# Date 2008-01-16 Time 01:16:17 PST -0800 (1200474977.34 s)
#phil __OFF__

Command line arguments: "../359.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25798
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 359

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 48.1033, 87.2539, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0501 1.97083
Completeness in resolution range: 0.92545
Completeness with d_max=infinity: 0.92266

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0501
                             d_min =   1.9708

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0501 1.97083
Completeness in resolution range: 0.92545
Completeness with d_max=infinity: 0.92266

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0505 -  4.2178 [2219/2247]  1992   227  10.2%
  bin  2:  4.2178 -  3.3600 [2130/2153]  1916   214  10.0%
  bin  3:  3.3600 -  2.9389 [2100/2125]  1897   203   9.7%
  bin  4:  2.9389 -  2.6718 [2092/2109]  1880   212  10.1%
  bin  5:  2.6718 -  2.4812 [2049/2092]  1842   207  10.1%
  bin  6:  2.4812 -  2.3355 [2070/2098]  1867   203   9.8%
  bin  7:  2.3355 -  2.2189 [2049/2085]  1847   202   9.9%
  bin  8:  2.2189 -  2.1226 [2050/2092]  1845   205  10.0%
  bin  9:  2.1226 -  2.0411 [2010/2070]  1809   201  10.0%
  bin 10:  2.0411 -  1.9708 [ 820/2096]   735    85  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_359/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:
        1.46 -     2.15: 9
        2.15 -     2.83: 982
        2.83 -     3.52: 4389
        3.52 -     4.21: 9213
        4.21 -     4.90: 13487
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.457 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.538 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.680 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.739 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28075 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_359/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_359/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 48.10325 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5117   r_free= 0.4959   ksol= 0.00   Bsol= 0.00   scale= 0.764    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.309327                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.7046 0.99   1441  160 0.4227 0.4401      6.6533      6.6977|
|  2:  4.7046 -  3.7533 0.99   1400  154 0.4528 0.4653      6.8657      6.9029|
|  3:  3.7533 -  3.2845 0.99   1350  151 0.4888 0.4570      6.7186      6.6965|
|  4:  3.2845 -  2.9867 0.99   1351  145 0.5120 0.4736      6.5502      6.5075|
|  5:  2.9867 -  2.7741 0.99   1336  152 0.5514 0.5345      6.3889      6.4185|
|  6:  2.7741 -  2.6114 0.99   1359  151 0.5421 0.5026       6.295      6.1861|
|  7:  2.6114 -  2.4812 0.98   1290  150 0.5215 0.5038      6.2389      6.1813|
|  8:  2.4812 -  2.3737 0.98   1332  137 0.5356 0.4716       6.184      6.1873|
|  9:  2.3737 -  2.2826 0.99   1343  150 0.5496 0.5762      6.1217       6.172|
| 10:  2.2826 -  2.2041 0.98   1322  144 0.5620 0.5370      6.1068       6.107|
| 11:  2.2041 -  2.1354 0.97   1297  147 0.5659 0.5622       6.036      6.0493|
| 12:  2.1354 -  2.0745 0.99   1304  155 0.5359 0.5045      5.9492       5.952|
| 13:  2.0745 -  2.0200 0.88   1179  122 0.5396 0.5621      5.8683      5.8449|
| 14:  2.0200 -  1.9708 0.24    326   41 0.6015 0.4187      5.9479      5.7192|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0505 -  4.7046  1441   160  0.62  41.34   0.78     0.63      96339.68|
|  2:  4.7046 -  3.7533  1400   154  0.62  42.29   0.85     0.67     136905.26|
|  3:  3.7533 -  3.2845  1350   151  0.51  51.12   0.79     0.63     140896.57|
|  4:  3.2845 -  2.9867  1351   145  0.43  57.28   0.76     0.53     115810.66|
|  5:  2.9867 -  2.7741  1336   152  0.35  63.56   0.70     0.44      91543.81|
|  6:  2.7741 -  2.6114  1359   151  0.34  64.32   0.70     0.40      75633.35|
|  7:  2.6114 -  2.4812  1290   150  0.31  66.80   0.72     0.36      70489.75|
|  8:  2.4812 -  2.3737  1332   137  0.30  67.95   0.71     0.34      62921.45|
|  9:  2.3737 -  2.2826  1343   150  0.25  71.30   0.69     0.31      62816.04|
| 10:  2.2826 -  2.2041  1322   144  0.25  71.00   0.71     0.31      54690.02|
| 11:  2.2041 -  2.1354  1297   147  0.25  71.32   0.72     0.33      52699.58|
| 12:  2.1354 -  2.0745  1304   155  0.27  69.93   0.74     0.36      46215.51|
| 13:  2.0745 -  2.0200  1179   122  0.27  70.06   0.70     0.35      39781.12|
| 14:  2.0200 -  1.9708   326    41  0.29  68.54   0.72     0.30      29427.62|
|alpha:            min =        0.30 max =            0.67 mean =         0.44|
|beta:             min =    29427.62 max =       140896.57 mean =     80474.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.96|
|phase err.(test): min =        0.00 max =           89.78 mean =        62.09|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.754005             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.482   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.874525              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.164   (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 |  1.136 -  1.513:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.513 -  1.889:       15 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.889 -  2.265:      152 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.265 -  2.642:      624 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.642 -  3.018:     1438 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.018 -  3.395:     2538 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.395 -  3.771:     3926 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.771 -  4.147:     5075 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.147 -  4.524:     6580 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.524 -  4.900:     7782 |
|-----------------------------------------------------------------------------|
|-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 |       54.030 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.136 |       2.091 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.013)------------------------------------------|
|    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 = 12.013)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5161   r_free= 0.4991   ksol= 0.00   Bsol= 0.00   scale= 0.736    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.309823                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5051   r_free= 0.4930   ksol= 0.33   Bsol= 20.00   scale= 0.956   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.12,11.80,8.12,0.00,0.00,0.00); trace/3= 8.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.303932                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.531584             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.870   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.782607              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.367   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5051      final r-factor (work) = 0.4432          |
| start r-factor (free) = 0.4930      final r-factor (free) = 0.4526          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 115.6157 = 19.53 * 0.50 * 6.3063 + 1.00 * 54.0299                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 61.2546 = 19.53 * 0.50 * 6.2568 + 1.00 * 0.1517                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4432      final r-factor (work) = 0.4025          |
| start r-factor (free) = 0.4526      final r-factor (free) = 0.4555          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1682 = 1.78 * 1.00 * 6.2568 + 1.00 * 0.0147                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0821 = 1.78 * 1.00 * 6.2034 + 1.00 * 0.0238                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.013)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.36  16.98    None  None   None       |
|    all(noH): 2823   0      0.00    114.36  16.98    None  None   None       |
|    Sol.    : 438    0      0.00    114.36  27.24    None  None   None       |
|    Mac.    : 2385   0      0.00    78.81   15.09    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 -  11.436: 1218   |   5:    57.182 -  68.618:   32        |
|      1:    11.436 -  22.873:  863   |   6:    68.618 -  80.054:   12        |
|      2:    22.873 -  34.309:  403   |   7:    80.054 -  91.491:    2        |
|      3:    34.309 -  45.745:  218   |   8:    91.491 - 102.927:    2        |
