# Date 2008-01-16 Time 00:52:01 PST -0800 (1200473521.41 s)
#phil __OFF__

Command line arguments: "../194.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13204
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 194

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 47.1647, 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: 3.35, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8121 1.96082
Completeness in resolution range: 0.934723
Completeness with d_max=infinity: 0.931878

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8121
                             d_min =   1.9608

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8121 1.96082
Completeness in resolution range: 0.934723
Completeness with d_max=infinity: 0.931878

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8125 -  4.1955 [2209/2237]  1986   223  10.1%
  bin  2:  4.1955 -  3.3426 [2102/2125]  1891   211  10.0%
  bin  3:  3.3426 -  2.9238 [2068/2090]  1865   203   9.8%
  bin  4:  2.9238 -  2.6582 [2087/2106]  1877   210  10.1%
  bin  5:  2.6582 -  2.4686 [2031/2060]  1823   208  10.2%
  bin  6:  2.4686 -  2.3236 [2057/2099]  1853   204   9.9%
  bin  7:  2.3236 -  2.2076 [2028/2064]  1830   198   9.8%
  bin  8:  2.2076 -  2.1118 [2026/2066]  1816   210  10.4%
  bin  9:  2.1118 -  2.0307 [2026/2055]  1832   194   9.6%
  bin 10:  2.0307 -  1.9608 [ 955/2055]   857    98  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_194/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.42 -     2.12: 13
        2.12 -     2.81: 825
        2.81 -     3.51: 4492
        3.51 -     4.20: 9344
        4.20 -     4.90: 13747
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.421 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.564 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.595 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.648 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.703 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 28416 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_194/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_194/model_refine_001.geo

