# Date 2008-01-16 Time 01:46:31 PST -0800 (1200476791.09 s)
#phil __OFF__

Command line arguments: "../561.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1304
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 561

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.3993, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95143
Completeness in resolution range: 0.935929
Completeness with d_max=infinity: 0.933076

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8359
                             d_min =   1.9514

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95143
Completeness in resolution range: 0.935929
Completeness with d_max=infinity: 0.933076

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8363 -  4.1759 [2203/2231]  1984   219   9.9%
  bin  2:  4.1759 -  3.3268 [2100/2123]  1891   209  10.0%
  bin  3:  3.3268 -  2.9099 [2085/2110]  1871   214  10.3%
  bin  4:  2.9099 -  2.6455 [2063/2079]  1863   200   9.7%
  bin  5:  2.6455 -  2.4568 [2049/2093]  1841   208  10.2%
  bin  6:  2.4568 -  2.3125 [2051/2079]  1849   202   9.8%
  bin  7:  2.3125 -  2.1971 [2008/2044]  1807   201  10.0%
  bin  8:  2.1971 -  2.1017 [2019/2061]  1817   202  10.0%
  bin  9:  2.1017 -  2.0210 [2017/2063]  1813   204  10.1%
  bin 10:  2.0210 -  1.9514 [ 994/2047]   894   100  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_561/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: 0.15 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:
        1.49 -     2.18: 25
        2.18 -     2.86: 1164
        2.86 -     3.54: 4477
        3.54 -     4.22: 9317
        4.22 -     4.90: 13632
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.494 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.595 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.603 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.630 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28610 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_561/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_561/model_refine_001.geo

CPU time processing inputs: 9.44


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.3993 84.23025 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: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4793   r_free= 0.4848   ksol= 0.00   Bsol= 0.00   scale= 0.799    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.282438                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6577 0.99   1426  161 0.3945 0.3895      6.5966      6.6195|
|  2:  4.6577 -  3.7161 0.99   1370  148 0.3975 0.4055      6.7844      6.7763|
|  3:  3.7161 -  3.2520 0.99   1346  154 0.4363 0.4379      6.6668      6.7373|
|  4:  3.2520 -  2.9572 0.99   1341  146 0.4516 0.4827      6.5094      6.5119|
|  5:  2.9572 -  2.7467 0.98   1332  148 0.4994 0.5327      6.3702       6.363|
|  6:  2.7467 -  2.5857 0.99   1320  146 0.5017 0.5428      6.2672      6.2117|
|  7:  2.5857 -  2.4568 0.98   1315  147 0.5226 0.4418      6.2558      6.1526|
|  8:  2.4568 -  2.3503 0.99   1307  147 0.5257 0.5402      6.1597      6.1877|
|  9:  2.3503 -  2.2601 0.99   1315  144 0.5411 0.5234      6.1323      6.1342|
| 10:  2.2601 -  2.1824 0.98   1306  145 0.5300 0.5388      6.1041      6.1491|
| 11:  2.1824 -  2.1143 0.97   1278  139 0.5310 0.5310      6.0357      6.0035|
| 12:  2.1143 -  2.0541 0.99   1302  153 0.5386 0.5916      5.9536      5.9975|
| 13:  2.0541 -  2.0001 0.93   1242  136 0.5410 0.5320      5.8843      5.8359|
| 14:  2.0001 -  1.9514 0.33    430   45 0.5579 0.5483      5.8394      5.7203|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6577  1426   161  0.69  35.53   0.80     0.71      74184.17|
|  2:  4.6577 -  3.7161  1370   148  0.68  36.61   0.88     0.75     111354.17|
|  3:  3.7161 -  3.2520  1346   154  0.57  46.20   0.84     0.70     122252.33|
|  4:  3.2520 -  2.9572  1341   146  0.48  53.73   0.81     0.59     109170.44|
|  5:  2.9572 -  2.7467  1332   148  0.39  60.78   0.74     0.48      89249.20|
|  6:  2.7467 -  2.5857  1320   146  0.39  60.81   0.74     0.46      72377.08|
|  7:  2.5857 -  2.4568  1315   147  0.40  60.16   0.74     0.45      62518.08|
|  8:  2.4568 -  2.3503  1307   147  0.38  61.59   0.72     0.45      57119.68|
|  9:  2.3503 -  2.2601  1315   144  0.32  65.90   0.72     0.39      55648.14|
| 10:  2.2601 -  2.1824  1306   145  0.26  70.96   0.77     0.31      55434.95|
| 11:  2.1824 -  2.1143  1278   139  0.19  75.76   0.76     0.24      53610.38|