|      4:    45.745 -  57.182:   71   |   9:   102.927 - 114.363:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4025 r_free = 0.4555             target_work(ml) = 6.195         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4020 r_free = 0.4556             target_work(ml) = 6.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4020   r_free= 0.4556   ksol= 0.33   Bsol= 20.00   scale= 1.112   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.12,11.80,8.12,0.00,0.00,0.00); trace/3= 8.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.194496                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3994   r_free= 0.4507   ksol= 0.29   Bsol= 20.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.21,6.59,4.14,0.00,0.00,0.00); trace/3= 4.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.196330                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.388391             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.185  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.622315              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.059  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3994      final r-factor (work) = 0.3357          |
| start r-factor (free) = 0.4507      final r-factor (free) = 0.4028          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.7449 = 14.39 * 0.50 * 6.1985 + 1.00 * 0.1515                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.1718 = 14.39 * 0.50 * 6.1242 + 1.00 * 0.1132                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3357      final r-factor (work) = 0.3224          |
| start r-factor (free) = 0.4028      final r-factor (free) = 0.3930          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8347 = 0.62 * 1.00 * 6.1242 + 1.00 * 0.0235                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7879 = 0.62 * 1.00 * 6.0686 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.013)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.55  15.57    None  None   None       |
|    all(noH): 2823   0      0.00    100.55  15.57    None  None   None       |
|    Sol.    : 438    0      0.00    100.55  27.85    None  None   None       |
|    Mac.    : 2385   0      0.00    75.48   13.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.055: 1148   |   5:    50.276 -  60.332:   24        |
|      1:    10.055 -  20.111:  905   |   6:    60.332 -  70.387:   17        |
|      2:    20.111 -  30.166:  438   |   7:    70.387 -  80.442:    2        |
|      3:    30.166 -  40.221:  213   |   8:    80.442 -  90.498:    3        |
|      4:    40.221 -  50.276:   71   |   9:    90.498 - 100.553:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3224 r_free = 0.3930             target_work(ml) = 6.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3222 r_free = 0.3929             target_work(ml) = 6.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3222   r_free= 0.3929   ksol= 0.29   Bsol= 20.00   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.21,6.59,4.14,0.00,0.00,0.00); trace/3= 4.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.055275                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3216   r_free= 0.3910   ksol= 0.32   Bsol= 47.94   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.03,4.60,2.73,0.00,0.00,0.00); trace/3= 2.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.054800                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.517873              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.337  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.350617              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.250  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3216      final r-factor (work) = 0.2651          |
| start r-factor (free) = 0.3910      final r-factor (free) = 0.3205          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9255 = 7.52 * 0.50 * 6.0688 + 1.00 * 0.1132                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.5852 = 7.52 * 0.50 * 5.9844 + 1.00 * 0.0904                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2651      final r-factor (work) = 0.2487          |
| start r-factor (free) = 0.3205      final r-factor (free) = 0.3026          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1093 = 0.35 * 1.00 * 5.9844 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0647 = 0.35 * 1.00 * 5.8600 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.013)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.10   15.09    None  None   None       |
|    all(noH): 2823   0      0.00    92.10   15.09    None  None   None       |
|    Sol.    : 438    0      1.54    92.10   31.56    None  None   None       |
|    Mac.    : 2385   0      0.00    70.88   12.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.210: 1182   |   5:    46.051 -  55.261:   55        |
|      1:     9.210 -  18.420:  850   |   6:    55.261 -  64.471:   16        |
|      2:    18.420 -  27.630:  378   |   7:    64.471 -  73.681:    8        |
|      3:    27.630 -  36.841:  200   |   8:    73.681 -  82.891:    3        |
|      4:    36.841 -  46.051:  129   |   9:    82.891 -  92.101:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2487 r_free = 0.3026             target_work(ml) = 5.839         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2486 r_free = 0.3027             target_work(ml) = 5.838         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2486   r_free= 0.3027   ksol= 0.32   Bsol= 47.94   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.03,4.60,2.73,0.00,0.00,0.00); trace/3= 2.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.838356                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2476   r_free= 0.3032   ksol= 0.32   Bsol= 47.94   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.31,2.76,1.66,0.00,0.00,0.00); trace/3= 1.37                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.838243                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.866273              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.689   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.619157              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.988  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2476      final r-factor (work) = 0.1903          |
| start r-factor (free) = 0.3032      final r-factor (free) = 0.2336          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3528 = 4.87 * 0.50 * 5.8618 + 1.00 * 0.0904                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0323 = 4.87 * 0.50 * 5.7325 + 1.00 * 0.0845                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1903      final r-factor (work) = 0.1711          |
| start r-factor (free) = 0.2336      final r-factor (free) = 0.2158          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5588 = 0.62 * 1.00 * 5.7325 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4376 = 0.62 * 1.00 * 5.5313 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.013)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.43   15.93    None  None   None       |
|    all(noH): 2823   0      0.00    88.43   15.93    None  None   None       |
|    Sol.    : 438    0      3.06    86.61   40.15    None  None   None       |
|    Mac.    : 2385   0      0.00    88.43   11.48    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 -   8.843: 1205   |   5:    44.216 -  53.059:  100        |
|      1:     8.843 -  17.686:  875   |   6:    53.059 -  61.902:   79        |
|      2:    17.686 -  26.529:  250   |   7:    61.902 -  70.745:   39        |
|      3:    26.529 -  35.373:  141   |   8:    70.745 -  79.588:   18        |
|      4:    35.373 -  44.216:  110   |   9:    79.588 -  88.431:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1711 r_free = 0.2158             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1709 r_free = 0.2163             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1709   r_free= 0.2163   ksol= 0.32   Bsol= 47.94   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.31,2.76,1.66,0.00,0.00,0.00); trace/3= 1.37                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.500797                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1708   r_free= 0.2165   ksol= 0.32   Bsol= 59.96   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,1.51,1.42,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.501595                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.689683              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.813   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.219146              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.385  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1708      final r-factor (work) = 0.1417          |
| start r-factor (free) = 0.2165      final r-factor (free) = 0.1891          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2930 = 3.69 * 0.50 * 5.5336 + 1.00 * 0.0845                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0801 = 3.69 * 0.50 * 5.4209 + 1.00 * 0.0794                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1417      final r-factor (work) = 0.1369          |