CPU time processing inputs: 9.00


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 47.16465 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: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4602   r_free= 0.4483   ksol= 0.00   Bsol= 0.00   scale= 0.808    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.261554                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8125 -  4.6793 0.99   1430  158 0.3702 0.3646      6.5554      6.5684|
|  2:  4.6793 -  3.7337 0.99   1385  154 0.3559 0.3864       6.687      6.7701|
|  3:  3.7337 -  3.2675 0.99   1338  149 0.4206 0.3844      6.6236      6.6167|
|  4:  3.2675 -  2.9714 0.99   1343  145 0.4482 0.4382      6.4787       6.452|
|  5:  2.9714 -  2.7599 0.99   1314  152 0.4811 0.4601      6.3349      6.3644|
|  6:  2.7599 -  2.5981 0.98   1336  143 0.4898 0.5283      6.2706      6.1931|
|  7:  2.5981 -  2.4686 0.99   1296  154 0.4901 0.5051      6.2137      6.1532|
|  8:  2.4686 -  2.3616 0.99   1340  138 0.5131 0.4371      6.1726      6.1451|
|  9:  2.3616 -  2.2710 0.98   1310  148 0.5192 0.4866      6.1126      6.1393|
| 10:  2.2710 -  2.1929 0.98   1306  144 0.5184 0.4846       6.106      6.0546|
| 11:  2.1929 -  2.1245 0.98   1286  152 0.5205 0.5135       6.021      6.0377|
| 12:  2.1245 -  2.0639 0.99   1306  139 0.5257 0.4837      5.9568      5.9454|
| 13:  2.0639 -  2.0097 0.94   1269  130 0.5264 0.5084      5.8843      5.8187|
| 14:  2.0097 -  1.9608 0.29    371   53 0.5348 0.4678      5.9154      5.7154|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8125 -  4.6793  1430   158  0.70  33.90   0.81     0.71      68129.84|
|  2:  4.6793 -  3.7337  1385   154  0.72  33.12   0.91     0.78      93279.67|
|  3:  3.7337 -  3.2675  1338   149  0.65  39.97   0.85     0.75      96331.76|
|  4:  3.2675 -  2.9714  1343   145  0.57  46.45   0.81     0.66      83623.49|
|  5:  2.9714 -  2.7599  1314   152  0.48  53.89   0.75     0.56      73189.54|
|  6:  2.7599 -  2.5981  1336   143  0.43  57.27   0.73     0.51      67524.71|
|  7:  2.5981 -  2.4686  1296   154  0.42  58.53   0.76     0.48      61994.11|
|  8:  2.4686 -  2.3616  1340   138  0.44  56.80   0.73     0.51      51370.02|
|  9:  2.3616 -  2.2710  1310   148  0.47  54.73   0.73     0.56      45095.71|
| 10:  2.2710 -  2.1929  1306   144  0.48  53.46   0.75     0.56      39541.20|
| 11:  2.1929 -  2.1245  1286   152  0.43  57.86   0.75     0.54      40945.53|
| 12:  2.1245 -  2.0639  1306   139  0.39  60.70   0.76     0.50      38938.45|
| 13:  2.0639 -  2.0097  1269   130  0.38  61.26   0.74     0.49      34156.08|
| 14:  2.0097 -  1.9608   371    53  0.47  54.93   0.75     0.48      24263.35|
|alpha:            min =        0.48 max =            0.78 mean =         0.59|
|beta:             min =    24263.35 max =        96331.76 mean =     60689.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           89.99 mean =        51.21|
|phase err.(test): min =        0.00 max =           89.99 mean =        51.32|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.868775              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.962   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.810725              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.980   (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 |  1.158 -  1.532:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.532 -  1.906:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.906 -  2.280:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.280 -  2.655:      665 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.655 -  3.029:     1456 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.029 -  3.403:     2595 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.403 -  3.777:     3961 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.777 -  4.151:     5119 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.151 -  4.526:     6671 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.526 -  4.900:     7802 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.554 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.158 |       2.384 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.751)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.751)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4670   r_free= 0.4501   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.264228                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4514   r_free= 0.4381   ksol= 0.34   Bsol= 13.54   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.33,8.31,9.37,0.00,0.00,0.00); trace/3= 8.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.252190                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.423275              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.418   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.829489              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.618   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4514      final r-factor (work) = 0.3532          |
| start r-factor (free) = 0.4381      final r-factor (free) = 0.3707          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 83.0759 = 9.42 * 0.50 * 6.2657 + 1.00 * 53.5540                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.0468 = 9.42 * 0.50 * 6.1366 + 1.00 * 0.1334                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3532      final r-factor (work) = 0.2995          |
| start r-factor (free) = 0.3707      final r-factor (free) = 0.3406          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1046 = 0.83 * 1.00 * 6.1366 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9908 = 0.83 * 1.00 * 6.0000 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.751)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.65   12.01    None  None   None       |
|    all(noH): 2823   0      0.00    63.65   12.01    None  None   None       |
|    Sol.    : 438    0      0.00    63.65   27.42    None  None   None       |
|    Mac.    : 2385   0      0.00    61.18   9.17     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.365: 1137   |   5:    31.823 -  38.188:   87        |
|      1:     6.365 -  12.729:  719   |   6:    38.188 -  44.553:   57        |
|      2:    12.729 -  19.094:  410   |   7:    44.553 -  50.917:   40        |
|      3:    19.094 -  25.459:  204   |   8:    50.917 -  57.282:   23        |
|      4:    25.459 -  31.823:  135   |   9:    57.282 -  63.646:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2995 r_free = 0.3406             target_work(ml) = 5.965         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2990 r_free = 0.3414             target_work(ml) = 5.964         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2990   r_free= 0.3414   ksol= 0.34   Bsol= 13.54   scale= 1.107   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.33,8.31,9.37,0.00,0.00,0.00); trace/3= 8.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.964212                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2941   r_free= 0.3370   ksol= 0.33   Bsol= 38.62   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.43,4.30,5.70,0.00,0.00,0.00); trace/3= 4.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.963963                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.229278              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.064   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.346061              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.692  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2941      final r-factor (work) = 0.1985          |
| start r-factor (free) = 0.3370      final r-factor (free) = 0.2417          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8303 = 5.23 * 0.50 * 6.0035 + 1.00 * 0.1334                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2422 = 5.23 * 0.50 * 5.8025 + 1.00 * 0.0707                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1985      final r-factor (work) = 0.1767          |
| start r-factor (free) = 0.2417      final r-factor (free) = 0.2216          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0431 = 0.35 * 1.00 * 5.8025 + 1.00 * 0.0351                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0042 = 0.35 * 1.00 * 5.5620 + 1.00 * 0.0794                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.751)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.67   12.13    None  None   None       |
|    all(noH): 2823   0      0.00    70.67   12.13    None  None   None       |
|    Sol.    : 438    0      0.83    62.92   32.66    None  None   None       |
|    Mac.    : 2385   0      0.00    70.67   8.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.068: 1374   |   5:    35.337 -  42.405:  102        |
|      1:     7.068 -  14.135:  730   |   6:    42.405 -  49.472:   72        |
|      2:    14.135 -  21.202:  229   |   7:    49.472 -  56.540:   40        |
|      3:    21.202 -  28.270:  132   |   8:    56.540 -  63.607:   21        |
|      4:    28.270 -  35.337:  120   |   9:    63.607 -  70.675:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1767 r_free = 0.2216             target_work(ml) = 5.520         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1765 r_free = 0.2217             target_work(ml) = 5.520         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1765   r_free= 0.2217   ksol= 0.33   Bsol= 38.62   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.43,4.30,5.70,0.00,0.00,0.00); trace/3= 4.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.519503                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1744   r_free= 0.2208   ksol= 0.31   Bsol= 38.62   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,3.09,4.14,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.517406                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.654013              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.419  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.259970              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.768   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1744      final r-factor (work) = 0.1320          |
| start r-factor (free) = 0.2208      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2524 = 3.65 * 0.50 * 5.5729 + 1.00 * 0.0707                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9380 = 3.65 * 0.50 * 5.4027 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1320      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1746      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.2426 = 2.26 * 1.00 * 5.4027 + 1.00 * 0.0327                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.8688 = 2.26 * 1.00 * 5.2439 + 1.00 * 0.0178                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.751)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.95   13.01    None  None   None       |
|    all(noH): 2823   0      0.00    89.95   13.01    None  None   None       |
|    Sol.    : 438    0      1.40    83.17   37.91    None  None   None       |
|    Mac.    : 2385   0      0.00    89.95   8.44     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:     0.000 -   8.995: 1708   |   5:    44.976 -  53.972:   87        |
|      1:     8.995 -  17.991:  539   |   6:    53.972 -  62.967:   62        |
|      2:    17.991 -  26.986:  174   |   7:    62.967 -  71.962:   32        |
|      3:    26.986 -  35.981:  100   |   8:    71.962 -  80.957:   14        |