| 12:  2.1143 -  2.0541  1302   153  0.17  77.61   0.75     0.22      50534.44|
| 13:  2.0541 -  2.0001  1242   136  0.22  73.84   0.74     0.28      40773.90|
| 14:  2.0001 -  1.9514   430    45  0.35  63.78   0.70     0.42      29273.49|
|alpha:            min =        0.22 max =            0.75 mean =         0.47|
|beta:             min =    29273.49 max =       122252.33 mean =     72812.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.98 mean =        59.68|
|phase err.(test): min =        0.00 max =           90.00 mean =        60.16|
|-----------------------------------------------------------------------------|

============================== 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 = 14.621162             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.230   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.383590              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.308   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      182 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      708 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1520 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2684 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3964 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5095 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6625 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7835 |
|-----------------------------------------------------------------------------|
|-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 |       53.266 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.170 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    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 = 11.644)------------------------------------------|
|    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: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4851   r_free= 0.4897   ksol= 0.00   Bsol= 0.00   scale= 0.768    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.284118                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4711   r_free= 0.4749   ksol= 0.36   Bsol= 17.39   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.46,8.72,9.24,0.00,0.00,0.00); trace/3= 8.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.280783                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.129737             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.310   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.234908              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.113   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4711      final r-factor (work) = 0.4017          |
| start r-factor (free) = 0.4749      final r-factor (free) = 0.4212          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.3592 = 12.13 * 0.50 * 6.2809 + 1.00 * 53.2661                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.7636 = 12.13 * 0.50 * 6.2031 + 1.00 * 0.1424                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4017      final r-factor (work) = 0.3584          |
| start r-factor (free) = 0.4212      final r-factor (free) = 0.4040          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6746 = 1.23 * 1.00 * 6.2031 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5869 = 1.23 * 1.00 * 6.1307 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.64   13.52    None  None   None       |
|    all(noH): 2823   0      0.00    74.64   13.52    None  None   None       |
|    Sol.    : 438    0      0.00    74.64   26.46    None  None   None       |
|    Mac.    : 2385   0      0.00    70.70   11.14    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 -   7.464: 1101   |   5:    37.320 -  44.784:   60        |
|      1:     7.464 -  14.928:  748   |   6:    44.784 -  52.248:   51        |
|      2:    14.928 -  22.392:  432   |   7:    52.248 -  59.712:   23        |
|      3:    22.392 -  29.856:  249   |   8:    59.712 -  67.175:   13        |