| start r-factor (free) = 0.1891      final r-factor (free) = 0.1814          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2007 = 0.22 * 1.00 * 5.4209 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1796 = 0.22 * 1.00 * 5.3362 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.013)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.56    88.93   15.40    None  None   None       |
|    all(noH): 2823   0      0.56    88.93   15.40    None  None   None       |
|    Sol.    : 438    0      3.24    84.52   39.37    None  None   None       |
|    Mac.    : 2385   0      0.56    88.93   10.99    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:     0.562 -   9.398: 1335   |   5:    44.745 -  53.582:   94        |
|      1:     9.398 -  18.235:  857   |   6:    53.582 -  62.419:   70        |
|      2:    18.235 -  27.072:  191   |   7:    62.419 -  71.255:   36        |
|      3:    27.072 -  35.908:  118   |   8:    71.255 -  80.092:   10        |
|      4:    35.908 -  44.745:  107   |   9:    80.092 -  88.929:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1369 r_free = 0.1814             target_work(ml) = 5.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1368 r_free = 0.1814             target_work(ml) = 5.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1368   r_free= 0.1814   ksol= 0.32   Bsol= 59.96   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,1.51,1.42,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.312027                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.7046 0.99   1441  160 0.1021 0.1422      5.4435       5.648|
|  2:  4.7046 -  3.7533 0.99   1400  154 0.0964 0.1189      5.5436      5.7408|
|  3:  3.7533 -  3.2845 0.99   1350  151 0.1310 0.1847       5.641       5.996|
|  4:  3.2845 -  2.9867 0.99   1351  145 0.1513 0.1892      5.6247      5.7699|
|  5:  2.9867 -  2.7741 0.99   1336  152 0.1688 0.1844      5.5169      5.6311|
|  6:  2.7741 -  2.6114 0.99   1359  151 0.1565 0.2381      5.3954      5.6364|
|  7:  2.6114 -  2.4812 0.98   1290  150 0.1572 0.1891      5.3402      5.5047|
|  8:  2.4812 -  2.3737 0.98   1332  137 0.1505 0.1919        5.26      5.4329|
|  9:  2.3737 -  2.2826 0.99   1343  150 0.1502 0.2221      5.1848      5.4551|
| 10:  2.2826 -  2.2041 0.98   1322  144 0.1423 0.2076      5.1264      5.3365|
| 11:  2.2041 -  2.1354 0.97   1297  147 0.1383 0.2030      5.0618      5.3371|
| 12:  2.1354 -  2.0745 0.99   1304  155 0.1454 0.1822      5.0283      5.2202|
| 13:  2.0745 -  2.0200 0.88   1179  122 0.1406 0.2049      4.9202      5.1631|
| 14:  2.0200 -  1.9708 0.24    326   41 0.1244 0.1723      4.8159       4.944|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0505 -  4.7046  1441   160  0.93  10.37   0.97     0.94       8616.53|
|  2:  4.7046 -  3.7533  1400   154  0.94   9.82   1.02     1.01      11483.49|
|  3:  3.7533 -  3.2845  1350   151  0.91  14.08   1.02     1.01      13933.30|
|  4:  3.2845 -  2.9867  1351   145  0.89  17.07   1.01     1.01      14282.87|
|  5:  2.9867 -  2.7741  1336   152  0.87  19.70   1.01     0.98      12035.94|
|  6:  2.7741 -  2.6114  1359   151  0.86  20.26   0.98     0.94      10061.23|
|  7:  2.6114 -  2.4812  1290   150  0.88  18.88   1.00     0.94       8206.48|
|  8:  2.4812 -  2.3737  1332   137  0.87  19.07   1.01     0.98       7650.01|
|  9:  2.3737 -  2.2826  1343   150  0.88  19.01   1.01     0.97       6628.34|
| 10:  2.2826 -  2.2041  1322   144  0.86  19.97   1.01     0.97       6214.75|
| 11:  2.2041 -  2.1354  1297   147  0.88  18.78   1.01     0.96       5605.61|
| 12:  2.1354 -  2.0745  1304   155  0.88  19.06   1.01     1.00       5068.61|
| 13:  2.0745 -  2.0200  1179   122  0.88  18.66   1.00     0.98       4186.03|
| 14:  2.0200 -  1.9708   326    41  0.89  16.79   0.97     0.92       3194.47|
|alpha:            min =        0.92 max =            1.01 mean =         0.98|
|beta:             min =     3194.47 max =        14282.87 mean =      8740.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.19|
|phase err.(test): min =        0.00 max =           89.34 mean =        16.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1371   r_free= 0.1820   ksol= 0.33   Bsol= 60.41   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,0.50,0.86,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.313705                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1371   r_free= 0.1820   ksol= 0.33   Bsol= 60.41   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,0.50,0.86,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.313705                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.7046 0.99   1441  160 0.1047 0.1452      5.4577      5.6574|
|  2:  4.7046 -  3.7533 0.99   1400  154 0.0973 0.1188      5.5516      5.7481|
|  3:  3.7533 -  3.2845 0.99   1350  151 0.1315 0.1842      5.6448      5.9913|
|  4:  3.2845 -  2.9867 0.99   1351  145 0.1516 0.1900      5.6258      5.7707|
|  5:  2.9867 -  2.7741 0.99   1336  152 0.1690 0.1848      5.5176      5.6305|
|  6:  2.7741 -  2.6114 0.99   1359  151 0.1563 0.2385      5.3941      5.6371|
|  7:  2.6114 -  2.4812 0.98   1290  150 0.1571 0.1893      5.3397      5.5035|
|  8:  2.4812 -  2.3737 0.98   1332  137 0.1501 0.1912      5.2588      5.4317|
|  9:  2.3737 -  2.2826 0.99   1343  150 0.1500 0.2219      5.1835      5.4535|
| 10:  2.2826 -  2.2041 0.98   1322  144 0.1419 0.2078      5.1245       5.338|
| 11:  2.2041 -  2.1354 0.97   1297  147 0.1380 0.2030       5.061      5.3357|
| 12:  2.1354 -  2.0745 0.99   1304  155 0.1456 0.1825       5.029      5.2201|
| 13:  2.0745 -  2.0200 0.88   1179  122 0.1408 0.2038      4.9195      5.1608|
| 14:  2.0200 -  1.9708 0.24    326   41 0.1243 0.1714      4.8147      4.9426|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0505 -  4.7046  1441   160  0.93  10.56   0.96     0.94       8804.55|
|  2:  4.7046 -  3.7533  1400   154  0.94   9.91   1.01     1.01      11654.64|
|  3:  3.7533 -  3.2845  1350   151  0.91  14.17   1.02     1.01      14097.32|
|  4:  3.2845 -  2.9867  1351   145  0.89  17.07   1.01     1.00      14267.74|
|  5:  2.9867 -  2.7741  1336   152  0.87  19.69   1.00     0.97      12032.03|
|  6:  2.7741 -  2.6114  1359   151  0.86  20.24   0.97     0.93      10057.47|
|  7:  2.6114 -  2.4812  1290   150  0.88  18.88   0.98     0.93       8209.73|
|  8:  2.4812 -  2.3737  1332   137  0.87  19.04   1.00     0.97       7634.27|
|  9:  2.3737 -  2.2826  1343   150  0.88  18.97   0.99     0.95       6613.37|
| 10:  2.2826 -  2.2041  1322   144  0.86  19.94   1.00     0.96       6200.84|
| 11:  2.2041 -  2.1354  1297   147  0.88  18.77   0.99     0.95       5602.44|
| 12:  2.1354 -  2.0745  1304   155  0.88  19.03   0.99     0.99       5064.74|
| 13:  2.0745 -  2.0200  1179   122  0.88  18.62   0.98     0.97       4166.48|
| 14:  2.0200 -  1.9708   326    41  0.89  16.74   0.96     0.91       3171.57|
|alpha:            min =        0.91 max =            1.01 mean =         0.97|
|beta:             min =     3171.57 max =        14267.74 mean =      8775.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.20|
|phase err.(test): min =        0.00 max =           89.91 mean =        16.59|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.013)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    89.38   15.85    None  None   None       |
|    all(noH): 2823   0      1.01    89.38   15.85    None  None   None       |
|    Sol.    : 438    0      3.69    84.97   39.82    None  None   None       |
|    Mac.    : 2385   0      1.01    89.38   11.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.010 -   9.847: 1335   |   5:    45.194 -  54.031:   94        |
|      1:     9.847 -  18.684:  857   |   6:    54.031 -  62.867:   70        |
|      2:    18.684 -  27.521:  191   |   7:    62.867 -  71.704:   36        |
|      3:    27.521 -  36.357:  118   |   8:    71.704 -  80.541:   10        |
|      4:    36.357 -  45.194:  107   |   9:    80.541 -  89.378:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 331         
Filter by distance & map next to the model:
   mapped sites are within: 0.637 - 5.093
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 331
   mapped sites are within: 0.713 - 5.093

peak=    8.203 closest distance to " CB  VAL A 230 " =    1.468
peak=    7.616 closest distance to " O   HOH Z 396 " =    1.507
peak=    7.532 closest distance to " O   HOH Z 400 " =    1.157
peak=    7.297 closest distance to " O   GLN A  11 " =    1.112
peak=    6.519 closest distance to " O   HOH Z 120 " =    1.429
peak=    6.507 closest distance to " CG1 ILE A 234 " =    1.451
peak=    6.026 closest distance to " O   HOH Z 404 " =    1.610
peak=    5.874 closest distance to " OD1 ASN A 301 " =    1.093