|      4:    35.981 -  44.976:  103   |   9:    80.957 -  89.953:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1235 r_free = 0.1690             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1233 r_free = 0.1689             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1233   r_free= 0.1689   ksol= 0.31   Bsol= 38.62   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,3.09,4.14,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.227392                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1233   r_free= 0.1689   ksol= 0.31   Bsol= 38.62   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.85,2.82,3.94,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.226678                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.522134              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.884  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.489875              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.768   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1233      final r-factor (work) = 0.1195          |
| start r-factor (free) = 0.1689      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0589 = 1.52 * 0.50 * 5.2447 + 1.00 * 0.0673                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0232 = 1.52 * 0.50 * 5.2165 + 1.00 * 0.0531                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1195      final r-factor (work) = 0.1185          |
| start r-factor (free) = 0.1635      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5717 = 0.49 * 1.00 * 5.2165 + 1.00 * 0.0162                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5616 = 0.49 * 1.00 * 5.2023 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.751)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.87   12.70    None  None   None       |
|    all(noH): 2823   0      0.00    90.87   12.70    None  None   None       |
|    Sol.    : 438    0      1.39    84.50   36.75    None  None   None       |
|    Mac.    : 2385   0      0.00    90.87   8.29     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 -   9.087: 1754   |   5:    45.435 -  54.522:   74        |
|      1:     9.087 -  18.174:  514   |   6:    54.522 -  63.609:   61        |
|      2:    18.174 -  27.261:  163   |   7:    63.609 -  72.696:   20        |
|      3:    27.261 -  36.348:  118   |   8:    72.696 -  81.783:   13        |
|      4:    36.348 -  45.435:  102   |   9:    81.783 -  90.870:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1185 r_free = 0.1618             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1184 r_free = 0.1618             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1618   ksol= 0.31   Bsol= 38.62   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.85,2.82,3.94,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.196443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1617   ksol= 0.32   Bsol= 43.15   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,2.82,3.98,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.196175                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.027415              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.969  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.284473              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.128  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1184      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1617      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9276 = 3.03 * 0.50 * 5.2022 + 1.00 * 0.0531                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8958 = 3.03 * 0.50 * 5.1683 + 1.00 * 0.0724                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4832 = 0.28 * 1.00 * 5.1683 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4779 = 0.28 * 1.00 * 5.1572 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.751)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.38   12.10    None  None   None       |
|    all(noH): 2823   0      0.00    88.38   12.10    None  None   None       |
|    Sol.    : 438    0      1.55    82.63   34.34    None  None   None       |
|    Mac.    : 2385   0      0.00    88.38   8.01     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 -   8.838: 1748   |   5:    44.192 -  53.030:   79        |
|      1:     8.838 -  17.677:  534   |   6:    53.030 -  61.868:   37        |
|      2:    17.677 -  26.515:  155   |   7:    61.868 -  70.707:   20        |
|      3:    26.515 -  35.353:  130   |   8:    70.707 -  79.545:    6        |
|      4:    35.353 -  44.192:  110   |   9:    79.545 -  88.383:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1567             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1116 r_free = 0.1566             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1566   ksol= 0.32   Bsol= 43.15   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,2.82,3.98,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151107                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8125 -  4.6793 0.99   1430  158 0.0979 0.1289      5.3832      5.5534|
|  2:  4.6793 -  3.7337 0.99   1385  154 0.0839 0.1075      5.4189      5.6289|
|  3:  3.7337 -  3.2675 0.99   1338  149 0.1057 0.1495      5.4588        5.81|
|  4:  3.2675 -  2.9714 0.99   1343  145 0.1196 0.1570      5.4333      5.6129|
|  5:  2.9714 -  2.7599 0.99   1314  152 0.1327 0.1548      5.3213      5.4798|
|  6:  2.7599 -  2.5981 0.98   1336  143 0.1225 0.2106      5.2129      5.5222|
|  7:  2.5981 -  2.4686 0.99   1296  154 0.1255 0.1615      5.1764      5.3497|
|  8:  2.4686 -  2.3616 0.99   1340  138 0.1148 0.1703       5.079      5.3173|
|  9:  2.3616 -  2.2710 0.98   1310  148 0.1194 0.1970      5.0302       5.361|
| 10:  2.2710 -  2.1929 0.98   1306  144 0.1126 0.1652      4.9594      5.1554|
| 11:  2.1929 -  2.1245 0.98   1286  152 0.1147 0.1765      4.9216      5.2696|
| 12:  2.1245 -  2.0639 0.99   1306  139 0.1144 0.1612      4.8634      5.0751|
| 13:  2.0639 -  2.0097 0.94   1269  130 0.1121 0.1672      4.7668      4.9744|
| 14:  2.0097 -  1.9608 0.29    371   53 0.1046 0.1763      4.6969      4.9257|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8125 -  4.6793  1430   158  0.94   9.13   0.98     0.96       7332.71|
|  2:  4.6793 -  3.7337  1385   154  0.95   7.98   1.02     1.00       8904.97|
|  3:  3.7337 -  3.2675  1338   149  0.93  11.40   1.03     1.02      10228.02|
|  4:  3.2675 -  2.9714  1343   145  0.92  13.60   1.01     1.00      10103.77|
|  5:  2.9714 -  2.7599  1314   152  0.90  15.98   1.00     0.96       8334.68|
|  6:  2.7599 -  2.5981  1336   143  0.89  16.56   0.98     0.95       7127.88|
|  7:  2.5981 -  2.4686  1296   154  0.90  15.83   0.99     0.95       6303.81|
|  8:  2.4686 -  2.3616  1340   138  0.90  15.74   1.00     0.97       5613.89|
|  9:  2.3616 -  2.2710  1310   148  0.90  16.16   1.01     0.98       5072.43|
| 10:  2.2710 -  2.1929  1306   144  0.90  16.18   1.00     0.96       4544.71|
| 11:  2.1929 -  2.1245  1286   152  0.90  16.29   1.00     0.97       4303.65|
| 12:  2.1245 -  2.0639  1306   139  0.90  15.97   1.01     1.00       3857.44|
| 13:  2.0639 -  2.0097  1269   130  0.91  15.79   1.00     0.98       3207.49|
| 14:  2.0097 -  1.9608   371    53  0.92  13.96   0.98     0.95       2619.12|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2619.12 max =        10228.02 mean =      6490.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.28|
|phase err.(test): min =        0.00 max =           89.74 mean =        13.81|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1566   ksol= 0.32   Bsol= 46.06   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.06,-0.08,1.14,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151148                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1566   ksol= 0.32   Bsol= 46.06   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.06,-0.08,1.14,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151148                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8125 -  4.6793 0.99   1430  158 0.0980 0.1289      5.3835      5.5537|
|  2:  4.6793 -  3.7337 0.99   1385  154 0.0839 0.1075       5.419      5.6289|
|  3:  3.7337 -  3.2675 0.99   1338  149 0.1057 0.1495      5.4587        5.81|
|  4:  3.2675 -  2.9714 0.99   1343  145 0.1196 0.1569      5.4333      5.6126|
|  5:  2.9714 -  2.7599 0.99   1314  152 0.1327 0.1548      5.3212      5.4797|
|  6:  2.7599 -  2.5981 0.98   1336  143 0.1225 0.2106      5.2128       5.522|
|  7:  2.5981 -  2.4686 0.99   1296  154 0.1255 0.1615      5.1764      5.3497|
|  8:  2.4686 -  2.3616 0.99   1340  138 0.1148 0.1702      5.0789      5.3173|
|  9:  2.3616 -  2.2710 0.98   1310  148 0.1194 0.1969      5.0302      5.3611|
| 10:  2.2710 -  2.1929 0.98   1306  144 0.1126 0.1652      4.9596      5.1556|
| 11:  2.1929 -  2.1245 0.98   1286  152 0.1147 0.1767      4.9218      5.2701|
| 12:  2.1245 -  2.0639 0.99   1306  139 0.1144 0.1613      4.8635      5.0753|
| 13:  2.0639 -  2.0097 0.94   1269  130 0.1122 0.1671      4.7668      4.9741|
| 14:  2.0097 -  1.9608 0.29    371   53 0.1046 0.1763      4.6966      4.9257|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8125 -  4.6793  1430   158  0.94   9.14   0.98     0.96       7336.27|
|  2:  4.6793 -  3.7337  1385   154  0.95   7.98   1.02     1.00       8906.53|
|  3:  3.7337 -  3.2675  1338   149  0.93  11.40   1.03     1.02      10226.52|
|  4:  3.2675 -  2.9714  1343   145  0.92  13.60   1.01     1.00      10102.25|
|  5:  2.9714 -  2.7599  1314   152  0.90  15.98   1.00     0.97       8331.15|
|  6:  2.7599 -  2.5981  1336   143  0.89  16.56   0.98     0.95       7127.43|
|  7:  2.5981 -  2.4686  1296   154  0.90  15.83   0.99     0.95       6302.63|
|  8:  2.4686 -  2.3616  1340   138  0.90  15.74   1.00     0.97       5612.84|
|  9:  2.3616 -  2.2710  1310   148  0.90  16.17   1.01     0.98       5072.85|
| 10:  2.2710 -  2.1929  1306   144  0.90  16.18   1.00     0.96       4546.88|
| 11:  2.1929 -  2.1245  1286   152  0.90  16.29   1.00     0.97       4307.36|
| 12:  2.1245 -  2.0639  1306   139  0.90  15.98   1.01     1.01       3859.58|
| 13:  2.0639 -  2.0097  1269   130  0.91  15.80   1.00     0.98       3207.43|
| 14:  2.0097 -  1.9608   371    53  0.92  13.96   0.98     0.95       2617.44|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2617.44 max =        10226.52 mean =      6491.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.28|
|phase err.(test): min =        0.00 max =           89.74 mean =        13.81|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.751)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.91    91.29   15.01    None  None   None       |
|    all(noH): 2823   0      2.91    91.29   15.01    None  None   None       |
|    Sol.    : 438    0      4.46    85.54   37.25    None  None   None       |
|    Mac.    : 2385   0      2.91    91.29   10.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.910 -  11.749: 1748   |   5:    47.102 -  55.940:   79        |
|      1:    11.749 -  20.587:  534   |   6:    55.940 -  64.779:   37        |
|      2:    20.587 -  29.425:  155   |   7:    64.779 -  73.617:   20        |
|      3:    29.425 -  38.264:  130   |   8:    73.617 -  82.455:    6        |
|      4:    38.264 -  47.102:  110   |   9:    82.455 -  91.294:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.201 - 4.720
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 300 from: 302
   mapped sites are within: 0.708 - 4.720