|      4:    29.856 -  37.320:  141   |   9:    67.175 -  74.639:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3584 r_free = 0.4040             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3578 r_free = 0.4038             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3578   r_free= 0.4038   ksol= 0.36   Bsol= 17.39   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.46,8.72,9.24,0.00,0.00,0.00); trace/3= 8.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.114837                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3548   r_free= 0.4014   ksol= 0.34   Bsol= 36.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,5.01,6.05,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.115659                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.847602              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.505   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.597044              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.004  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3548      final r-factor (work) = 0.2627          |
| start r-factor (free) = 0.4014      final r-factor (free) = 0.3209          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.3101 = 9.85 * 0.50 * 6.1269 + 1.00 * 0.1424                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.6450 = 9.85 * 0.50 * 6.0010 + 1.00 * 0.0971                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2627      final r-factor (work) = 0.2365          |
| start r-factor (free) = 0.3209      final r-factor (free) = 0.2940          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5991 = 0.60 * 1.00 * 6.0010 + 1.00 * 0.0162                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4909 = 0.60 * 1.00 * 5.8266 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.59   13.87    None  None   None       |
|    all(noH): 2823   0      0.00    69.59   13.87    None  None   None       |
|    Sol.    : 438    0      1.10    68.07   32.84    None  None   None       |
|    Mac.    : 2385   0      0.00    69.59   10.39    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 -   6.959: 1064   |   5:    34.793 -  41.752:  108        |
|      1:     6.959 -  13.917:  821   |   6:    41.752 -  48.710:   79        |
|      2:    13.917 -  20.876:  336   |   7:    48.710 -  55.669:   52        |
|      3:    20.876 -  27.834:  202   |   8:    55.669 -  62.627:   23        |
|      4:    27.834 -  34.793:  127   |   9:    62.627 -  69.586:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2365 r_free = 0.2940             target_work(ml) = 5.789         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2363 r_free = 0.2942             target_work(ml) = 5.788         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2363   r_free= 0.2942   ksol= 0.34   Bsol= 36.00   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,5.01,6.05,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.788080                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2338   r_free= 0.2916   ksol= 0.32   Bsol= 39.24   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.54,2.86,3.28,0.00,0.00,0.00); trace/3= 2.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.785091                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.880226              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.813   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.454797              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.639  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2338      final r-factor (work) = 0.1742          |
| start r-factor (free) = 0.2916      final r-factor (free) = 0.2305          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4096 = 3.88 * 0.50 * 5.8309 + 1.00 * 0.0971                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0662 = 3.88 * 0.50 * 5.6703 + 1.00 * 0.0652                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1742      final r-factor (work) = 0.1598          |
| start r-factor (free) = 0.2305      final r-factor (free) = 0.2148          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5907 = 0.45 * 1.00 * 5.6703 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5096 = 0.45 * 1.00 * 5.4947 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.43   13.96    None  None   None       |
|    all(noH): 2823   0      0.00    76.43   13.96    None  None   None       |
|    Sol.    : 438    0      3.45    69.45   36.68    None  None   None       |
|    Mac.    : 2385   0      0.00    76.43   9.79     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 -   7.643: 1261   |   5:    38.213 -  45.855:  110        |
|      1:     7.643 -  15.285:  824   |   6:    45.855 -  53.498:   87        |
|      2:    15.285 -  22.928:  240   |   7:    53.498 -  61.140:   51        |