peak=    5.653 closest distance to " O   HOH Z 403 " =    2.076
peak=    5.592 closest distance to " O   HOH Z 210 " =    1.677
peak=    5.326 closest distance to " O   HOH Z 248 " =    1.643
peak=    5.272 closest distance to " O   HOH Z  46 " =    1.214
peak=    5.214 closest distance to " CG  LEU A   5 " =    1.449
peak=    5.137 closest distance to " NH2 ARG A 156 " =    1.213
peak=    5.126 closest distance to " O   HOH Z  44 " =    1.715
peak=    5.051 closest distance to " O   HOH Z 124 " =    1.650
peak=    5.032 closest distance to " O   HOH Z 126 " =    1.693
peak=    4.872 closest distance to " O   HOH Z 154 " =    1.896
peak=    4.814 closest distance to " CG1 VAL A 296 " =    1.210
peak=    4.761 closest distance to " O   HOH Z 102 " =    1.652
peak=    4.760 closest distance to " CB  SER A  63 " =    1.170
peak=    4.714 closest distance to " O   HOH Z 128 " =    1.937
peak=    4.713 closest distance to " CB  VAL A 296 " =    1.480
peak=    4.702 closest distance to " O   HOH Z 117 " =    1.190
peak=    4.692 closest distance to " O   HOH Z 415 " =    1.229
peak=    4.647 closest distance to " O   HOH Z 146 " =    1.649
peak=    4.632 closest distance to " O   HOH Z 412 " =    3.320
peak=    4.627 closest distance to " NE2 GLN A  11 " =    1.042
peak=    4.617 closest distance to " NH2 ARG A  56 " =    2.252
peak=    4.596 closest distance to " O   HOH Z 142 " =    2.534
peak=    4.540 closest distance to " CD2 TRP A 179 " =    1.252
peak=    4.538 closest distance to " OE1 GLN A  55 " =    1.555
peak=    4.526 closest distance to " O   HOH Z 425 " =    1.607
peak=    4.523 closest distance to " CD  ARG A  36 " =    1.136
peak=    4.480 closest distance to " CB  ARG A 275 " =    0.851
peak=    4.471 closest distance to " CG  PRO A 280 " =    0.860
peak=    4.464 closest distance to " O   HOH Z 422 " =    0.940
peak=    4.460 closest distance to " O   HOH Z  53 " =    1.240
peak=    4.454 closest distance to " CB  ASN A 285 " =    0.978
peak=    4.421 closest distance to " O   HOH Z  54 " =    1.269
peak=    4.417 closest distance to " CB  GLU A 175 " =    1.270
peak=    4.368 closest distance to " O   HOH Z 193 " =    1.791
peak=    4.356 closest distance to " CD2 LEU A 228 " =    1.243
peak=    4.313 closest distance to " ND2 ASN A 249 " =    2.222
peak=    4.311 closest distance to " O   HOH Z 130 " =    2.446
peak=    4.276 closest distance to " NZ  LYS A  76 " =    0.992
peak=    4.273 closest distance to " N   SER A 164 " =    0.996
peak=    4.259 closest distance to " CB  VAL A 230 " =    1.239
peak=    4.258 closest distance to " OE1 GLN A  11 " =    2.130
peak=    4.228 closest distance to " O   HOH Z  80 " =    2.337
peak=    4.212 closest distance to " CG  PRO A  54 " =    1.294
peak=    4.159 closest distance to " CG  GLN A  77 " =    0.823
peak=    4.146 closest distance to " O   HOH Z 431 " =    1.715
peak=    4.140 closest distance to " O   HOH Z  43 " =    2.070
peak=    4.140 closest distance to " O   HOH Z 234 " =    3.495
peak=    4.132 closest distance to " CB  ALA A 299 " =    1.196
peak=    4.114 closest distance to " O   HOH Z 357 " =    2.114
peak=    4.114 closest distance to " O   HOH Z 183 " =    1.842
peak=    4.108 closest distance to " OE1 GLU A   2 " =    1.328
peak=    4.102 closest distance to " O   HOH Z 394 " =    1.808
peak=    4.100 closest distance to " CB  TRP A 179 " =    1.253
peak=    4.100 closest distance to " NE  ARG A  36 " =    1.160
peak=    4.097 closest distance to " CD  LYS A 166 " =    1.658
peak=    4.091 closest distance to " CB  THR A  31 " =    1.382
peak=    4.084 closest distance to " O   HOH Z 426 " =    1.196
peak=    4.082 closest distance to " O   HOH Z 402 " =    1.507
peak=    4.076 closest distance to " CA  SER A  12 " =    1.315
peak=    4.068 closest distance to " CE  LYS A 119 " =    1.306
peak=    4.063 closest distance to " CA  VAL A  41 " =    0.919
peak=    4.045 closest distance to " CG AARG A 275 " =    1.200
peak=    4.029 closest distance to " CB  GLN A 183 " =    1.198
peak=    4.027 closest distance to " O   HOH Z  49 " =    1.520
peak=    3.988 closest distance to " CD  GLN A 194 " =    1.646
peak=    3.983 closest distance to " O   HOH Z 327 " =    1.658
peak=    3.980 closest distance to " O   HOH Z 414 " =    2.514
peak=    3.951 closest distance to " CB  GLN A 223 " =    1.521
peak=    3.945 closest distance to " O   HOH Z  85 " =    1.667
peak=    3.942 closest distance to " CA  TYR A  30 " =    0.941
peak=    3.937 closest distance to " O   HOH Z 130 " =    1.168
peak=    3.927 closest distance to " CA  ALA A 100 " =    1.288
peak=    3.926 closest distance to " O   ASP A 124 " =    1.638
peak=    3.915 closest distance to " O   HOH Z  40 " =    2.010
peak=    3.891 closest distance to " O   ASP A 200 " =    1.581
peak=    3.890 closest distance to " CB  ASN A 148 " =    1.240
peak=    3.889 closest distance to " O   HOH Z 433 " =    2.030
peak=    3.872 closest distance to " CE1 HIS A 108 " =    1.199
peak=    3.861 closest distance to " CG  PRO A 243 " =    1.194
peak=    3.855 closest distance to " O   HOH Z 134 " =    2.315
peak=    3.829 closest distance to " NE1 TRP A  92 " =    1.387
peak=    3.824 closest distance to " CB  ASN A 187 " =    1.201
peak=    3.810 closest distance to " O   HOH Z 427 " =    2.779
peak=    3.808 closest distance to " O   HOH Z 108 " =    1.300
peak=    3.784 closest distance to " O   HOH Z 126 " =    2.259
peak=    3.760 closest distance to " CG  ARG A  66 " =    1.001
peak=    3.749 closest distance to " CG1 ILE A 120 " =    1.107
peak=    3.742 closest distance to " CG2AVAL A  72 " =    1.835
peak=    3.742 closest distance to " NH1AARG A 145 " =    1.228
peak=    3.742 closest distance to " O   HOH Z 144 " =    1.728
peak=    3.734 closest distance to " O   HOH Z 111 " =    1.822
peak=    3.730 closest distance to " N   ALA A   1 " =    1.462
peak=    3.725 closest distance to " N   THR A  42 " =    1.470
peak=    3.718 closest distance to " CA  ALA A  51 " =    1.078
peak=    3.715 closest distance to " O   HOH Z 277 " =    1.329
peak=    3.715 closest distance to " CB  VAL A 202 " =    1.315
peak=    3.712 closest distance to " CA  ARG A 195 " =    1.222
peak=    3.712 closest distance to " OG  SER A  62 " =    2.660
peak=    3.711 closest distance to " N   ASN A  39 " =    1.319
peak=    3.710 closest distance to " CG  ARG A  36 " =    1.067
peak=    3.709 closest distance to " NH1 ARG A  36 " =    1.236
peak=    3.702 closest distance to " CB  SER A  62 " =    0.999
peak=    3.701 closest distance to " CD  GLN A  73 " =    1.274
peak=    3.700 closest distance to " O   HOH Z 139 " =    1.188
peak=    3.699 closest distance to " O   HOH Z 227 " =    1.747
peak=    3.695 closest distance to " CB BVAL A  41 " =    1.112
peak=    3.695 closest distance to " O   HOH Z  76 " =    1.131
peak=    3.694 closest distance to " O   HOH Z 369 " =    1.569
peak=    3.691 closest distance to " O   HOH Z  44 " =    2.440
peak=    3.671 closest distance to " CB  ASN A  45 " =    1.198
peak=    3.669 closest distance to " O   HOH Z 247 " =    1.383
peak=    3.665 closest distance to " O   ARG A  14 " =    1.576
peak=    3.665 closest distance to " O   HOH Z 418 " =    3.072
peak=    3.658 closest distance to " O   HOH Z 209 " =    2.480
peak=    3.657 closest distance to " CB  SER A 141 " =    1.048
peak=    3.657 closest distance to " CG  LEU A 228 " =    1.311
peak=    3.656 closest distance to " CA  TRP A  85 " =    1.126
peak=    3.654 closest distance to " CB  SER A  26 " =    1.690
peak=    3.654 closest distance to " CG2 THR A 220 " =    0.820
peak=    3.647 closest distance to " O   HOH Z 142 " =    1.720
peak=    3.646 closest distance to " CG AARG A 275 " =    1.270
peak=    3.639 closest distance to " CD  PRO A  54 " =    0.974
peak=    3.636 closest distance to " OD2 ASP A 298 " =    0.885
peak=    3.630 closest distance to " CB  GLU A 152 " =    1.238
peak=    3.627 closest distance to " CG2 VAL A 197 " =    1.213
peak=    3.621 closest distance to " O   HOH Z 272 " =    2.017
peak=    3.617 closest distance to " O   HOH Z 158 " =    1.312
peak=    3.613 closest distance to " O   HOH Z 421 " =    2.035
peak=    3.608 closest distance to " O   HOH Z  78 " =    1.699
peak=    3.605 closest distance to " O   ALA A 165 " =    1.258
peak=    3.603 closest distance to " O   HOH Z 423 " =    1.848
peak=    3.598 closest distance to " CB  TRP A 150 " =    1.459
peak=    3.598 closest distance to " CA  ASP A 191 " =    1.073
peak=    3.596 closest distance to " CB  PRO A  54 " =    0.876
peak=    3.591 closest distance to " O   HOH Z 368 " =    3.087
peak=    3.575 closest distance to " O   HOH Z 236 " =    1.656
peak=    3.572 closest distance to " N   GLU A  44 " =    1.405
peak=    3.572 closest distance to " O   HOH Z 418 " =    1.572
peak=    3.560 closest distance to " O   HOH Z 131 " =    2.455