peak=   11.375 closest distance to " CB  VAL A 230 " =    1.484
peak=    7.965 closest distance to " CG2 VAL A 296 " =    1.245
peak=    6.365 closest distance to " CG  LEU A   5 " =    1.239
peak=    5.695 closest distance to " NH2 ARG A  56 " =    2.197
peak=    5.421 closest distance to " CG  PRO A  54 " =    1.252
peak=    5.233 closest distance to " NE2 GLN A  11 " =    1.153
peak=    5.228 closest distance to " CG  LEU A 228 " =    1.200
peak=    5.183 closest distance to " CD2 LEU A   5 " =    1.132
peak=    4.986 closest distance to " CB  VAL A 296 " =    0.998
peak=    4.966 closest distance to " CB  ARG A 275 " =    0.924
peak=    4.941 closest distance to " O   HOH Z 142 " =    1.760
peak=    4.876 closest distance to " CB  GLN A 223 " =    1.508
peak=    4.802 closest distance to " CB  GLN A 183 " =    1.267
peak=    4.776 closest distance to " O   HOH Z 232 " =    2.298
peak=    4.745 closest distance to " O   HOH Z 346 " =    1.531
peak=    4.733 closest distance to " O   HOH Z 209 " =    2.291
peak=    4.720 closest distance to " O   HOH Z 193 " =    1.758
peak=    4.703 closest distance to " O   HOH Z  85 " =    1.594
peak=    4.659 closest distance to " O   HOH Z 402 " =    1.437
peak=    4.560 closest distance to " O   HOH Z 248 " =    1.342
peak=    4.540 closest distance to " O   SER A  87 " =    2.181
peak=    4.530 closest distance to " CB  SER A  63 " =    1.162
peak=    4.524 closest distance to " ND2 ASN A 187 " =    1.594
peak=    4.521 closest distance to " CB  ARG A  79 " =    1.445
peak=    4.501 closest distance to " O   HOH Z  63 " =    2.005
peak=    4.479 closest distance to " O   HOH Z  61 " =    1.675
peak=    4.448 closest distance to " O   HOH Z 272 " =    1.861
peak=    4.356 closest distance to " O   HOH Z 126 " =    1.821
peak=    4.334 closest distance to " CD2 TRP A 179 " =    1.337
peak=    4.333 closest distance to " O   HOH Z 287 " =    1.928
peak=    4.333 closest distance to " O   HOH Z 265 " =    2.135
peak=    4.314 closest distance to " CB  PRO A  54 " =    0.968
peak=    4.279 closest distance to " O   HOH Z 403 " =    1.753
peak=    4.244 closest distance to " C   PRO A 198 " =    1.469
peak=    4.235 closest distance to " CG  PRO A 213 " =    1.213
peak=    4.213 closest distance to " CB  GLU A 152 " =    1.143
peak=    4.195 closest distance to " O   HOH Z 130 " =    2.618
peak=    4.188 closest distance to " O   HOH Z 369 " =    2.361
peak=    4.181 closest distance to " CB  GLU A 277 " =    3.598
peak=    4.138 closest distance to " CB  VAL A 230 " =    1.189
peak=    4.114 closest distance to " O   HOH Z 251 " =    1.567
peak=    4.095 closest distance to " O   HOH Z 368 " =    2.156
peak=    4.089 closest distance to " CB  ASN A 148 " =    1.426
peak=    4.076 closest distance to " CB  ALA A   9 " =    1.636
peak=    4.064 closest distance to " O   HOH Z 188 " =    2.734
peak=    4.057 closest distance to " O   HOH Z 423 " =    1.908
peak=    4.052 closest distance to " O   HOH Z 154 " =    1.624
peak=    4.046 closest distance to " CG  PRO A 243 " =    1.140
peak=    4.036 closest distance to " O   HOH Z 234 " =    3.580
peak=    4.035 closest distance to " O   HOH Z 411 " =    3.827
peak=    4.030 closest distance to " O   HOH Z 298 " =    1.740
peak=    4.024 closest distance to " O   HOH Z  59 " =    2.067
peak=    4.003 closest distance to " O   HOH Z 427 " =    2.867
peak=    3.998 closest distance to " CA  ALA A  51 " =    0.975
peak=    3.996 closest distance to " CZ  PHE A 218 " =    1.147
peak=    3.992 closest distance to " O   HOH Z 422 " =    2.531
peak=    3.991 closest distance to " O   HOH Z 188 " =    1.380
peak=    3.991 closest distance to " CB  SER A  26 " =    1.841
peak=    3.983 closest distance to " O   HOH Z 313 " =    1.888
peak=    3.978 closest distance to " O   HOH Z  97 " =    1.958
peak=    3.970 closest distance to " N   ASN A  39 " =    1.278
peak=    3.962 closest distance to " O   HOH Z 303 " =    2.125
peak=    3.957 closest distance to " O   HOH Z 124 " =    1.334
peak=    3.953 closest distance to " O   HOH Z  80 " =    1.745
peak=    3.935 closest distance to " O   HOH Z 126 " =    1.759
peak=    3.929 closest distance to " O   HOH Z 126 " =    1.521
peak=    3.914 closest distance to " O   HOH Z  43 " =    2.231
peak=    3.909 closest distance to " O   HOH Z  78 " =    1.630
peak=    3.908 closest distance to " CG2 ILE A  20 " =    1.414
peak=    3.896 closest distance to " CD2 LEU A 228 " =    1.339
peak=    3.874 closest distance to " CB  ASN A 142 " =    1.143
peak=    3.869 closest distance to " N   ALA A   1 " =    3.026
peak=    3.852 closest distance to " O   HOH Z 261 " =    2.116
peak=    3.835 closest distance to " CA  TYR A  30 " =    0.964
peak=    3.828 closest distance to " CB  ASN A 187 " =    1.239
peak=    3.826 closest distance to " O   HOH Z  97 " =    2.314
peak=    3.815 closest distance to " O   HOH Z 214 " =    2.502
peak=    3.813 closest distance to " O   HOH Z 345 " =    3.073
peak=    3.811 closest distance to " CB  VAL A 265 " =    1.302
peak=    3.811 closest distance to " O   HOH Z  44 " =    1.908
peak=    3.806 closest distance to " CB  TRP A 266 " =    1.055
peak=    3.791 closest distance to " O   HOH Z 102 " =    1.318
peak=    3.790 closest distance to " CB  ARG A 139 " =    1.048
peak=    3.787 closest distance to " O   HOH Z 359 " =    1.444
peak=    3.785 closest distance to " CB  SER A   3 " =    1.246
peak=    3.783 closest distance to " CB  ASN A  39 " =    0.861
peak=    3.766 closest distance to " CA  ARG A  36 " =    1.054
peak=    3.757 closest distance to " CB  ARG A 190 " =    1.702
peak=    3.753 closest distance to " O   HOH Z  88 " =    2.714
peak=    3.747 closest distance to " CD  LYS A 166 " =    1.316
peak=    3.742 closest distance to " O   HOH Z 158 " =    3.014
peak=    3.741 closest distance to " O   HOH Z  40 " =    1.695
peak=    3.731 closest distance to " CB  VAL A 202 " =    1.519
peak=    3.727 closest distance to " OE1 GLU A   2 " =    2.219
peak=    3.723 closest distance to " O   HOH Z 273 " =    2.893
peak=    3.720 closest distance to " O   HOH Z 128 " =    2.523
peak=    3.708 closest distance to " O   HOH Z 371 " =    3.029
peak=    3.698 closest distance to " O   HOH Z 406 " =    1.382
peak=    3.695 closest distance to " O   ASP A 124 " =    1.403
peak=    3.694 closest distance to " CG1 ILE A  49 " =    1.479
peak=    3.686 closest distance to " O   HOH Z 250 " =    1.386
peak=    3.680 closest distance to " OG ASER A 258 " =    3.058
peak=    3.678 closest distance to " CB  TYR A 169 " =    0.779
peak=    3.674 closest distance to " CB  TRP A 179 " =    1.311
peak=    3.652 closest distance to " CD  ARG A 269 " =    0.930
peak=    3.650 closest distance to " CG  PRO A 198 " =    1.207
peak=    3.633 closest distance to " NZ  LYS A 117 " =    2.740
peak=    3.626 closest distance to " CD2 LEU A 297 " =    0.923
peak=    3.616 closest distance to " CG2AVAL A 121 " =    2.248
peak=    3.600 closest distance to " N   PHE A 130 " =    1.342
peak=    3.585 closest distance to " O   HOH Z 180 " =    2.168
peak=    3.583 closest distance to " O   HOH Z 128 " =    1.901
peak=    3.582 closest distance to " O   HOH Z 238 " =    0.925
peak=    3.582 closest distance to " CD  LYS A  76 " =    1.749
peak=    3.582 closest distance to " O   HOH Z 145 " =    2.388
peak=    3.578 closest distance to " NH2BARG A 145 " =    2.154
peak=    3.572 closest distance to " CB  THR A  31 " =    1.552
peak=    3.571 closest distance to " O   HOH Z 327 " =    1.524
peak=    3.567 closest distance to " O   HOH Z 389 " =    1.750
peak=    3.565 closest distance to " CG  LEU A 167 " =    1.218
peak=    3.565 closest distance to " O   HOH Z 404 " =    2.247
peak=    3.558 closest distance to " O   HOH Z 130 " =    2.510
peak=    3.556 closest distance to " OD2 ASP A 298 " =    3.949
peak=    3.548 closest distance to " O   HOH Z 425 " =    1.987
peak=    3.543 closest distance to " O   HOH Z  21 " =    1.833
peak=    3.538 closest distance to " CB  ASN A 110 " =    1.093
peak=    3.526 closest distance to " CB  ALA A 248 " =    1.273
peak=    3.526 closest distance to " NH2AARG A 275 " =    3.578
peak=    3.525 closest distance to " OG BSER A 164 " =    2.202
peak=    3.525 closest distance to " CB  GLU A  46 " =    1.020
peak=    3.523 closest distance to " O   HOH Z 425 " =    1.347
peak=    3.522 closest distance to " O   HOH Z 130 " =    2.226
peak=    3.521 closest distance to " CB  PHE A 204 " =    0.843
peak=    3.509 closest distance to " N   SER A 135 " =    1.400
peak=    3.508 closest distance to " OD1 ASN A  69 " =    2.435
peak=    3.507 closest distance to " CG  MET A 185 " =    1.097
peak=    3.506 closest distance to " CG  GLN A  58 " =    2.926
peak=    3.506 closest distance to " O   HOH Z 322 " =    2.146
peak=    3.498 closest distance to " CB  THR A  52 " =    1.007
peak=    3.493 closest distance to " O   HOH Z  54 " =    1.567
peak=    3.492 closest distance to " CG1BVAL A  72 " =    1.666
peak=    3.492 closest distance to " CA  ALA A 291 " =    0.823
peak=    3.489 closest distance to " N   ASP A 162 " =    1.236
peak=    3.487 closest distance to " CD  LYS A 119 " =    1.967
peak=    3.481 closest distance to " CB  ASP A 140 " =    1.048
peak=    3.476 closest distance to " O   HOH Z 141 " =    1.597
peak=    3.468 closest distance to " O   HOH Z 421 " =    1.593
peak=    3.463 closest distance to " O   HOH Z  15 " =    2.023
peak=    3.458 closest distance to " O   HOH Z 299 " =    4.163
peak=    3.457 closest distance to " O   HOH Z 130 " =    1.086
