1_xyz:  41.251 0.6268  0.9037    39024.336
   1_adp:  34.324 0.7099  1.0203    29571.483
   1_occ:  34.240 0.7109  1.0203    29454.094
   2_bss:  33.876 0.7148  0.9065    28870.343
   2_xyz:  24.002 0.8213  1.0052    14985.341
   2_adp:  21.300 0.8496  1.0313    12608.492
   2_occ:  21.255 0.8500  1.0311    12547.377
   3_bss:  21.140 0.8510  0.9761    12398.240
   3_xyz:  16.050 0.8975  1.0007     7624.441
   3_adp:  14.916 0.9076  1.0054     6981.102
   3_occ:  14.904 0.9077  1.0053     6974.210
   4_bss:  14.869 0.9079  0.9863     6931.813
   4_xyz:  14.080 0.9147  0.9890     6405.314
   4_adp:  14.051 0.9150  0.9907     6396.005
   4_occ:  14.050 0.9150  0.9905     6395.635
   5_bss:  14.034 0.9151  0.9863     6384.908
   5_xyz:  13.664 0.9176  0.9870     6107.197
   5_adp:  13.768 0.9170  0.9818     6150.271
   5_occ:  13.764 0.9170  0.9818     6147.528
   5_bss:  13.757 0.9171  0.9866     6143.063
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3069e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3069e+01
   1_xyz:   1.628  0.013  0.106 17.937  0.006  4.106   1.3245e-01
   1_adp:   1.628  0.013  0.106 17.937  0.006  4.106   1.3245e-01
   1_occ:   1.628  0.013  0.106 17.937  0.006  4.106   1.3245e-01
   2_bss:   1.628  0.013  0.106 17.937  0.006  4.106   1.3245e-01
   2_xyz:   0.999  0.006  0.075 15.830  0.004  4.116   6.2925e-02
   2_adp:   0.999  0.006  0.075 15.830  0.004  4.116   6.2925e-02
   2_occ:   0.999  0.006  0.075 15.830  0.004  4.116   6.2925e-02
   3_bss:   0.999  0.006  0.075 15.830  0.004  4.116   6.2925e-02
   3_xyz:   1.018  0.006  0.076 15.677  0.003  4.108   6.0817e-02
   3_adp:   1.018  0.006  0.076 15.677  0.003  4.108   6.0817e-02
   3_occ:   1.018  0.006  0.076 15.677  0.003  4.108   6.0817e-02
   4_bss:   1.018  0.006  0.076 15.677  0.003  4.108   6.0817e-02
   4_xyz:   0.898  0.005  0.069 15.329  0.003  4.108   5.1140e-02
   4_adp:   0.898  0.005  0.069 15.329  0.003  4.108   5.1140e-02
   4_occ:   0.898  0.005  0.069 15.329  0.003  4.108   5.1140e-02
   5_bss:   0.898  0.005  0.069 15.329  0.003  4.108   5.1140e-02
   5_xyz:   1.174  0.008  0.091 15.808  0.005  4.109   7.6829e-02
   5_adp:   1.174  0.008  0.091 15.808  0.005  4.109   7.6829e-02
   5_occ:   1.174  0.008  0.091 15.808  0.005  4.109   7.6829e-02
   5_bss:   1.174  0.008  0.091 15.808  0.005  4.109   7.6829e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.130   6.8747e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.130   6.8747e+00
   1_xyz:  14.558  0.159  0.489 86.574  0.043  2.257   9.5804e-02
   1_adp:  14.558  0.159  0.489 86.574  0.043  2.257   9.5804e-02
   1_occ:  14.558  0.159  0.489 86.574  0.043  2.257   9.5804e-02
   2_bss:  14.558  0.159  0.489 86.574  0.043  2.257   9.5804e-02
   2_xyz:   6.250  0.060  0.310 83.054  0.029  2.345   4.6636e-02
   2_adp:   6.250  0.060  0.310 83.054  0.029  2.345   4.6636e-02
   2_occ:   6.250  0.060  0.310 83.054  0.029  2.345   4.6636e-02
   3_bss:   6.250  0.060  0.310 83.054  0.029  2.345   4.6636e-02
   3_xyz:   7.277  0.041  0.475 84.218  0.033  2.302   4.4725e-02
   3_adp:   7.277  0.041  0.475 84.218  0.033  2.302   4.4725e-02
   3_occ:   7.277  0.041  0.475 84.218  0.033  2.302   4.4725e-02
   4_bss:   7.277  0.041  0.475 84.218  0.033  2.302   4.4725e-02
   4_xyz:   5.892  0.033  0.363 82.297  0.031  2.382   2.8234e-02
   4_adp:   5.892  0.033  0.363 82.297  0.031  2.382   2.8234e-02
   4_occ:   5.892  0.033  0.363 82.297  0.031  2.382   2.8234e-02
   5_bss:   5.892  0.033  0.363 82.297  0.031  2.382   2.8234e-02
   5_xyz:   7.279  0.048  0.667 83.227  0.038  2.246   5.8390e-02
   5_adp:   7.279  0.048  0.667 83.227  0.038  2.246   5.8390e-02
   5_occ:   7.279  0.048  0.667 83.227  0.038  2.246   5.8390e-02
   5_bss:   7.279  0.048  0.667 83.227  0.038  2.246   5.8390e-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:  74.82   0.00  11.68  70.01   0.00   8.71  74.82   0.00  27.83