peak=    3.557 closest distance to " CG1 ILE A  20 " =    1.350
peak=    3.549 closest distance to " O   GLU A   2 " =    1.702
peak=    3.547 closest distance to " O   HOH Z  39 " =    1.592
peak=    3.543 closest distance to " O   HOH Z 279 " =    1.196
peak=    3.538 closest distance to " O   SER A  87 " =    2.289
peak=    3.535 closest distance to " O   HOH Z 298 " =    5.093
peak=    3.531 closest distance to " CG2 VAL A 296 " =    1.024
peak=    3.527 closest distance to " CB  PRO A 243 " =    1.105
peak=    3.526 closest distance to " O   PRO A 198 " =    1.524
peak=    3.523 closest distance to " O   HOH Z 155 " =    3.028
peak=    3.522 closest distance to " CB  PRO A 198 " =    1.071
peak=    3.521 closest distance to " ND2 ASN A 301 " =    0.971
peak=    3.519 closest distance to " NH2AARG A 145 " =    1.053
peak=    3.516 closest distance to " O   HOH Z 152 " =    2.319
peak=    3.509 closest distance to " O   HOH Z 255 " =    1.471
peak=    3.506 closest distance to " O   HOH Z 339 " =    1.538
peak=    3.499 closest distance to " CG  PRO A 198 " =    1.306
peak=    3.497 closest distance to " CB  MET A  40 " =    0.904
peak=    3.481 closest distance to " CB  MET A 105 " =    1.068
peak=    3.481 closest distance to " O   HOH Z 438 " =    3.173
peak=    3.480 closest distance to " CA  ARG A  66 " =    0.929
peak=    3.478 closest distance to " O   HOH Z  88 " =    3.075
peak=    3.477 closest distance to " CZ  PHE A 218 " =    1.173
peak=    3.472 closest distance to " O   HOH Z  61 " =    1.450
peak=    3.472 closest distance to " CB  THR A 235 " =    1.196
peak=    3.469 closest distance to " O   HOH Z 435 " =    1.887
peak=    3.467 closest distance to " CB  GLU A 277 " =    0.999
peak=    3.463 closest distance to " CD2 TRP A 179 " =    2.426
peak=    3.461 closest distance to " O   HOH Z 196 " =    1.387
peak=    3.459 closest distance to " OG  SER A  62 " =    3.111
peak=    3.452 closest distance to " CG1 ILE A  33 " =    1.306
peak=    3.446 closest distance to " CB  TRP A 179 " =    1.739
peak=    3.443 closest distance to " O   HOH Z  38 " =    1.466
peak=    3.441 closest distance to " O   HOH Z 250 " =    1.208
peak=    3.441 closest distance to " NE2 HIS A 115 " =    1.111
peak=    3.437 closest distance to " O   VAL A  72 " =    1.244
peak=    3.436 closest distance to " OG  SER A 245 " =    1.481
peak=    3.435 closest distance to " CB  ARG A  79 " =    0.861
peak=    3.431 closest distance to " O   HOH Z  59 " =    2.046
peak=    3.425 closest distance to " O   HOH Z 370 " =    1.117
peak=    3.421 closest distance to " O   HOH Z 409 " =    3.435
peak=    3.420 closest distance to " CB  VAL A 126 " =    0.883
peak=    3.420 closest distance to " O   HOH Z 214 " =    1.434
peak=    3.418 closest distance to " CG  ARG A  66 " =    1.374
peak=    3.414 closest distance to " O   HOH Z 301 " =    1.972
peak=    3.408 closest distance to " NE2 HIS A 108 " =    0.810
peak=    3.407 closest distance to " O   HOH Z 289 " =    1.654
peak=    3.403 closest distance to " CD2 LEU A 297 " =    0.895
peak=    3.402 closest distance to " O   HOH Z 280 " =    3.121
peak=    3.398 closest distance to " O   HOH Z 402 " =    1.133
peak=    3.395 closest distance to " CB  GLN A  73 " =    1.282
peak=    3.393 closest distance to " CB  SER A 146 " =    1.006
peak=    3.388 closest distance to " CB  GLN A  88 " =    1.328
peak=    3.386 closest distance to " CZ3 TRP A 266 " =    1.070
peak=    3.384 closest distance to " O   HOH Z 141 " =    1.653
peak=    3.382 closest distance to " CB  GLN A  73 " =    1.406
peak=    3.373 closest distance to " O   HOH Z   7 " =    1.098
peak=    3.369 closest distance to " O   HOH Z 263 " =    1.359
peak=    3.367 closest distance to " O   HOH Z  63 " =    2.141
peak=    3.366 closest distance to " NH1 ARG A  14 " =    1.139
peak=    3.362 closest distance to " CZ2 TRP A 274 " =    1.100
peak=    3.358 closest distance to " OG  SER A  97 " =    3.192
peak=    3.353 closest distance to " O   HOH Z 147 " =    1.684
peak=    3.352 closest distance to " O  BHOH Z 338 " =    2.427
peak=    3.341 closest distance to " O   HOH Z 332 " =    1.675
peak=    3.341 closest distance to " CA  ILE A 120 " =    1.210
peak=    3.341 closest distance to " CG2 ILE A  20 " =    1.417
peak=    3.341 closest distance to " O   HOH Z 136 " =    1.334
peak=    3.336 closest distance to " CB  PHE A  16 " =    1.228
peak=    3.336 closest distance to " N   ASP A 298 " =    1.032
peak=    3.335 closest distance to " CD  ARG A 159 " =    0.822
peak=    3.335 closest distance to " O   HOH Z 383 " =    2.117
peak=    3.334 closest distance to " O   HOH Z 361 " =    2.700
peak=    3.333 closest distance to " CG2 VAL A 126 " =    1.101
peak=    3.329 closest distance to " O   HOH Z  68 " =    2.076
peak=    3.329 closest distance to " CG1BVAL A 121 " =    1.371
peak=    3.321 closest distance to " O   HOH Z 132 " =    2.152
peak=    3.319 closest distance to " O   HOH Z  48 " =    1.748
peak=    3.319 closest distance to " CB  ALA A 100 " =    1.245
peak=    3.319 closest distance to " CB  ARG A 269 " =    1.854
peak=    3.318 closest distance to " CB  VAL A 265 " =    1.313
peak=    3.317 closest distance to " CZ  PHE A  38 " =    1.128
peak=    3.314 closest distance to " O   HOH Z 267 " =    1.167
peak=    3.312 closest distance to " CE1 TYR A  30 " =    1.092
peak=    3.312 closest distance to " O   HOH Z 132 " =    2.834
peak=    3.312 closest distance to " CB  PHE A 283 " =    0.969
peak=    3.311 closest distance to " CD1 TRP A 274 " =    1.221
peak=    3.303 closest distance to " O   HOH Z 139 " =    4.550
peak=    3.299 closest distance to " CZ3 TRP A  85 " =    0.926
peak=    3.293 closest distance to " N   ASP A 162 " =    2.242
peak=    3.288 closest distance to " O   HOH Z 371 " =    3.043
peak=    3.284 closest distance to " OD1 ASN A  60 " =    0.966
peak=    3.278 closest distance to " CD  ARG A  24 " =    1.141
peak=    3.277 closest distance to " O   HOH Z 265 " =    1.782
peak=    3.274 closest distance to " O   HOH Z 291 " =    1.456
peak=    3.273 closest distance to " CE3 TRP A  85 " =    1.253
peak=    3.273 closest distance to " CB  ARG A  79 " =    1.101
peak=    3.267 closest distance to " NH2BARG A 190 " =    1.800
peak=    3.266 closest distance to " O   HOH Z 358 " =    2.259
peak=    3.264 closest distance to " O   HOH Z 238 " =    1.706
peak=    3.261 closest distance to " C   ALA A 299 " =    0.869
peak=    3.261 closest distance to " O   HOH Z 322 " =    2.320
peak=    3.260 closest distance to " O   HOH Z  80 " =    3.145
peak=    3.256 closest distance to " CA  ILE A 106 " =    0.770
peak=    3.253 closest distance to " NH2 ARG A  36 " =    1.794
peak=    3.251 closest distance to " O   PRO A 213 " =    1.367
peak=    3.251 closest distance to " CG2 THR A 221 " =    1.229
peak=    3.250 closest distance to " CB  GLN A  58 " =    1.155
peak=    3.250 closest distance to " O   HOH Z 344 " =    3.074
peak=    3.250 closest distance to " CA  ASP A 149 " =    1.169
peak=    3.250 closest distance to " O   HOH Z 214 " =    2.397
peak=    3.250 closest distance to " CG  MET A 185 " =    1.202
peak=    3.248 closest distance to " O   HOH Z 365 " =    2.164
peak=    3.246 closest distance to " CG  ARG A 219 " =    1.402
peak=    3.246 closest distance to " NZ  LYS A  48 " =    1.132
peak=    3.242 closest distance to " CG1 VAL A 153 " =    1.050
peak=    3.241 closest distance to " O   HOH Z 380 " =    1.950
peak=    3.240 closest distance to " CD  LYS A 119 " =    2.023
peak=    3.240 closest distance to " CA  LEU A  83 " =    1.433
peak=    3.238 closest distance to " CA  ALA A 295 " =    0.982
peak=    3.235 closest distance to " CA  CYS A 260 " =    1.433
peak=    3.235 closest distance to " O   HOH Z 116 " =    2.603
peak=    3.233 closest distance to " CA  THR A 294 " =    2.081
peak=    3.233 closest distance to " O   HOH Z  15 " =    2.244
peak=    3.230 closest distance to " CG2 ILE A  33 " =    1.243
peak=    3.227 closest distance to " O   HOH Z 359 " =    1.489
peak=    3.225 closest distance to " CD ALYS A 290 " =    1.076
peak=    3.225 closest distance to " CZ2 TRP A 150 " =    1.078
peak=    3.223 closest distance to " CB  GLU A  46 " =    1.126
peak=    3.222 closest distance to " CG  PRO A 213 " =    1.240
peak=    3.220 closest distance to " CB  GLU A 236 " =    1.204
peak=    3.217 closest distance to " N   ASP A 162 " =    1.213
peak=    3.217 closest distance to " CD  ARG A 195 " =    1.156
peak=    3.214 closest distance to " CA  GLY A 196 " =    0.713
peak=    3.212 closest distance to " CG2 THR A  29 " =    1.435
peak=    3.209 closest distance to " CB  PHE A 155 " =    0.945
peak=    3.209 closest distance to " O   HOH Z 271 " =    1.561
peak=    3.208 closest distance to " O   HOH Z 232 " =    2.283
peak=    3.205 closest distance to " CB  ARG A 190 " =    1.942