peak=    3.451 closest distance to " CG BARG A 102 " =    1.714
peak=    3.448 closest distance to " O   HOH Z 357 " =    1.929
peak=    3.443 closest distance to " OG  SER A 276 " =    1.369
peak=    3.428 closest distance to " O   HOH Z 407 " =    2.803
peak=    3.423 closest distance to " O   HOH Z 380 " =    1.922
peak=    3.421 closest distance to " CA  VAL A  41 " =    0.766
peak=    3.415 closest distance to " O   HOH Z 325 " =    2.079
peak=    3.414 closest distance to " CB  ASN A 215 " =    1.109
peak=    3.411 closest distance to " O   HOH Z   3 " =    1.642
peak=    3.410 closest distance to " O   HOH Z  94 " =    2.201
peak=    3.408 closest distance to " CD  ARG A 159 " =    0.711
peak=    3.406 closest distance to " O   HOH Z 148 " =    3.273
peak=    3.401 closest distance to " NZ  LYS A  48 " =    1.148
peak=    3.400 closest distance to " CB  ARG A 219 " =    1.129
peak=    3.398 closest distance to " O   HOH Z 258 " =    2.301
peak=    3.393 closest distance to " NE2 GLN A  77 " =    3.189
peak=    3.385 closest distance to " CA  ALA A  21 " =    1.132
peak=    3.385 closest distance to " CB  LEU A  83 " =    0.710
peak=    3.383 closest distance to " O   ASN A  74 " =    1.539
peak=    3.379 closest distance to " CA  TYR A 116 " =    1.511
peak=    3.377 closest distance to " CA  ASN A 215 " =    1.031
peak=    3.377 closest distance to " CG2 ILE A 120 " =    1.318
peak=    3.376 closest distance to " O   HOH Z  19 " =    1.708
peak=    3.373 closest distance to " O   HOH Z 419 " =    1.763
peak=    3.371 closest distance to " CA  ALA A 158 " =    1.352
peak=    3.371 closest distance to " CB  TRP A 150 " =    1.415
peak=    3.368 closest distance to " CA  ASP A 162 " =    1.056
peak=    3.364 closest distance to " O   HOH Z 365 " =    2.763
peak=    3.363 closest distance to " O   HOH Z 246 " =    1.311
peak=    3.362 closest distance to " CG AARG A 275 " =    1.254
peak=    3.361 closest distance to " O   HOH Z  68 " =    2.172
peak=    3.356 closest distance to " O   HOH Z 147 " =    1.761
peak=    3.350 closest distance to " O   TRP A 274 " =    1.811
peak=    3.349 closest distance to " O   HOH Z 173 " =    2.299
peak=    3.346 closest distance to " O   HOH Z 392 " =    2.861
peak=    3.345 closest distance to " O   HOH Z 203 " =    1.548
peak=    3.344 closest distance to " CB BVAL A  41 " =    1.142
peak=    3.339 closest distance to " CA  ASP A 149 " =    1.059
peak=    3.339 closest distance to " O   HOH Z 406 " =    1.641
peak=    3.339 closest distance to " O   HOH Z 298 " =    4.235
peak=    3.337 closest distance to " O   HOH Z  35 " =    2.417
peak=    3.336 closest distance to " CA  LYS A 117 " =    1.255
peak=    3.335 closest distance to " CA  ALA A 233 " =    1.321
peak=    3.334 closest distance to " O   HOH Z 193 " =    1.792
peak=    3.333 closest distance to " CB  ALA A 295 " =    1.203
peak=    3.330 closest distance to " O   HOH Z  10 " =    1.742
peak=    3.329 closest distance to " O   HOH Z 361 " =    3.041
peak=    3.328 closest distance to " CB  SER A  62 " =    1.249
peak=    3.327 closest distance to " O   HOH Z 128 " =    1.531
peak=    3.322 closest distance to " CA  SER A  32 " =    1.681
peak=    3.321 closest distance to " O   HOH Z 383 " =    1.869
peak=    3.318 closest distance to " CG  MET A 185 " =    0.967
peak=    3.316 closest distance to " O   HOH Z  88 " =    2.851
peak=    3.316 closest distance to " CB  ALA A 104 " =    0.708
peak=    3.299 closest distance to " CB  GLU A 128 " =    0.993
peak=    3.294 closest distance to " O   HOH Z 353 " =    2.713
peak=    3.291 closest distance to " O   HOH Z 137 " =    1.640
peak=    3.290 closest distance to " CG2 THR A 221 " =    1.125
peak=    3.290 closest distance to " CG1 VAL A 296 " =    1.171
peak=    3.287 closest distance to " O   THR A  31 " =    1.809
peak=    3.286 closest distance to " CB  HIS A 108 " =    0.831
peak=    3.282 closest distance to " O   SER A 164 " =    1.131
peak=    3.280 closest distance to " O  BHOH Z 338 " =    2.433
peak=    3.279 closest distance to " CG  GLN A  88 " =    1.069
peak=    3.278 closest distance to " O   HOH Z 293 " =    1.813
peak=    3.276 closest distance to " CA  ARG A 195 " =    1.189
peak=    3.273 closest distance to " N   ARG A 156 " =    1.362
peak=    3.272 closest distance to " OG1 THR A 294 " =    2.329
peak=    3.268 closest distance to " CD2 TYR A 186 " =    1.059
peak=    3.265 closest distance to " O   HOH Z   9 " =    2.076
peak=    3.265 closest distance to " O   HOH Z  88 " =    3.153
peak=    3.263 closest distance to " CG2 VAL A 257 " =    0.785
peak=    3.260 closest distance to " O   HOH Z 329 " =    4.016
peak=    3.256 closest distance to " CA  LEU A 282 " =    1.276
peak=    3.255 closest distance to " O   HOH Z 301 " =    1.787
peak=    3.254 closest distance to " CG2 THR A 294 " =    1.640
peak=    3.251 closest distance to " O   HOH Z 188 " =    2.189
peak=    3.250 closest distance to " CA  GLY A 133 " =    3.598
peak=    3.248 closest distance to " CB  ASP A 132 " =    0.979
peak=    3.247 closest distance to " O   ILE A  20 " =    2.182
peak=    3.246 closest distance to " CG2 THR A  18 " =    1.526
peak=    3.246 closest distance to " O   HOH Z 344 " =    2.873
peak=    3.245 closest distance to " CD1 ILE A 106 " =    1.131
peak=    3.244 closest distance to " O   HOH Z 435 " =    1.916
peak=    3.241 closest distance to " CZ3 TRP A  85 " =    0.973
peak=    3.241 closest distance to " NH2 ARG A  79 " =    1.338
peak=    3.240 closest distance to " O   HOH Z 109 " =    2.060
peak=    3.239 closest distance to " CB  PRO A  90 " =    1.119
peak=    3.238 closest distance to " O   HOH Z 368 " =    3.543
peak=    3.232 closest distance to " O   HOH Z 388 " =    2.221
peak=    3.231 closest distance to " CG  GLN A  55 " =    2.384
peak=    3.221 closest distance to " O   HOH Z 171 " =    2.003
peak=    3.220 closest distance to " O   LEU A 228 " =    1.782
peak=    3.220 closest distance to " CE1 HIS A 108 " =    1.153
peak=    3.217 closest distance to " CB  ARG A 190 " =    1.122
peak=    3.215 closest distance to " O   HOH Z 282 " =    2.038
peak=    3.214 closest distance to " CB  THR A 235 " =    1.204
peak=    3.213 closest distance to " CZ2 TRP A 150 " =    1.137
peak=    3.210 closest distance to " O   HOH Z 352 " =    1.274
peak=    3.207 closest distance to " ND2 ASN A 249 " =    0.890
peak=    3.205 closest distance to " CE1 TYR A 186 " =    1.253
peak=    3.204 closest distance to " OE2 GLU A  53 " =    2.076
peak=    3.203 closest distance to " CD1 LEU A  96 " =    0.752
peak=    3.202 closest distance to " O   HOH Z 234 " =    1.872
peak=    3.192 closest distance to " O   HOH Z 245 " =    1.441
peak=    3.185 closest distance to " O   HOH Z 227 " =    2.102
peak=    3.184 closest distance to " CA  SER A 146 " =    1.942
peak=    3.179 closest distance to " NH2 ARG A 156 " =    1.083
peak=    3.177 closest distance to " O   HOH Z 417 " =    3.466
peak=    3.168 closest distance to " NH1AARG A 145 " =    1.228
peak=    3.168 closest distance to " CA  PHE A  59 " =    0.933
peak=    3.166 closest distance to " OG  SER A  62 " =    2.745
peak=    3.162 closest distance to " CE  LYS A  76 " =    0.895
peak=    3.158 closest distance to " O   HOH Z 132 " =    2.724
peak=    3.158 closest distance to " CB  LYS A 290 " =    1.025
peak=    3.158 closest distance to " CA  GLY A 267 " =    0.804
peak=    3.157 closest distance to " CB  ARG A 156 " =    1.143
peak=    3.156 closest distance to " CG  LYS A 119 " =    1.113
peak=    3.154 closest distance to " O   HOH Z 263 " =    1.717
peak=    3.152 closest distance to " O   ASN A 284 " =    1.755
peak=    3.152 closest distance to " O   HOH Z 337 " =    1.671
peak=    3.151 closest distance to " O   HOH Z 236 " =    1.662
peak=    3.151 closest distance to " O   ILE A  33 " =    1.146
peak=    3.148 closest distance to " CA  ASN A 176 " =    1.101
peak=    3.148 closest distance to " CZ  PHE A  38 " =    1.121
peak=    3.147 closest distance to " O   HOH Z 116 " =    2.556
peak=    3.144 closest distance to " O   HOH Z 183 " =    1.734
peak=    3.136 closest distance to " CB  ALA A 291 " =    1.322
peak=    3.131 closest distance to " O   HOH Z 118 " =    1.504
peak=    3.128 closest distance to " O   HOH Z 368 " =    4.720
peak=    3.126 closest distance to " O   HOH Z 209 " =    2.374
peak=    3.116 closest distance to " O   HOH Z 244 " =    1.598
peak=    3.116 closest distance to " O   HOH Z 361 " =    3.500
peak=    3.115 closest distance to " O   HOH Z 134 " =    1.247
peak=    3.107 closest distance to " O   HOH Z  47 " =    1.827
peak=    3.105 closest distance to " CD  ARG A  79 " =    1.865
peak=    3.103 closest distance to " O   HOH Z 394 " =    3.679
peak=    3.102 closest distance to " O   HOH Z  40 " =    2.653
peak=    3.096 closest distance to " O   HOH Z 426 " =    1.456
peak=    3.095 closest distance to " CZ2 TRP A 274 " =    1.606
peak=    3.093 closest distance to " CD1 LEU A   5 " =    1.517
peak=    3.087 closest distance to " O   HOH Z  99 " =    1.880
peak=    3.080 closest distance to " CB  ALA A  71 " =    1.265
peak=    3.078 closest distance to " OG  SER A  22 " =    2.660
peak=    3.077 closest distance to " CA  ILE A 106 " =    0.751
peak=    3.076 closest distance to " O   HOH Z  49 " =    3.531
peak=    3.062 closest distance to " O   HOH Z  63 " =    2.096
peak=    3.052 closest distance to " O   HOH Z 423 " =    3.237
peak=    3.042 closest distance to " CD1 LEU A 228 " =    1.839
peak=    3.039 closest distance to " O   ALA A   1 " =    1.795