   1_occ:  74.82   0.00  11.68  70.01   0.00   8.71  74.82   0.00  27.83
   2_bss:  74.82   0.00  11.68  70.01   0.00   8.71  74.82   0.00  27.83
   2_xyz:  74.82   0.00  11.68  70.01   0.00   8.71  74.82   0.00  27.83
   2_adp:  77.74   0.00  11.98  77.74   0.00   8.25  74.98   1.16  32.26
   2_occ:  77.74   0.00  11.98  77.74   0.00   8.25  74.98   1.16  32.26
   3_bss:  77.74   0.00  11.98  77.74   0.00   8.25  74.98   1.16  32.26
   3_xyz:  77.74   0.00  11.98  77.74   0.00   8.25  74.98   1.16  32.26
   3_adp:  79.85   0.00  11.88  79.85   0.00   7.98  68.88   1.90  33.09
   3_occ:  79.85   0.00  11.88  79.85   0.00   7.98  68.88   1.90  33.09
   4_bss:  79.85   0.00  11.88  79.85   0.00   7.98  68.88   1.90  33.09
   4_xyz:  79.85   0.00  11.88  79.85   0.00   7.98  68.88   1.90  33.09
   4_adp:  79.86   0.00  11.91  79.86   0.00   8.02  68.84   1.68  33.09
   4_occ:  79.86   0.00  11.91  79.86   0.00   8.02  68.84   1.68  33.09
   5_bss:  79.86   0.00  11.91  79.86   0.00   8.02  68.84   1.68  33.09
   5_xyz:  79.86   0.00  11.91  79.86   0.00   8.02  68.84   1.68  33.09
   5_adp:  85.81   0.00  12.23  85.81   0.00   8.05  70.59   1.32  35.05
   5_occ:  85.81   0.00  12.23  85.81   0.00   8.05  70.59   1.32  35.05
   5_bss:  88.56   2.76  14.99  88.56   2.76  10.80  73.35   4.08  37.81
------------------------------------------------------------------------
 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:    1.218    0.012    0.410
   1_adp:    1.218    0.012    0.410
   1_occ:    1.218    0.012    0.410
   2_bss:    1.218    0.012    0.410
   2_xyz:    1.568    0.024    0.533
   2_adp:    1.568    0.024    0.533
   2_occ:    1.568    0.024    0.533
   3_bss:    1.568    0.024    0.533
   3_xyz:    1.520    0.043    0.585
   3_adp:    1.520    0.043    0.585
   3_occ:    1.520    0.043    0.585
   4_bss:    1.520    0.043    0.585
   4_xyz:    1.626    0.041    0.605
   4_adp:    1.626    0.041    0.605
   4_occ:    1.626    0.041    0.605
   5_bss:    1.626    0.041    0.605
   5_xyz:    1.547    0.038    0.617
   5_adp:    1.547    0.038    0.617
   5_occ:    1.547    0.038    0.617
   5_bss:    1.547    0.038    0.617
------------------------------------------------------------------------

CPU time actual refinement: 335.56


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_179/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_179/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_179/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_179/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_179/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.40 
  Macro-tasks:
    bulk solvent and scale       = 40.57  
    individual site refinement   = 139.76 
    weights calculation          = 32.24  
    collect and process          = 6.56   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 219.25 
  Micro-tasks:
    mask                            = 1.89   
    f_calc                          = 103.66 
    alpha_beta                      = 8.28   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 113.86 
    fmodel                         = 7.36   
    r_factors                      = 0.29   
    phase_errors                   = 10.49  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 247.29 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.702 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    647 calls, 103.34 s
gradients_fft:          591 calls, 100.27 s

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

# Date 2008-01-16 Time 00:57:24 PST -0800 (1200473844.06 s)
Start R-work = 0.4539, R-free = 0.4465 (no bulk solvent and anisotropic scale)
Final R-work = 0.1257, R-free = 0.1718 (no bulk solvent and anisotropic scale)

Start R-work = 0.4446, R-free = 0.4393
Final R-work = 0.1075, R-free = 0.1559