peak=    3.202 closest distance to " O   HOH Z 150 " =    2.094
peak=    3.202 closest distance to " O   HOH Z 188 " =    4.775
peak=    3.201 closest distance to " O   HOH Z  47 " =    1.367
peak=    3.200 closest distance to " N   ARG A 102 " =    2.030
peak=    3.198 closest distance to " CD1 LEU A   5 " =    1.520
peak=    3.196 closest distance to " CD  LYS A  76 " =    1.851
peak=    3.193 closest distance to " OH  TYR A 116 " =    1.207
peak=    3.193 closest distance to " CB  TRP A 266 " =    1.075
peak=    3.188 closest distance to " CB  SER A  97 " =    1.507
peak=    3.187 closest distance to " CA  ALA A 248 " =    1.207
peak=    3.187 closest distance to " CG2 VAL A 268 " =    1.191
peak=    3.179 closest distance to " N   ASP A 286 " =    0.894
peak=    3.178 closest distance to " O   HOH Z 251 " =    1.375
peak=    3.175 closest distance to " CE1 TYR A 186 " =    1.357
peak=    3.168 closest distance to " O   GLY A  23 " =    2.417
peak=    3.166 closest distance to " CG  LYS A  76 " =    1.061
peak=    3.161 closest distance to " CD1 LEU A 222 " =    0.903
peak=    3.159 closest distance to " O   THR A 220 " =    1.037
peak=    3.159 closest distance to " O   HOH Z 285 " =    1.722
peak=    3.157 closest distance to " CB  LYS A 289 " =    1.186
peak=    3.155 closest distance to " O   HOH Z  77 " =    1.456
peak=    3.148 closest distance to " O   HOH Z 316 " =    2.923
peak=    3.148 closest distance to " CB  SER A  62 " =    3.771
peak=    3.132 closest distance to " NZ  LYS A 117 " =    2.660
peak=    3.132 closest distance to " CB  LYS A 119 " =    1.250
peak=    3.129 closest distance to " CG2 THR A 294 " =    1.346
peak=    3.128 closest distance to " CG2 THR A  42 " =    0.810
peak=    3.128 closest distance to " OG BSER A 164 " =    1.956
peak=    3.126 closest distance to " CG  LEU A 167 " =    1.110
peak=    3.122 closest distance to " CG2 ILE A 234 " =    1.279
peak=    3.120 closest distance to " O   HOH Z 152 " =    1.835
peak=    3.109 closest distance to " O   HOH Z  57 " =    2.171
peak=    3.108 closest distance to " ND2 ASN A 249 " =    0.909
peak=    3.087 closest distance to " CB  PHE A 225 " =    0.931
peak=    3.077 closest distance to " O   HOH Z 331 " =    1.153
peak=    3.075 closest distance to " CB  ALA A 242 " =    1.022
peak=    3.072 closest distance to " CG  PHE A 204 " =    1.032
peak=    3.069 closest distance to " O   HOH Z 345 " =    2.831
peak=    3.060 closest distance to " CA  ASP A 162 " =    1.071
peak=    3.059 closest distance to " O   HOH Z 371 " =    2.688
peak=    3.057 closest distance to " CB  PRO A  90 " =    1.210
peak=    3.054 closest distance to " CA  GLN A  11 " =    0.940

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.467 - 5.430
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 212
   mapped sites are within: 0.722 - 5.430

peak=   -5.911 closest distance to " CG2 VAL A 230 " =    0.774
peak=   -5.137 closest distance to " O   GLN A  11 " =    0.920
peak=   -4.804 closest distance to " NH2 ARG A  36 " =    1.084
peak=   -4.693 closest distance to " CD  ARG A  14 " =    3.068
peak=   -4.670 closest distance to " OD1 ASN A 301 " =    0.757
peak=   -4.413 closest distance to " CD  GLN A  58 " =    0.970
peak=   -4.219 closest distance to " CD1 PHE A  59 " =    1.937
peak=   -4.161 closest distance to " CD  GLN A 223 " =    1.568
peak=   -4.142 closest distance to " O   HOH Z 155 " =    1.733
peak=   -4.125 closest distance to " CG2BVAL A  41 " =    2.083
peak=   -4.107 closest distance to " O   PRO A 198 " =    1.242
peak=   -4.048 closest distance to " CA  ASP A 298 " =    1.065
peak=   -4.033 closest distance to " CG  PRO A 243 " =    1.764
peak=   -4.033 closest distance to " O   ASP A 298 " =    1.534
peak=   -4.022 closest distance to " O   HOH Z 411 " =    5.396
peak=   -4.011 closest distance to " CG2 ILE A  49 " =    2.633
peak=   -4.010 closest distance to " CB  ALA A 161 " =    2.460
peak=   -3.966 closest distance to " O   HOH Z 422 " =    1.128
peak=   -3.938 closest distance to " CG1 VAL A 112 " =    2.454
peak=   -3.924 closest distance to " O   HOH Z 151 " =    0.808
peak=   -3.919 closest distance to " NH2 ARG A  36 " =    1.081
peak=   -3.912 closest distance to " O   HOH Z  67 " =    1.491
peak=   -3.899 closest distance to " O   HOH Z 425 " =    0.998
peak=   -3.861 closest distance to " CD2 LEU A 237 " =    2.349
peak=   -3.830 closest distance to " O   HOH Z  60 " =    2.071
peak=   -3.824 closest distance to " CD  ARG A  14 " =    2.700
peak=   -3.820 closest distance to " N   ALA A   1 " =    2.544
peak=   -3.804 closest distance to " O   HOH Z 221 " =    1.041
peak=   -3.786 closest distance to " OD2 ASP A 298 " =    0.892
peak=   -3.780 closest distance to " O   HOH Z 290 " =    0.842
peak=   -3.738 closest distance to " C   VAL A 265 " =    1.066
peak=   -3.734 closest distance to " C   THR A 279 " =    1.111
peak=   -3.718 closest distance to " CG1 VAL A 296 " =    1.018
peak=   -3.713 closest distance to " O   HOH Z 174 " =    1.790
peak=   -3.704 closest distance to " O   HOH Z 351 " =    1.791
peak=   -3.702 closest distance to " O   HOH Z 407 " =    3.123
peak=   -3.698 closest distance to " CD  ARG A  36 " =    1.040
peak=   -3.684 closest distance to " C   ASN A 285 " =    2.212
peak=   -3.674 closest distance to " CG  GLN A 103 " =    2.333
peak=   -3.673 closest distance to " O   HOH Z 101 " =    1.480
peak=   -3.673 closest distance to " O   HOH Z 411 " =    1.584
peak=   -3.664 closest distance to " CD2 TYR A  30 " =    2.636
peak=   -3.664 closest distance to " O   HOH Z 250 " =    1.902
peak=   -3.663 closest distance to " CD  GLN A  11 " =    1.196
peak=   -3.660 closest distance to " O   HOH Z   7 " =    1.241
peak=   -3.658 closest distance to " CZ3 TRP A  70 " =    1.557
peak=   -3.652 closest distance to " O   HOH Z  37 " =    1.264
peak=   -3.646 closest distance to " O   HOH Z 205 " =    0.767
peak=   -3.645 closest distance to " O   HOH Z 231 " =    1.982
peak=   -3.639 closest distance to " CD1 TRP A 179 " =    1.117
peak=   -3.637 closest distance to " O   HOH Z 124 " =    1.273
peak=   -3.637 closest distance to " O   HOH Z 384 " =    1.500
peak=   -3.634 closest distance to " CB  ALA A 248 " =    2.272
peak=   -3.634 closest distance to " O   HOH Z 198 " =    1.097
peak=   -3.625 closest distance to " O   HOH Z   6 " =    2.399
peak=   -3.608 closest distance to " O   GLY A 241 " =    2.366
peak=   -3.606 closest distance to " O   HOH Z 432 " =    0.837
peak=   -3.602 closest distance to " O   HOH Z  52 " =    2.191
peak=   -3.590 closest distance to " CG  LEU A   5 " =    0.940
peak=   -3.586 closest distance to " CA  SER A 164 " =    2.145
peak=   -3.584 closest distance to " ND2 ASN A  60 " =    1.377
peak=   -3.581 closest distance to " OD1 ASP A 298 " =    2.357
peak=   -3.570 closest distance to " O   HOH Z 152 " =    1.346
peak=   -3.567 closest distance to " CA  SER A 276 " =    1.522
peak=   -3.554 closest distance to " CG2 THR A 182 " =    2.281
peak=   -3.553 closest distance to " O   HOH Z 368 " =    1.873
peak=   -3.549 closest distance to " O   HOH Z 210 " =    0.949
peak=   -3.543 closest distance to " O   SER A  95 " =    1.729
peak=   -3.538 closest distance to " O   HOH Z 234 " =    4.047
peak=   -3.536 closest distance to " O   HOH Z 196 " =    1.539
peak=   -3.535 closest distance to " CG  ASP A 231 " =    0.723
peak=   -3.534 closest distance to " O   SER A 258 " =    2.385
peak=   -3.516 closest distance to " CG  ASP A 286 " =    1.122
peak=   -3.507 closest distance to " O   HOH Z  92 " =    1.341
peak=   -3.497 closest distance to " CD  GLN A 223 " =    0.722
peak=   -3.494 closest distance to " CG  GLN A  73 " =    0.910
peak=   -3.493 closest distance to " OH  TYR A 169 " =    0.812
peak=   -3.491 closest distance to " OE2 GLU A 128 " =    1.927
peak=   -3.474 closest distance to " OD1 ASN A 148 " =    1.309
peak=   -3.472 closest distance to " O   HOH Z 423 " =    2.834
peak=   -3.470 closest distance to " CD1 LEU A 167 " =    2.086
peak=   -3.466 closest distance to " O   HOH Z  30 " =    1.604
peak=   -3.466 closest distance to " CD  GLN A  77 " =    1.088
peak=   -3.463 closest distance to " O   HOH Z 388 " =    2.023
peak=   -3.453 closest distance to " OG  SER A  97 " =    2.353
peak=   -3.447 closest distance to " CD  LYS A 289 " =    2.331
peak=   -3.445 closest distance to " CA  VAL A 197 " =    0.939
peak=   -3.439 closest distance to " O   HOH Z 166 " =    1.590
peak=   -3.439 closest distance to " CZ  ARG A 259 " =    0.846
peak=   -3.437 closest distance to " CG2 VAL A 189 " =    2.097
peak=   -3.433 closest distance to " O   HOH Z 119 " =    1.948
peak=   -3.431 closest distance to " O   HOH Z 103 " =    2.308
peak=   -3.424 closest distance to " OXT GLY A 302 " =    2.861
peak=   -3.424 closest distance to " NE  ARG A 156 " =    1.923
peak=   -3.412 closest distance to " O   HOH Z 120 " =    1.249