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.484 - 5.628
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 200
   mapped sites are within: 0.826 - 5.628

peak=   -4.793 closest distance to " CG  GLN A  58 " =    1.105
peak=   -4.652 closest distance to " CD  ARG A  14 " =    3.244
peak=   -4.416 closest distance to " OG BSER A 134 " =    1.264
peak=   -4.373 closest distance to " O   HOH Z 266 " =    5.266
peak=   -4.356 closest distance to " CD  ARG A 156 " =    2.029
peak=   -4.267 closest distance to " O   PRO A 163 " =    2.180
peak=   -4.264 closest distance to " CD1 LEU A 101 " =    2.353
peak=   -4.238 closest distance to " C   HIS A 108 " =    1.243
peak=   -4.195 closest distance to " OXT GLY A 302 " =    2.824
peak=   -4.134 closest distance to " CB  ALA A 248 " =    2.298
peak=   -4.101 closest distance to " O   HOH Z 351 " =    1.477
peak=   -4.076 closest distance to " CG  GLN A 223 " =    2.147
peak=   -4.056 closest distance to " O   HOH Z 166 " =    1.887
peak=   -4.053 closest distance to " O   HOH Z 193 " =    1.407
peak=   -4.046 closest distance to " O   VAL A  67 " =    2.476
peak=   -4.045 closest distance to " CE2 TYR A  30 " =    2.740
peak=   -4.043 closest distance to " O   HOH Z 290 " =    1.045
peak=   -4.037 closest distance to " O   HOH Z 114 " =    3.217
peak=   -4.012 closest distance to " CD2 PHE A 192 " =    2.052
peak=   -3.968 closest distance to " ND2 ASN A 187 " =    1.595
peak=   -3.947 closest distance to " NE2 GLN A  88 " =    1.053
peak=   -3.934 closest distance to " O   HOH Z 394 " =    1.582
peak=   -3.920 closest distance to " O   HOH Z 387 " =    2.672
peak=   -3.898 closest distance to " CE  MET A 105 " =    2.379
peak=   -3.823 closest distance to " CD1 ILE A 263 " =    2.757
peak=   -3.817 closest distance to " CD2 TYR A 293 " =    1.963
peak=   -3.794 closest distance to " O   HOH Z 196 " =    2.085
peak=   -3.763 closest distance to " CG2 THR A 178 " =    2.322
peak=   -3.745 closest distance to " N   ALA A 248 " =    2.139
peak=   -3.742 closest distance to " CA  ASP A 298 " =    1.083
peak=   -3.721 closest distance to " CZ3 TRP A 179 " =    1.304
peak=   -3.715 closest distance to " CD1 PHE A 130 " =    2.311
peak=   -3.708 closest distance to " O   PHE A 218 " =    1.593
peak=   -3.676 closest distance to " O   SER A 210 " =    1.905
peak=   -3.676 closest distance to " O   HOH Z 103 " =    1.851
peak=   -3.673 closest distance to " O   HOH Z 435 " =    2.645
peak=   -3.654 closest distance to " CB  ALA A 161 " =    2.440
peak=   -3.647 closest distance to " CB  PRO A 163 " =    2.490
peak=   -3.644 closest distance to " NH2AARG A 275 " =    4.890
peak=   -3.637 closest distance to " CB  ALA A 248 " =    2.074
peak=   -3.633 closest distance to " O   PRO A 198 " =    1.192
peak=   -3.626 closest distance to " CB  ASP A 132 " =    2.330
peak=   -3.626 closest distance to " O   ASN A  45 " =    1.900
peak=   -3.625 closest distance to " CA  VAL A  67 " =    2.887
peak=   -3.617 closest distance to " CG1 VAL A 112 " =    2.670
peak=   -3.616 closest distance to " CG  ASP A 231 " =    0.826
peak=   -3.613 closest distance to " O   HOH Z 211 " =    1.490
peak=   -3.604 closest distance to " ND2 ASN A  45 " =    1.151
peak=   -3.589 closest distance to " CB  ALA A  43 " =    2.415
peak=   -3.586 closest distance to " O   HOH Z 407 " =    2.823
peak=   -3.569 closest distance to " OD1 ASN A 301 " =    2.004
peak=   -3.563 closest distance to " CG  TRP A 266 " =    1.903
peak=   -3.557 closest distance to " CE BMET A  47 " =    1.374
peak=   -3.553 closest distance to " N   SER A 276 " =    1.337
peak=   -3.551 closest distance to " CB  ALA A 291 " =    2.245
peak=   -3.539 closest distance to " O   GLY A  80 " =    2.526
peak=   -3.529 closest distance to " CG2 VAL A 296 " =    1.483
peak=   -3.521 closest distance to " O   HOH Z 423 " =    2.186
peak=   -3.515 closest distance to " O   HOH Z 165 " =    1.917
peak=   -3.510 closest distance to " N   ALA A 226 " =    1.962
peak=   -3.509 closest distance to " CB  TYR A  15 " =    2.195
peak=   -3.509 closest distance to " O   ALA A   8 " =    1.945
peak=   -3.505 closest distance to " NE2 GLN A  88 " =    1.952
peak=   -3.503 closest distance to " O   HOH Z 216 " =    1.414
peak=   -3.503 closest distance to " CA  GLY A 241 " =    2.510
peak=   -3.497 closest distance to " O   SER A 276 " =    1.713
peak=   -3.494 closest distance to " OG  SER A  97 " =    2.315
peak=   -3.493 closest distance to " O   HOH Z 166 " =    1.611
peak=   -3.490 closest distance to " CG  LEU A   5 " =    0.913
peak=   -3.484 closest distance to " O   GLY A 196 " =    1.123
peak=   -3.483 closest distance to " CA  GLY A 133 " =    2.288
peak=   -3.482 closest distance to " C   SER A 206 " =    1.478
peak=   -3.481 closest distance to " O   HOH Z 191 " =    5.628
peak=   -3.462 closest distance to " CA  GLY A 133 " =    1.945
peak=   -3.454 closest distance to " O   HOH Z  11 " =    1.926
peak=   -3.453 closest distance to " O   HOH Z 185 " =    2.470
peak=   -3.444 closest distance to " O   ASN A 187 " =    1.569
peak=   -3.442 closest distance to " O   HOH Z  15 " =    1.527
peak=   -3.442 closest distance to " O   HOH Z 136 " =    2.490
peak=   -3.441 closest distance to " O   HOH Z 131 " =    4.092
peak=   -3.440 closest distance to " O   HOH Z 154 " =    1.527
peak=   -3.439 closest distance to " CG2 ILE A 263 " =    2.221
peak=   -3.435 closest distance to " CG1 VAL A 112 " =    2.840
peak=   -3.427 closest distance to " N   ALA A 248 " =    1.677
peak=   -3.417 closest distance to " OG ASER A 134 " =    1.407
peak=   -3.399 closest distance to " ND2 ASN A  39 " =    1.101
peak=   -3.398 closest distance to " CG  PHE A  59 " =    2.026
peak=   -3.393 closest distance to " O   HOH Z 116 " =    1.342
peak=   -3.393 closest distance to " O   ALA A 227 " =    1.456
peak=   -3.384 closest distance to " CB  ASP A 132 " =    2.375
peak=   -3.379 closest distance to " N   HIS A 115 " =    2.168
peak=   -3.377 closest distance to " C   ILE A 239 " =    2.142
peak=   -3.375 closest distance to " N   THR A  52 " =    1.710
peak=   -3.374 closest distance to " O   HOH Z  88 " =    4.270
peak=   -3.368 closest distance to " C   ASN A 285 " =    2.192
peak=   -3.355 closest distance to " O   HOH Z 102 " =    1.683
peak=   -3.346 closest distance to " CG  GLU A  53 " =    1.662