|      3:    22.928 -  30.570:  122   |   8:    61.140 -  68.783:   17        |
|      4:    30.570 -  38.213:  103   |   9:    68.783 -  76.425:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1598 r_free = 0.2148             target_work(ml) = 5.453         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1596 r_free = 0.2147             target_work(ml) = 5.453         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1596   r_free= 0.2147   ksol= 0.32   Bsol= 39.24   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.54,2.86,3.28,0.00,0.00,0.00); trace/3= 2.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.452965                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1592   r_free= 0.2139   ksol= 0.32   Bsol= 37.66   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.85,1.87,1.98,0.00,0.00,0.00); trace/3= 1.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.452728                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.015122              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.019  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.314967              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.674  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1592      final r-factor (work) = 0.1366          |
| start r-factor (free) = 0.2139      final r-factor (free) = 0.1833          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6073 = 2.02 * 0.50 * 5.5005 + 1.00 * 0.0652                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4850 = 2.02 * 0.50 * 5.3905 + 1.00 * 0.0537                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1366      final r-factor (work) = 0.1319          |
| start r-factor (free) = 0.1833      final r-factor (free) = 0.1774          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7084 = 0.31 * 1.00 * 5.3905 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6796 = 0.31 * 1.00 * 5.2934 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.54   13.85    None  None   None       |
|    all(noH): 2823   0      0.00    78.54   13.85    None  None   None       |
|    Sol.    : 438    0      2.61    70.37   36.96    None  None   None       |
|    Mac.    : 2385   0      0.00    78.54   9.60     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 -   7.855: 1317   |   5:    39.272 -  47.127:  111        |
|      1:     7.855 -  15.709:  817   |   6:    47.127 -  54.981:   86        |
|      2:    15.709 -  23.563:  210   |   7:    54.981 -  62.835:   40        |
|      3:    23.563 -  31.418:  115   |   8:    62.835 -  70.690:   17        |
|      4:    31.418 -  39.272:  105   |   9:    70.690 -  78.544:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1319 r_free = 0.1774             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1316 r_free = 0.1771             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1771   ksol= 0.32   Bsol= 37.66   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.85,1.87,1.98,0.00,0.00,0.00); trace/3= 1.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.275889                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1320   r_free= 0.1772   ksol= 0.32   Bsol= 38.85   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.76,1.62,1.63,0.00,0.00,0.00); trace/3= 1.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.278046                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.265950              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.475  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.514330              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.579   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1320      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1772      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0519 = 2.27 * 0.50 * 5.2943 + 1.00 * 0.0537                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9972 = 2.27 * 0.50 * 5.2394 + 1.00 * 0.0611                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1660      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7170 = 0.51 * 1.00 * 5.2394 + 1.00 * 0.0222                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7085 = 0.51 * 1.00 * 5.1990 + 1.00 * 0.0345                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.16   13.89    None  None   None       |