peak=   -3.394 closest distance to " CD2 HIS A 115 " =    1.119
peak=   -3.394 closest distance to " ND2 ASN A 249 " =    1.961
peak=   -3.381 closest distance to " O   HOH Z 418 " =    1.296
peak=   -3.380 closest distance to " C   TRP A 274 " =    1.116
peak=   -3.372 closest distance to " CA  GLY A 203 " =    2.307
peak=   -3.372 closest distance to " O   HOH Z 362 " =    4.422
peak=   -3.356 closest distance to " O   HOH Z 417 " =    1.178
peak=   -3.356 closest distance to " O   HOH Z 136 " =    1.289
peak=   -3.353 closest distance to " O   HOH Z  35 " =    0.870
peak=   -3.349 closest distance to " OG BSER A 210 " =    1.189
peak=   -3.349 closest distance to " N   ALA A 226 " =    2.105
peak=   -3.339 closest distance to " CD2 LEU A 143 " =    2.540
peak=   -3.339 closest distance to " O   HOH Z 401 " =    1.151
peak=   -3.334 closest distance to " CD  ARG A 138 " =    2.623
peak=   -3.333 closest distance to " O   HOH Z 227 " =    0.806
peak=   -3.331 closest distance to " CG  ARG A  24 " =    2.092
peak=   -3.326 closest distance to " O   HOH Z 422 " =    0.977
peak=   -3.324 closest distance to " O   HOH Z   5 " =    1.853
peak=   -3.306 closest distance to " CZ  ARG A 156 " =    1.431
peak=   -3.304 closest distance to " O   LEU A 300 " =    2.413
peak=   -3.301 closest distance to " O   HOH Z 171 " =    3.140
peak=   -3.296 closest distance to " CD  ARG A 269 " =    2.468
peak=   -3.290 closest distance to " O   HOH Z 151 " =    0.930
peak=   -3.288 closest distance to " CZ  TYR A 172 " =    1.854
peak=   -3.284 closest distance to " CG  PRO A 280 " =    2.084
peak=   -3.283 closest distance to " O   HOH Z 265 " =    1.249
peak=   -3.283 closest distance to " OE2 GLU A 277 " =    2.682
peak=   -3.282 closest distance to " O   SER A 273 " =    1.039
peak=   -3.279 closest distance to " O   LYS A  76 " =    1.401
peak=   -3.278 closest distance to " CG  LEU A  83 " =    2.048
peak=   -3.275 closest distance to " O   HOH Z 384 " =    0.997
peak=   -3.275 closest distance to " O   HOH Z  31 " =    2.205
peak=   -3.275 closest distance to " O   SER A 271 " =    2.087
peak=   -3.272 closest distance to " NE2 GLN A  58 " =    2.185
peak=   -3.271 closest distance to " CD  ARG A 139 " =    1.096
peak=   -3.270 closest distance to " O   HOH Z 435 " =    1.281
peak=   -3.268 closest distance to " CB  HIS A  86 " =    2.383
peak=   -3.267 closest distance to " O   HOH Z 109 " =    3.492
peak=   -3.264 closest distance to " O   HOH Z 145 " =    2.619
peak=   -3.260 closest distance to " O   HOH Z 378 " =    0.955
peak=   -3.257 closest distance to " CA  GLU A 277 " =    1.235
peak=   -3.256 closest distance to " CE  MET A 105 " =    2.146
peak=   -3.255 closest distance to " O   HOH Z 196 " =    2.370
peak=   -3.250 closest distance to " O   HOH Z 259 " =    1.236
peak=   -3.242 closest distance to " O   HOH Z 331 " =    1.503
peak=   -3.240 closest distance to " OG  SER A  87 " =    1.750
peak=   -3.238 closest distance to " O   HOH Z 277 " =    1.361
peak=   -3.238 closest distance to " O   HOH Z 131 " =    4.257
peak=   -3.237 closest distance to " C   LYS A  76 " =    1.866
peak=   -3.236 closest distance to " OD2 ASP A 171 " =    2.082
peak=   -3.231 closest distance to " OG  SER A  32 " =    1.223
peak=   -3.228 closest distance to " O   ALA A  34 " =    2.414
peak=   -3.225 closest distance to " CG1 VAL A 197 " =    2.359
peak=   -3.224 closest distance to " O   HOH Z 176 " =    1.701
peak=   -3.219 closest distance to " NE1 TRP A 266 " =    2.028
peak=   -3.215 closest distance to " O   HOH Z 252 " =    1.273
peak=   -3.214 closest distance to " O   HOH Z  11 " =    1.751
peak=   -3.211 closest distance to " OG  SER A  63 " =    1.036
peak=   -3.203 closest distance to " NE2 GLN A 278 " =    1.926
peak=   -3.199 closest distance to " O   HOH Z 387 " =    2.849
peak=   -3.192 closest distance to " O   HOH Z 353 " =    1.461
peak=   -3.189 closest distance to " O   GLN A  94 " =    2.308
peak=   -3.187 closest distance to " O   HOH Z 401 " =    1.450
peak=   -3.180 closest distance to " CB  ALA A  10 " =    2.093
peak=   -3.179 closest distance to " CG2 ILE A 263 " =    2.142
peak=   -3.178 closest distance to " O   HOH Z  44 " =    1.922
peak=   -3.173 closest distance to " O   ALA A   1 " =    1.872
peak=   -3.173 closest distance to " CG  LYS A 119 " =    2.965
peak=   -3.171 closest distance to " N   THR A 235 " =    1.220
peak=   -3.166 closest distance to " CD1 TYR A 247 " =    2.490
peak=   -3.164 closest distance to " N   ALA A 295 " =    0.996
peak=   -3.164 closest distance to " SG  CYS A 260 " =    1.865
peak=   -3.163 closest distance to " O   HOH Z 285 " =    1.458
peak=   -3.163 closest distance to " O   GLN A 144 " =    1.765
peak=   -3.160 closest distance to " O   HOH Z  29 " =    1.278
peak=   -3.156 closest distance to " CE2 PHE A  61 " =    2.549
peak=   -3.155 closest distance to " CG2 VAL A 296 " =    1.181
peak=   -3.155 closest distance to " CB  PHE A 130 " =    1.227
peak=   -3.151 closest distance to " CD1 ILE A 151 " =    2.523
peak=   -3.150 closest distance to " O   HOH Z 137 " =    1.393
peak=   -3.148 closest distance to " CG2 THR A  18 " =    2.730
peak=   -3.147 closest distance to " O   ASP A 200 " =    1.178
peak=   -3.146 closest distance to " OG BSER A 134 " =    1.481
peak=   -3.145 closest distance to " O   HOH Z 165 " =    2.003
peak=   -3.144 closest distance to " CB  ALA A  43 " =    2.688
peak=   -3.144 closest distance to " O   HOH Z 426 " =    1.938
peak=   -3.143 closest distance to " O   HOH Z 166 " =    1.218
peak=   -3.141 closest distance to " OE1 GLN A  88 " =    1.030
peak=   -3.141 closest distance to " O   HOH Z 424 " =    3.063
peak=   -3.139 closest distance to " CG2 THR A 235 " =    2.668
peak=   -3.139 closest distance to " O   TRP A  92 " =    2.255
peak=   -3.139 closest distance to " CH2 TRP A 150 " =    0.995
peak=   -3.138 closest distance to " CD2 PHE A  59 " =    2.313
peak=   -3.135 closest distance to " O   TYR A  15 " =    1.846
peak=   -3.134 closest distance to " NH2 ARG A  79 " =    2.065
peak=   -3.123 closest distance to " OD1 ASP A 171 " =    1.449
peak=   -3.117 closest distance to " O   HOH Z 377 " =    2.188
peak=   -3.113 closest distance to " O   HOH Z 109 " =    0.980
peak=   -3.104 closest distance to " CD2 TYR A 293 " =    1.835
peak=   -3.103 closest distance to " C   HIS A 108 " =    1.204
peak=   -3.093 closest distance to " O   HOH Z  57 " =    0.856
peak=   -3.082 closest distance to " N   SER A   3 " =    2.488
peak=   -3.080 closest distance to " O   HOH Z 108 " =    2.230
peak=   -3.073 closest distance to " CB  ALA A 129 " =    2.701
peak=   -3.071 closest distance to " CG  ASN A 110 " =    0.875
peak=   -3.059 closest distance to " OG BSER A  99 " =    1.213
peak=   -3.056 closest distance to " OD2 ASP A 132 " =    2.389
peak=   -3.052 closest distance to " O   HOH Z  39 " =    1.193
peak=   -3.046 closest distance to " O   HOH Z 394 " =    5.430
peak=   -3.027 closest distance to " O   HOH Z  39 " =    2.117

================= 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    :  0.5117 0.4959   6.309327e+00   6.298402e+00
   1_bss:  0.5051 0.4930   6.303932e+00   6.298097e+00
   1_xyz:  0.4432 0.4526   6.246185e+00   6.259231e+00
   1_adp:  0.4025 0.4555   6.194933e+00   6.255324e+00
   1_occ:  0.4020 0.4556   6.194496e+00   6.256050e+00
   2_bss:  0.3994 0.4507   6.196330e+00   6.256481e+00
   2_xyz:  0.3357 0.4028   6.079086e+00   6.195423e+00
   2_adp:  0.3224 0.3930   6.055589e+00   6.174137e+00
   2_occ:  0.3222 0.3929   6.055275e+00   6.174116e+00
   3_bss:  0.3216 0.3910   6.054800e+00   6.173046e+00
   3_xyz:  0.2651 0.3205   5.884377e+00   6.036172e+00
   3_adp:  0.2487 0.3026   5.838752e+00   5.994273e+00
   3_occ:  0.2486 0.3027   5.838356e+00   5.994885e+00
   4_bss:  0.2476 0.3032   5.838243e+00   5.994345e+00
   4_xyz:  0.1903 0.2336   5.584212e+00   5.764801e+00
   4_adp:  0.1711 0.2158   5.500808e+00   5.696213e+00
   4_occ:  0.1709 0.2163   5.500797e+00   5.696616e+00
   5_bss:  0.1708 0.2165   5.501595e+00   5.695727e+00
   5_xyz:  0.1417 0.1891   5.348771e+00   5.568109e+00
   5_adp:  0.1369 0.1814   5.312224e+00   5.523199e+00
   5_occ:  0.1368 0.1814   5.312027e+00   5.523141e+00
   5_bss:  0.1371 0.1820   5.313705e+00   5.523708e+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:  0.331  20.000   6.120  11.800   8.120   0.000   0.000   0.000
   1_xyz:  0.331  20.000   6.120  11.800   8.120   0.000   0.000   0.000
   1_adp:  0.331  20.000   6.120  11.800   8.120   0.000   0.000   0.000
   1_occ:  0.331  20.000   6.120  11.800   8.120   0.000   0.000   0.000
   2_bss:  0.287  20.000   2.208   6.594   4.144   0.000   0.000   0.000
   2_xyz:  0.287  20.000   2.208   6.594   4.144   0.000   0.000   0.000
   2_adp:  0.287  20.000   2.208   6.594   4.144   0.000   0.000   0.000