peak=   -3.343 closest distance to " O   VAL A 174 " =    2.199
peak=   -3.341 closest distance to " CD1 PHE A  59 " =    2.014
peak=   -3.336 closest distance to " O   HOH Z 389 " =    2.004
peak=   -3.336 closest distance to " CB  SER A 210 " =    1.240
peak=   -3.336 closest distance to " OD2 ASP A 191 " =    1.452
peak=   -3.331 closest distance to " OXT GLY A 302 " =    3.516
peak=   -3.331 closest distance to " O   HOH Z  13 " =    1.864
peak=   -3.329 closest distance to " O   HOH Z 174 " =    3.976
peak=   -3.326 closest distance to " NH2 ARG A  79 " =    2.043
peak=   -3.325 closest distance to " CE3 TRP A 150 " =    2.177
peak=   -3.313 closest distance to " O   HOH Z 193 " =    2.046
peak=   -3.311 closest distance to " C   GLN A 205 " =    1.878
peak=   -3.310 closest distance to " NE  ARG A  66 " =    4.194
peak=   -3.304 closest distance to " O   HOH Z 281 " =    2.875
peak=   -3.300 closest distance to " CZ  PHE A  38 " =    2.022
peak=   -3.299 closest distance to " O   GLY A  80 " =    2.591
peak=   -3.297 closest distance to " O   HOH Z 374 " =    1.851
peak=   -3.296 closest distance to " C   MET A 188 " =    1.460
peak=   -3.292 closest distance to " C   ILE A 234 " =    1.279
peak=   -3.288 closest distance to " N   GLN A  58 " =    2.077
peak=   -3.282 closest distance to " O   HOH Z  11 " =    2.083
peak=   -3.280 closest distance to " CD1 ILE A 199 " =    2.355
peak=   -3.280 closest distance to " C   ASP A 231 " =    2.420
peak=   -3.276 closest distance to " CD  ARG A 139 " =    1.727
peak=   -3.274 closest distance to " O   HOH Z 252 " =    3.941
peak=   -3.274 closest distance to " O   HOH Z 275 " =    1.832
peak=   -3.273 closest distance to " N   ASP A 171 " =    2.292
peak=   -3.269 closest distance to " CB  ASN A  39 " =    2.289
peak=   -3.264 closest distance to " N   THR A 157 " =    1.489
peak=   -3.264 closest distance to " ND2 ASN A  69 " =    1.823
peak=   -3.263 closest distance to " O   HOH Z 111 " =    4.328
peak=   -3.262 closest distance to " CG1 VAL A 230 " =    1.914
peak=   -3.252 closest distance to " O   PRO A 198 " =    1.284
peak=   -3.247 closest distance to " O   TRP A  92 " =    1.942
peak=   -3.247 closest distance to " O   HOH Z 301 " =    2.309
peak=   -3.244 closest distance to " O   ILE A 106 " =    1.896
peak=   -3.244 closest distance to " O   SER A 271 " =    2.127
peak=   -3.237 closest distance to " O   HOH Z 174 " =    2.249
peak=   -3.233 closest distance to " CA  GLY A  23 " =    1.836
peak=   -3.232 closest distance to " NH2 ARG A 159 " =    2.322
peak=   -3.231 closest distance to " O   VAL A 189 " =    2.623
peak=   -3.231 closest distance to " O   HOH Z 421 " =    3.443
peak=   -3.231 closest distance to " CZ  TYR A 169 " =    1.866
peak=   -3.229 closest distance to " O   HOH Z 238 " =    0.915
peak=   -3.227 closest distance to " CZ2 TRP A 274 " =    1.169
peak=   -3.222 closest distance to " O   HOH Z 295 " =    1.478
peak=   -3.220 closest distance to " OE1 GLN A 183 " =    1.485
peak=   -3.220 closest distance to " CB  TRP A  85 " =    2.653
peak=   -3.216 closest distance to " CG1 VAL A  78 " =    2.597
peak=   -3.214 closest distance to " OG BSER A 134 " =    1.792
peak=   -3.206 closest distance to " O   HOH Z 283 " =    2.206
peak=   -3.200 closest distance to " O   HOH Z 139 " =    3.280
peak=   -3.199 closest distance to " CZ  TYR A 172 " =    1.846
peak=   -3.198 closest distance to " CD2 LEU A 237 " =    2.748
peak=   -3.193 closest distance to " ND2 ASN A 187 " =    0.905
peak=   -3.190 closest distance to " O   ARG A  24 " =    2.000
peak=   -3.189 closest distance to " CG  PRO A 163 " =    2.620
peak=   -3.184 closest distance to " OD1 ASN A 148 " =    1.514
peak=   -3.179 closest distance to " O   HOH Z 371 " =    2.064
peak=   -3.176 closest distance to " CD2 PHE A 225 " =    1.217
peak=   -3.174 closest distance to " O   HOH Z 139 " =    5.023
peak=   -3.174 closest distance to " C   LEU A 143 " =    0.986
peak=   -3.173 closest distance to " O   HOH Z 431 " =    1.951
peak=   -3.171 closest distance to " O   HOH Z 285 " =    1.804
peak=   -3.164 closest distance to " O   HOH Z 243 " =    1.933
peak=   -3.162 closest distance to " CE1 TYR A 247 " =    2.592
peak=   -3.162 closest distance to " O   HOH Z 313 " =    1.859
peak=   -3.156 closest distance to " O   HOH Z 348 " =    2.292
peak=   -3.153 closest distance to " N   LYS A 289 " =    1.631
peak=   -3.152 closest distance to " CG  ARG A 219 " =    2.644
peak=   -3.149 closest distance to " OE2 GLU A 152 " =    1.434
peak=   -3.147 closest distance to " O   GLY A  80 " =    2.545
peak=   -3.139 closest distance to " CG  GLU A 277 " =    1.231
peak=   -3.138 closest distance to " ND2 ASN A  60 " =    1.265
peak=   -3.134 closest distance to " O   HOH Z 353 " =    2.225
peak=   -3.132 closest distance to " OD1 ASN A 249 " =    2.396
peak=   -3.132 closest distance to " CG2 THR A  18 " =    2.886
peak=   -3.126 closest distance to " O   HOH Z  63 " =    1.281
peak=   -3.124 closest distance to " CD  PRO A 243 " =    2.109
peak=   -3.124 closest distance to " O   HOH Z 426 " =    1.782
peak=   -3.124 closest distance to " O   HOH Z  52 " =    1.660
peak=   -3.121 closest distance to " O   GLY A  75 " =    1.779
peak=   -3.116 closest distance to " CB  TYR A 172 " =    2.447
peak=   -3.115 closest distance to " O   HOH Z 137 " =    1.559
peak=   -3.114 closest distance to " CA  PRO A 243 " =    2.217
peak=   -3.109 closest distance to " O   ASN A 301 " =    1.487
peak=   -3.106 closest distance to " O   HOH Z 372 " =    2.380
peak=   -3.104 closest distance to " CG  PHE A 283 " =    2.657
peak=   -3.103 closest distance to " O   HOH Z 110 " =    1.486
peak=   -3.102 closest distance to " CA  GLY A 241 " =    3.124
peak=   -3.098 closest distance to " O   HOH Z 369 " =    2.298
peak=   -3.098 closest distance to " O   HOH Z 357 " =    2.052
peak=   -3.096 closest distance to " CG  ARG A 269 " =    2.158
peak=   -3.079 closest distance to " O   HOH Z  64 " =    2.584
peak=   -3.057 closest distance to " CD2 PHE A  61 " =    2.061
peak=   -3.053 closest distance to " CB  ALA A 291 " =    2.151
peak=   -3.053 closest distance to " O   HOH Z 310 " =    3.379
peak=   -3.034 closest distance to " CH2 TRP A 150 " =    1.141
peak=   -3.017 closest distance to " O   HOH Z 111 " =    2.051