|    all(noH): 2823   0      0.00    88.16   13.89    None  None   None       |
|    Sol.    : 438    0      1.75    75.13   37.53    None  None   None       |
|    Mac.    : 2385   0      0.00    88.16   9.55     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 -   8.816: 1522   |   5:    44.078 -  52.894:   96        |
|      1:     8.816 -  17.631:  699   |   6:    52.894 -  61.709:   57        |
|      2:    17.631 -  26.447:  187   |   7:    61.709 -  70.525:   27        |
|      3:    26.447 -  35.262:  109   |   8:    70.525 -  79.340:   11        |
|      4:    35.262 -  44.078:  111   |   9:    79.340 -  88.156:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1657             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1176 r_free = 0.1656             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1656   ksol= 0.32   Bsol= 38.85   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.76,1.62,1.63,0.00,0.00,0.00); trace/3= 1.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.195858                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6577 0.99   1426  161 0.0969 0.1272      5.3751      5.5528|
|  2:  4.6577 -  3.7161 0.99   1370  148 0.0899 0.1172      5.4697      5.6852|
|  3:  3.7161 -  3.2520 0.99   1346  154 0.1110 0.1636      5.5106      5.8769|
|  4:  3.2520 -  2.9572 0.99   1341  146 0.1311 0.1561      5.4914      5.6319|
|  5:  2.9572 -  2.7467 0.98   1332  148 0.1378 0.1748      5.3542      5.4983|
|  6:  2.7467 -  2.5857 0.99   1320  146 0.1306 0.2186      5.2739       5.583|
|  7:  2.5857 -  2.4568 0.98   1315  147 0.1332 0.1762      5.2287      5.4134|
|  8:  2.4568 -  2.3503 0.99   1307  147 0.1222 0.1741      5.1128      5.3354|
|  9:  2.3503 -  2.2601 0.99   1315  144 0.1252 0.1866      5.0687      5.3005|
| 10:  2.2601 -  2.1824 0.98   1306  145 0.1177 0.1904      5.0251      5.3557|
| 11:  2.1824 -  2.1143 0.97   1278  139 0.1221 0.1894      4.9812      5.2618|
| 12:  2.1143 -  2.0541 0.99   1302  153 0.1196 0.1797      4.9073      5.1399|
| 13:  2.0541 -  2.0001 0.93   1242  136 0.1200 0.1872      4.8263       5.046|
| 14:  2.0001 -  1.9514 0.33    430   45 0.1186 0.1837      4.7304      5.0345|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6577  1426   161  0.94   9.21   0.98     0.96       7383.07|
|  2:  4.6577 -  3.7161  1370   148  0.95   8.41   1.02     1.00       9471.20|
|  3:  3.7161 -  3.2520  1346   154  0.93  12.19   1.03     1.03      11405.76|
|  4:  3.2520 -  2.9572  1341   146  0.91  14.48   1.01     0.99      10861.45|
|  5:  2.9572 -  2.7467  1332   148  0.89  17.05   1.00     0.96       8848.86|
|  6:  2.7467 -  2.5857  1320   146  0.89  17.08   0.99     0.97       8142.02|
|  7:  2.5857 -  2.4568  1315   147  0.89  16.84   0.99     0.96       7066.34|
|  8:  2.4568 -  2.3503  1307   147  0.90  16.65   1.00     0.97       6070.23|
|  9:  2.3503 -  2.2601  1315   144  0.89  17.41   1.01     0.98       5567.32|
| 10:  2.2601 -  2.1824  1306   145  0.90  16.04   1.01     0.97       5057.49|
| 11:  2.1824 -  2.1143  1278   139  0.89  17.56   1.00     0.96       4801.88|
| 12:  2.1143 -  2.0541  1302   153  0.91  16.11   1.01     1.00       4207.70|
| 13:  2.0541 -  2.0001  1242   136  0.89  17.33   1.01     1.00       3632.76|
| 14:  2.0001 -  1.9514   430    45  0.89  17.33   0.99     0.96       2974.26|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2974.26 max =        11405.76 mean =      7062.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.70 mean =        15.08|
|phase err.(test): min =        0.00 max =           89.73 mean =        14.66|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1657   ksol= 0.32   Bsol= 41.95   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.58,0.29,0.30,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.195869                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1657   ksol= 0.32   Bsol= 41.95   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.58,0.29,0.30,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.195869                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6577 0.99   1426  161 0.0969 0.1273      5.3763      5.5545|
|  2:  4.6577 -  3.7161 0.99   1370  148 0.0901 0.1173       5.471      5.6869|
|  3:  3.7161 -  3.2520 0.99   1346  154 0.1110 0.1638      5.5113      5.8774|
|  4:  3.2520 -  2.9572 0.99   1341  146 0.1311 0.1561      5.4915      5.6322|
|  5:  2.9572 -  2.7467 0.98   1332  148 0.1377 0.1747       5.354      5.4979|