   2_occ:  0.287  20.000   2.208   6.594   4.144   0.000   0.000   0.000
   3_bss:  0.317  47.936   1.029   4.604   2.732   0.000   0.000   0.000
   3_xyz:  0.317  47.936   1.029   4.604   2.732   0.000   0.000   0.000
   3_adp:  0.317  47.936   1.029   4.604   2.732   0.000   0.000   0.000
   3_occ:  0.317  47.936   1.029   4.604   2.732   0.000   0.000   0.000
   4_bss:  0.316  47.936  -0.307   2.757   1.663   0.000   0.000   0.000
   4_xyz:  0.316  47.936  -0.307   2.757   1.663   0.000   0.000   0.000
   4_adp:  0.316  47.936  -0.307   2.757   1.663   0.000   0.000   0.000
   4_occ:  0.316  47.936  -0.307   2.757   1.663   0.000   0.000   0.000
   5_bss:  0.324  59.962  -0.732   1.512   1.423   0.000   0.000   0.000
   5_xyz:  0.324  59.962  -0.732   1.512   1.423   0.000   0.000   0.000
   5_adp:  0.324  59.962  -0.732   1.512   1.423   0.000   0.000   0.000
   5_occ:  0.324  59.962  -0.732   1.512   1.423   0.000   0.000   0.000
   5_bss:  0.328  60.411  -1.354   0.499   0.855   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.977 0.3692  0.4381    80460.014
   1_bss:  62.615 0.3598  0.5472    80353.147
   1_xyz:  54.947 0.4573  0.6784    64443.071
   1_adp:  53.721 0.4726  0.7859    62733.437
   1_occ:  53.804 0.4715  0.7824    62844.051
   2_bss:  53.653 0.4734  0.6809    62730.842
   2_xyz:  46.846 0.5585  0.8034    49689.196
   2_adp:  44.603 0.5868  0.8374    46424.454
   2_occ:  44.613 0.5866  0.8367    46379.270
   3_bss:  44.288 0.5906  0.8005    45870.729
   3_xyz:  34.894 0.7019  0.9246    29541.581
   3_adp:  32.355 0.7318  0.9445    26440.743
   3_occ:  32.375 0.7315  0.9438    26434.660
   4_bss:  32.291 0.7325  0.8987    26367.595
   4_xyz:  23.333 0.8282  0.9706    14296.179
   4_adp:  21.319 0.8488  0.9752    12366.364
   4_occ:  21.330 0.8487  0.9752    12400.217
   5_bss:  21.292 0.8492  0.9548    12399.997
   5_xyz:  18.237 0.8780  0.9729     9408.131
   5_adp:  17.124 0.8885  0.9758     8726.824
   5_occ:  17.124 0.8885  0.9757     8739.268
   5_bss:  17.139 0.8885  0.9664     8773.666
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.4030e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.4030e+01
   1_xyz:   1.737  0.014  0.109 18.349  0.007  4.121   1.5173e-01
   1_adp:   1.737  0.014  0.109 18.349  0.007  4.121   1.5173e-01
   1_occ:   1.737  0.014  0.109 18.349  0.007  4.121   1.5173e-01
   2_bss:   1.737  0.014  0.109 18.349  0.007  4.121   1.5173e-01
   2_xyz:   1.382  0.010  0.090 17.112  0.005  4.108   1.1320e-01
   2_adp:   1.382  0.010  0.090 17.112  0.005  4.108   1.1320e-01
   2_occ:   1.382  0.010  0.090 17.112  0.005  4.108   1.1320e-01
   3_bss:   1.382  0.010  0.090 17.112  0.005  4.108   1.1320e-01
   3_xyz:   1.225  0.010  0.087 15.832  0.005  4.108   9.0375e-02
   3_adp:   1.225  0.010  0.087 15.832  0.005  4.108   9.0375e-02
   3_occ:   1.225  0.010  0.087 15.832  0.005  4.108   9.0375e-02
   4_bss:   1.225  0.010  0.087 15.832  0.005  4.108   9.0375e-02
   4_xyz:   1.186  0.010  0.080 15.408  0.005  4.125   8.4471e-02
   4_adp:   1.186  0.010  0.080 15.408  0.005  4.125   8.4471e-02
   4_occ:   1.186  0.010  0.080 15.408  0.005  4.125   8.4471e-02
   5_bss:   1.186  0.010  0.080 15.408  0.005  4.125   8.4471e-02
   5_xyz:   1.167  0.009  0.086 15.344  0.004  4.111   7.9405e-02
   5_adp:   1.167  0.009  0.086 15.344  0.004  4.111   7.9405e-02
   5_occ:   1.167  0.009  0.086 15.344  0.004  4.111   7.9405e-02
   5_bss:   1.167  0.009  0.086 15.344  0.004  4.111   7.9405e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.136   7.0022e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.136   7.0022e+00
   1_xyz:  15.993  0.163  0.508 88.853  0.054  2.226   1.0658e-01
   1_adp:  15.993  0.163  0.508 88.853  0.054  2.226   1.0658e-01
   1_occ:  15.993  0.163  0.508 88.853  0.054  2.226   1.0658e-01
   2_bss:  15.993  0.163  0.508 88.853  0.054  2.226   1.0658e-01
   2_xyz:   7.741  0.096  0.294 89.604  0.034  2.114   7.4994e-02
   2_adp:   7.741  0.096  0.294 89.604  0.034  2.114   7.4994e-02
   2_occ:   7.741  0.096  0.294 89.604  0.034  2.114   7.4994e-02
   3_bss:   7.741  0.096  0.294 89.604  0.034  2.114   7.4994e-02
   3_xyz:   7.748  0.074  0.327 84.408  0.029  2.213   1.4953e-01
   3_adp:   7.748  0.074  0.327 84.408  0.029  2.213   1.4953e-01
   3_occ:   7.748  0.074  0.327 84.408  0.029  2.213   1.4953e-01
   4_bss:   7.748  0.074  0.327 84.408  0.029  2.213   1.4953e-01
   4_xyz:   7.322  0.067  0.228 82.103  0.036  2.134   1.0874e-01
   4_adp:   7.322  0.067  0.228 82.103  0.036  2.134   1.0874e-01
   4_occ:   7.322  0.067  0.228 82.103  0.036  2.134   1.0874e-01
   5_bss:   7.322  0.067  0.228 82.103  0.036  2.134   1.0874e-01
   5_xyz:   7.993  0.053  0.473 81.637  0.036  2.188   5.6742e-02
   5_adp:   7.993  0.053  0.473 81.637  0.036  2.188   5.6742e-02
   5_occ:   7.993  0.053  0.473 81.637  0.036  2.188   5.6742e-02
   5_bss:   7.993  0.053  0.473 81.637  0.036  2.188   5.6742e-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: 114.36   0.00  16.98  78.81   0.00  15.09 114.36   0.00  27.24
   1_occ: 114.36   0.00  16.98  78.81   0.00  15.09 114.36   0.00  27.24
   2_bss: 114.36   0.00  16.98  78.81   0.00  15.09 114.36   0.00  27.24
   2_xyz: 114.36   0.00  16.98  78.81   0.00  15.09 114.36   0.00  27.24
   2_adp: 100.55   0.00  15.57  75.48   0.00  13.31 100.55   0.00  27.85
   2_occ: 100.55   0.00  15.57  75.48   0.00  13.31 100.55   0.00  27.85
   3_bss: 100.55   0.00  15.57  75.48   0.00  13.31 100.55   0.00  27.85
   3_xyz: 100.55   0.00  15.57  75.48   0.00  13.31 100.55   0.00  27.85
   3_adp:  92.10   0.00  15.09  70.88   0.00  12.07  92.10   1.54  31.56
   3_occ:  92.10   0.00  15.09  70.88   0.00  12.07  92.10   1.54  31.56
   4_bss:  92.10   0.00  15.09  70.88   0.00  12.07  92.10   1.54  31.56
   4_xyz:  92.10   0.00  15.09  70.88   0.00  12.07  92.10   1.54  31.56
   4_adp:  88.43   0.00  15.93  88.43   0.00  11.48  86.61   3.06  40.15
   4_occ:  88.43   0.00  15.93  88.43   0.00  11.48  86.61   3.06  40.15
   5_bss:  88.43   0.00  15.93  88.43   0.00  11.48  86.61   3.06  40.15
   5_xyz:  88.43   0.00  15.93  88.43   0.00  11.48  86.61   3.06  40.15
   5_adp:  88.93   0.56  15.40  88.93   0.56  10.99  84.52   3.24  39.37
   5_occ:  88.93   0.56  15.40  88.93   0.56  10.99  84.52   3.24  39.37
   5_bss:  89.38   1.01  15.85  89.38   1.01  11.44  84.97   3.69  39.82
------------------------------------------------------------------------
 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:    1.190    0.022    0.412
   1_adp:    1.190    0.022    0.412
   1_occ:    1.190    0.022    0.412
   2_bss:    1.190    0.022    0.412
   2_xyz:    1.544    0.019    0.603
   2_adp:    1.544    0.019    0.603
   2_occ:    1.544    0.019    0.603
   3_bss:    1.544    0.019    0.603
   3_xyz:    1.702    0.063    0.723
   3_adp:    1.702    0.063    0.723
   3_occ:    1.702    0.063    0.723
   4_bss:    1.702    0.063    0.723
   4_xyz:    2.110    0.064    0.859
   4_adp:    2.110    0.064    0.859
   4_occ:    2.110    0.064    0.859
   5_bss:    2.110    0.064    0.859
   5_xyz:    2.151    0.075    0.907
   5_adp:    2.151    0.075    0.907
   5_occ:    2.151    0.075    0.907
   5_bss:    2.151    0.075    0.907
------------------------------------------------------------------------

CPU time actual refinement: 356.17


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_359/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_359/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_359/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_359/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_359/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.01 
  Macro-tasks:
    bulk solvent and scale       = 46.70  
    individual site refinement   = 149.02 
    weights calculation          = 32.52  
    collect and process          = 6.41   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 234.77 
  Micro-tasks:
    mask                            = 2.98   
    f_calc                          = 110.48 
    alpha_beta                      = 8.37   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 121.04 
    fmodel                         = 8.14   
    r_factors                      = 0.29   
    phase_errors                   = 10.01  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 262.67 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.983 micro seconds
Total CPU time: 6.16 minutes
from_scatterers_fft:    642 calls, 110.06 s
gradients_fft:          588 calls, 107.85 s

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

# Date 2008-01-16 Time 01:22:26 PST -0800 (1200475346.81 s)
Start R-work = 0.5117, R-free = 0.4959 (no bulk solvent and anisotropic scale)
Final R-work = 0.1544, R-free = 0.1973 (no bulk solvent and anisotropic scale)

Start R-work = 0.5051, R-free = 0.4930
Final R-work = 0.1371, R-free = 0.1820