================= 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    :  0.4602 0.4483   6.261554e+00   6.245231e+00
   1_bss:  0.4514 0.4381   6.252190e+00   6.237671e+00
   1_xyz:  0.3532 0.3707   6.090799e+00   6.131223e+00
   1_adp:  0.2995 0.3406   5.964956e+00   6.064197e+00
   1_occ:  0.2990 0.3414   5.964212e+00   6.065644e+00
   2_bss:  0.2941 0.3370   5.963963e+00   6.065038e+00
   2_xyz:  0.1985 0.2417   5.622525e+00   5.790150e+00
   2_adp:  0.1767 0.2216   5.519668e+00   5.704686e+00
   2_occ:  0.1765 0.2217   5.519503e+00   5.704946e+00
   3_bss:  0.1744 0.2208   5.517406e+00   5.701981e+00
   3_xyz:  0.1320 0.1746   5.274128e+00   5.488626e+00
   3_adp:  0.1235 0.1690   5.227874e+00   5.456225e+00
   3_occ:  0.1233 0.1689   5.227392e+00   5.455946e+00
   4_bss:  0.1233 0.1689   5.226678e+00   5.453125e+00
   4_xyz:  0.1195 0.1635   5.205232e+00   5.431024e+00
   4_adp:  0.1185 0.1618   5.196482e+00   5.420297e+00
   4_occ:  0.1184 0.1618   5.196443e+00   5.420499e+00
   5_bss:  0.1184 0.1617   5.196175e+00   5.420136e+00
   5_xyz:  0.1113 0.1581   5.155114e+00   5.397514e+00
   5_adp:  0.1116 0.1567   5.151493e+00   5.387770e+00
   5_occ:  0.1116 0.1566   5.151107e+00   5.387478e+00
   5_bss:  0.1116 0.1566   5.151148e+00   5.387503e+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:  0.338  13.538   8.326   8.314   9.370   0.000   0.000   0.000
   1_xyz:  0.338  13.538   8.326   8.314   9.370   0.000   0.000   0.000
   1_adp:  0.338  13.538   8.326   8.314   9.370   0.000   0.000   0.000
   1_occ:  0.338  13.538   8.326   8.314   9.370   0.000   0.000   0.000
   2_bss:  0.326  38.618   4.433   4.303   5.698   0.000   0.000   0.000
   2_xyz:  0.326  38.618   4.433   4.303   5.698   0.000   0.000   0.000
   2_adp:  0.326  38.618   4.433   4.303   5.698   0.000   0.000   0.000
   2_occ:  0.326  38.618   4.433   4.303   5.698   0.000   0.000   0.000
   3_bss:  0.310  38.619   2.182   3.089   4.138   0.000   0.000   0.000
   3_xyz:  0.310  38.619   2.182   3.089   4.138   0.000   0.000   0.000
   3_adp:  0.310  38.619   2.182   3.089   4.138   0.000   0.000   0.000
   3_occ:  0.310  38.619   2.182   3.089   4.138   0.000   0.000   0.000
   4_bss:  0.310  38.619   1.852   2.824   3.938   0.000   0.000   0.000
   4_xyz:  0.310  38.619   1.852   2.824   3.938   0.000   0.000   0.000
   4_adp:  0.310  38.619   1.852   2.824   3.938   0.000   0.000   0.000
   4_occ:  0.310  38.619   1.852   2.824   3.938   0.000   0.000   0.000
   5_bss:  0.319  43.145   1.826   2.820   3.979   0.000   0.000   0.000
   5_xyz:  0.319  43.145   1.826   2.820   3.979   0.000   0.000   0.000
   5_adp:  0.319  43.145   1.826   2.820   3.979   0.000   0.000   0.000
   5_occ:  0.319  43.145   1.826   2.820   3.979   0.000   0.000   0.000
   5_bss:  0.319  46.056  -1.056  -0.081   1.137  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.221 0.5069  0.5859    60682.422
   1_bss:  51.256 0.5048  0.7603    58780.773
   1_xyz:  41.148 0.6281  0.9113    39080.249
   1_adp:  35.939 0.6905  1.0150    31850.327
   1_occ:  36.007 0.6897  1.0127    31958.118
   2_bss:  35.813 0.6920  0.8872    31854.738
   2_xyz:  24.321 0.8178  1.0009    15190.429
   2_adp:  21.520 0.8469  1.0254    12635.219
   2_occ:  21.534 0.8467  1.0254    12639.019
   3_bss:  21.432 0.8477  0.9642    12522.393
   3_xyz:  16.434 0.8940  0.9882     7909.827
   3_adp:  15.710 0.9006  0.9860     7424.708
   3_occ:  15.703 0.9007  0.9859     7414.801
   4_bss:  15.657 0.9010  0.9766     7366.614
   4_xyz:  15.072 0.9065  0.9784     7042.855
   4_adp:  14.826 0.9086  0.9768     6920.102
   4_occ:  14.830 0.9086  0.9766     6918.293
   5_bss:  14.824 0.9086  0.9770     6915.705
   5_xyz:  14.458 0.9113  0.9786     6615.478
   5_adp:  14.238 0.9131  0.9766     6497.092
   5_occ:  14.230 0.9132  0.9765     6490.228
   5_bss:  14.231 0.9132  0.9777     6490.526
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3554e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3554e+01
   1_xyz:   1.646  0.013  0.106 17.876  0.006  4.108   1.3337e-01
   1_adp:   1.646  0.013  0.106 17.876  0.006  4.108   1.3337e-01
   1_occ:   1.646  0.013  0.106 17.876  0.006  4.108   1.3337e-01
   2_bss:   1.646  0.013  0.106 17.876  0.006  4.108   1.3337e-01
   2_xyz:   1.084  0.008  0.078 16.075  0.004  4.124   7.0713e-02
   2_adp:   1.084  0.008  0.078 16.075  0.004  4.124   7.0713e-02
   2_occ:   1.084  0.008  0.078 16.075  0.004  4.124   7.0713e-02
   3_bss:   1.084  0.008  0.078 16.075  0.004  4.124   7.0713e-02
   3_xyz:   1.074  0.007  0.083 15.671  0.004  4.134   6.7291e-02
   3_adp:   1.074  0.007  0.083 15.671  0.004  4.134   6.7291e-02
   3_occ:   1.074  0.007  0.083 15.671  0.004  4.134   6.7291e-02
   4_bss:   1.074  0.007  0.083 15.671  0.004  4.134   6.7291e-02
   4_xyz:   0.918  0.005  0.072 15.253  0.003  4.117   5.3093e-02
   4_adp:   0.918  0.005  0.072 15.253  0.003  4.117   5.3093e-02
   4_occ:   0.918  0.005  0.072 15.253  0.003  4.117   5.3093e-02
   5_bss:   0.918  0.005  0.072 15.253  0.003  4.117   5.3093e-02
   5_xyz:   1.122  0.009  0.088 15.520  0.004  4.120   7.2435e-02
   5_adp:   1.122  0.009  0.088 15.520  0.004  4.120   7.2435e-02
   5_occ:   1.122  0.009  0.088 15.520  0.004  4.120   7.2435e-02
   5_bss:   1.122  0.009  0.088 15.520  0.004  4.120   7.2435e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.158   6.9382e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.158   6.9382e+00
   1_xyz:  14.698  0.159  0.475 85.092  0.034  2.278   9.8405e-02
   1_adp:  14.698  0.159  0.475 85.092  0.034  2.278   9.8405e-02
   1_occ:  14.698  0.159  0.475 85.092  0.034  2.278   9.8405e-02
   2_bss:  14.698  0.159  0.475 85.092  0.034  2.278   9.8405e-02
   2_xyz:   6.476  0.061  0.358 81.989  0.044  2.305   6.2498e-02
   2_adp:   6.476  0.061  0.358 81.989  0.044  2.305   6.2498e-02
   2_occ:   6.476  0.061  0.358 81.989  0.044  2.305   6.2498e-02
   3_bss:   6.476  0.061  0.358 81.989  0.044  2.305   6.2498e-02
   3_xyz:   7.244  0.047  0.551 82.227  0.041  2.293   4.9099e-02
   3_adp:   7.244  0.047  0.551 82.227  0.041  2.293   4.9099e-02
   3_occ:   7.244  0.047  0.551 82.227  0.041  2.293   4.9099e-02
   4_bss:   7.244  0.047  0.551 82.227  0.041  2.293   4.9099e-02
   4_xyz:   6.009  0.040  0.376 80.369  0.035  2.341   3.8723e-02
   4_adp:   6.009  0.040  0.376 80.369  0.035  2.341   3.8723e-02
   4_occ:   6.009  0.040  0.376 80.369  0.035  2.341   3.8723e-02
   5_bss:   6.009  0.040  0.376 80.369  0.035  2.341   3.8723e-02
   5_xyz:   7.448  0.051  0.577 81.574  0.039  2.283   5.1285e-02
   5_adp:   7.448  0.051  0.577 81.574  0.039  2.283   5.1285e-02
   5_occ:   7.448  0.051  0.577 81.574  0.039  2.283   5.1285e-02
   5_bss:   7.448  0.051  0.577 81.574  0.039  2.283   5.1285e-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:  63.65   0.00  12.01  61.18   0.00   9.17  63.65   0.00  27.42
   1_occ:  63.65   0.00  12.01  61.18   0.00   9.17  63.65   0.00  27.42
   2_bss:  63.65   0.00  12.01  61.18   0.00   9.17  63.65   0.00  27.42
   2_xyz:  63.65   0.00  12.01  61.18   0.00   9.17  63.65   0.00  27.42
   2_adp:  70.67   0.00  12.13  70.67   0.00   8.36  62.92   0.83  32.66
   2_occ:  70.67   0.00  12.13  70.67   0.00   8.36  62.92   0.83  32.66
   3_bss:  70.67   0.00  12.13  70.67   0.00   8.36  62.92   0.83  32.66
   3_xyz:  70.67   0.00  12.13  70.67   0.00   8.36  62.92   0.83  32.66
   3_adp:  89.95   0.00  13.01  89.95   0.00   8.44  83.17   1.40  37.91
   3_occ:  89.95   0.00  13.01  89.95   0.00   8.44  83.17   1.40  37.91
   4_bss:  89.95   0.00  13.01  89.95   0.00   8.44  83.17   1.40  37.91
   4_xyz:  89.95   0.00  13.01  89.95   0.00   8.44  83.17   1.40  37.91
   4_adp:  90.87   0.00  12.70  90.87   0.00   8.29  84.50   1.39  36.75
   4_occ:  90.87   0.00  12.70  90.87   0.00   8.29  84.50   1.39  36.75
   5_bss:  90.87   0.00  12.70  90.87   0.00   8.29  84.50   1.39  36.75
   5_xyz:  90.87   0.00  12.70  90.87   0.00   8.29  84.50   1.39  36.75
   5_adp:  88.38   0.00  12.10  88.38   0.00   8.01  82.63   1.55  34.34
   5_occ:  88.38   0.00  12.10  88.38   0.00   8.01  82.63   1.55  34.34
   5_bss:  91.29   2.91  15.01  91.29   2.91  10.92  85.54   4.46  37.25
------------------------------------------------------------------------
 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:    1.269    0.026    0.412
   1_adp:    1.269    0.026    0.412
   1_occ:    1.269    0.026    0.412
   2_bss:    1.269    0.026    0.412
   2_xyz:    1.681    0.022    0.559
   2_adp:    1.681    0.022    0.559
   2_occ:    1.681    0.022    0.559
   3_bss:    1.681    0.022    0.559
   3_xyz:    1.671    0.040    0.605
   3_adp:    1.671    0.040    0.605
   3_occ:    1.671    0.040    0.605
   4_bss:    1.671    0.040    0.605
   4_xyz:    1.858    0.035    0.623
   4_adp:    1.858    0.035    0.623
   4_occ:    1.858    0.035    0.623
   5_bss:    1.858    0.035    0.623
   5_xyz:    1.841    0.061    0.634
   5_adp:    1.841    0.061    0.634
   5_occ:    1.841    0.061    0.634
   5_bss:    1.841    0.061    0.634
------------------------------------------------------------------------

CPU time actual refinement: 346.39


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_194/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_194/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_194/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_194/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_194/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.25 
  Macro-tasks:
    bulk solvent and scale       = 44.17  
    individual site refinement   = 143.65 
    weights calculation          = 32.81  
    collect and process          = 6.73   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 227.46 
  Micro-tasks:
    mask                            = 1.71   
    f_calc                          = 108.61 
    alpha_beta                      = 8.57   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 114.11 
    fmodel                         = 7.76   
    r_factors                      = 0.25   
    phase_errors                   = 11.71  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 254.22 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.802 micro seconds
Total CPU time: 5.99 minutes
from_scatterers_fft:    664 calls, 108.10 s
gradients_fft:          608 calls, 102.42 s

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

# Date 2008-01-16 Time 00:58:01 PST -0800 (1200473881.39 s)
Start R-work = 0.4602, R-free = 0.4483 (no bulk solvent and anisotropic scale)
Final R-work = 0.1300, R-free = 0.1727 (no bulk solvent and anisotropic scale)

Start R-work = 0.4514, R-free = 0.4381
Final R-work = 0.1116, R-free = 0.1566