|  6:  2.7467 -  2.5857 0.99   1320  146 0.1305 0.2185      5.2736      5.5826|
|  7:  2.5857 -  2.4568 0.98   1315  147 0.1331 0.1762      5.2282      5.4132|
|  8:  2.4568 -  2.3503 0.99   1307  147 0.1222 0.1739      5.1123      5.3346|
|  9:  2.3503 -  2.2601 0.99   1315  144 0.1252 0.1867      5.0684      5.3004|
| 10:  2.2601 -  2.1824 0.98   1306  145 0.1177 0.1903      5.0247      5.3552|
| 11:  2.1824 -  2.1143 0.97   1278  139 0.1220 0.1894      4.9809      5.2617|
| 12:  2.1143 -  2.0541 0.99   1302  153 0.1196 0.1797      4.9071      5.1396|
| 13:  2.0541 -  2.0001 0.93   1242  136 0.1200 0.1870      4.8259      5.0455|
| 14:  2.0001 -  1.9514 0.33    430   45 0.1186 0.1837      4.7298      5.0339|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6577  1426   161  0.94   9.23   0.98     0.96       7414.59|
|  2:  4.6577 -  3.7161  1370   148  0.95   8.43   1.02     1.00       9502.43|
|  3:  3.7161 -  3.2520  1346   154  0.93  12.21   1.03     1.03      11430.78|
|  4:  3.2520 -  2.9572  1341   146  0.91  14.49   1.01     0.99      10869.10|
|  5:  2.9572 -  2.7467  1332   148  0.89  17.05   1.00     0.96       8847.84|
|  6:  2.7467 -  2.5857  1320   146  0.89  17.08   0.99     0.97       8137.63|
|  7:  2.5857 -  2.4568  1315   147  0.89  16.84   0.99     0.96       7059.67|
|  8:  2.4568 -  2.3503  1307   147  0.90  16.64   1.00     0.97       6063.01|
|  9:  2.3503 -  2.2601  1315   144  0.89  17.40   1.01     0.98       5561.27|
| 10:  2.2601 -  2.1824  1306   145  0.90  16.03   1.01     0.97       5053.07|
| 11:  2.1824 -  2.1143  1278   139  0.89  17.55   1.00     0.96       4799.23|
| 12:  2.1143 -  2.0541  1302   153  0.91  16.10   1.01     1.00       4205.12|
| 13:  2.0541 -  2.0001  1242   136  0.89  17.32   1.01     1.00       3628.76|
| 14:  2.0001 -  1.9514   430    45  0.89  17.31   0.99     0.96       2969.10|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2969.10 max =        11430.78 mean =      7067.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.76 mean =        15.08|
|phase err.(test): min =        0.00 max =           89.55 mean =        14.66|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.644)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.34    89.49   15.23    None  None   None       |
|    all(noH): 2823   0      1.34    89.49   15.23    None  None   None       |
|    Sol.    : 438    0      3.09    76.46   38.87    None  None   None       |
|    Mac.    : 2385   0      1.34    89.49   10.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.337 -  10.153: 1522   |   5:    45.415 -  54.231:   96        |
|      1:    10.153 -  18.969:  699   |   6:    54.231 -  63.046:   57        |
|      2:    18.969 -  27.784:  187   |   7:    63.046 -  71.862:   27        |
|      3:    27.784 -  36.600:  109   |   8:    71.862 -  80.678:   11        |
|      4:    36.600 -  45.415:  111   |   9:    80.678 -  89.493:    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)= 342         
Filter by distance & map next to the model:
   mapped sites are within: 0.668 - 5.843
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 341 from: 342
   mapped sites are within: 0.741 - 5.843

peak=   10.184 closest distance to " CB  VAL A 230 " =    1.443
peak=    9.275 closest distance to " O   HOH Z 138 " =    1.237
peak=    9.107 closest distance to " CG2 VAL A 296 " =    1.309
peak=    7.561 closest distance to " O   HOH Z 120 " =    1.256
peak=    6.877 closest distance to " O   HOH Z 279 " =    1.375
peak=    6.075 closest distance to " CG  LEU A   5 " =    1.348
peak=    5.968 closest distance to " NH2 ARG A  56 " =    2.178
peak=    5.839 closest distance to " O   HOH Z 278 " =    1.464
peak=    5.512 closest distance to " O   HOH Z 124 " =    1.558
peak=    5.365 closest distance to " CD2 LEU A   5 " =    1.166
peak=    5.239 closest distance to " O   HOH Z 199 " =    1.104
peak=    5.228 closest distance to " O   HOH Z 247 " =    1.361
peak=    5.179 closest distance to " O   HOH Z 132 " =    1.588
peak=    5.000 closest distance to " CB  GLN A 223 " =    1.397
peak=    4.991 closest distance to " CD1AILE A 234 " =    1.020
peak=    4.948 closest distance to " O   HOH Z  97 " =    1.910
peak=    4.884 closest distance to " O   HOH Z 202 " =    1.257
peak=    4.846 closest distance to " O   HOH Z 316 " =    1.016
peak=    4.842 closest distance to " O   HOH Z  48 " =    1.729
peak=    4.758 closest distance to " CG  PRO A 213 " =    1.231
peak=    4.735 closest distance to " O   HOH Z 316 " =    2.276
peak=    4.730 closest distance to " O   HOH Z 193 " =    1.756
peak=    4.714 closest distance to " CG  PRO A  54 " =    1.193
peak=    4.693 closest distance to " O   HOH Z 411 " =    3.684
peak=    4.679 closest distance to " O   SER A  87 " =    2.289
peak=    4.618 closest distance to " CG  LEU A 228 " =    1.223
peak=    4.611 closest distance to " CB  GLN A 183 " =    1.341
peak=    4.597 closest distance to " CB  ASN A 187 " =    1.997
peak=    4.567 closest distance to " O   HOH Z 272 " =    1.953
peak=    4.561 closest distance to " NE2 GLN A  11 " =    1.067
peak=    4.535 closest distance to " CB  SER A  63 " =    1.286
peak=    4.523 closest distance to " O   HOH Z  59 " =    2.260
peak=    4.516 closest distance to " O   HOH Z 142 " =    1.756
peak=    4.508 closest distance to " CG  PRO A 198 " =    1.198
peak=    4.479 closest distance to " CA  ALA A  21 " =    1.198
peak=    4.464 closest distance to " CB  ARG A 275 " =    0.900
peak=    4.417 closest distance to " C   PRO A 198 " =    1.465
peak=    4.400 closest distance to " O   HOH Z 263 " =    1.434
peak=    4.333 closest distance to " CB  PRO A  54 " =    0.818
peak=    4.312 closest distance to " O   ASP A 132 " =    3.884
peak=    4.308 closest distance to " O   HOH Z 389 " =    1.763
peak=    4.294 closest distance to " CA  VAL A  41 " =    0.880
peak=    4.290 closest distance to " O   HOH Z 108 " =    1.404
peak=    4.289 closest distance to " CB  SER A   3 " =    1.355
peak=    4.286 closest distance to " O   HOH Z 346 " =    1.505
peak=    4.284 closest distance to " O   HOH Z 326 " =    1.502
peak=    4.282 closest distance to " O   HOH Z 371 " =    3.341
peak=    4.275 closest distance to " CB  TRP A 179 " =    1.300
peak=    4.273 closest distance to " O   HOH Z  11 " =    1.304
peak=    4.229 closest distance to " O   HOH Z  37 " =    1.194
peak=    4.220 closest distance to " O   HOH Z 192 " =    1.495
peak=    4.200 closest distance to " O   HOH Z 423 " =    1.964
peak=    4.190 closest distance to " O   HOH Z 128 " =    1.887
peak=    4.179 closest distance to " O   HOH Z 134 " =    1.733
peak=    4.176 closest distance to " CB  GLU A 152 " =    1.080
peak=    4.161 closest distance to " CG1BVAL A  72 " =    1.556
peak=    4.158 closest distance to " CD2 LEU A 228 " =    1.188
peak=    4.139 closest distance to " CB  VAL A 230 " =    1.193
peak=    4.113 closest distance to " O   HOH Z 284 " =    2.934
peak=    4.107 closest distance to " O   HOH Z 232 " =    2.242
peak=    4.087 closest distance to " O   HOH Z  78 " =    1.796
peak=    4.058 closest distance to " O   HOH Z 236 " =    1.649
peak=    4.052 closest distance to " O   HOH Z 426 " =    1.440
peak=    4.024 closest distance to " CG2 THR A 221 " =    1.058
peak=    4.011 closest distance to " CA  TYR A  30 " =    1.037
peak=    4.001 closest distance to " O   HOH Z 136 " =    1.341
peak=    3.996 closest distance to " CB  ASN A 148 " =    1.246
peak=    3.996 closest distance to " O   HOH Z 214 " =    2.229
peak=    3.995 closest distance to " O   HOH Z 155 " =    1.709
peak=    3.983 closest distance to " O   HOH Z 203 " =    1.583
peak=    3.977 closest distance to " CB  TYR A 169 " =    0.962
peak=    3.964 closest distance to " O   HOH Z 344 " =    2.729
peak=    3.963 closest distance to " CG AARG A 275 " =    1.102
peak=    3.959 closest distance to " O   HOH Z 394 " =    1.537
peak=    3.958 closest distance to " O   HOH Z  80 " =    1.718
peak=    3.952 closest distance to " O   HOH Z 280 " =    1.602
peak=    3.945 closest distance to " O   HOH Z 112 " =    1.549
peak=    3.929 closest distance to " O   HOH Z 189 " =    2.391
peak=    3.908 closest distance to " O   HOH Z  20 " =    1.605
peak=    3.906 closest distance to " O   HOH Z 260 " =    1.250
peak=    3.893 closest distance to " OE1 GLN A  11 " =    1.804
peak=    3.889 closest distance to " CB  LEU A 228 " =    1.440
peak=    3.888 closest distance to " O   HOH Z 427 " =    2.888
peak=    3.886 closest distance to " O   HOH Z  61 " =    1.580
peak=    3.884 closest distance to " O   HOH Z 403 " =    1.740
peak=    3.857 closest distance to " O   HOH Z 154 " =    1.406
peak=    3.839 closest distance to " OE1 GLN A  58 " =    5.843
peak=    3.835 closest distance to " O   HOH Z 217 " =    1.625
peak=    3.819 closest distance to " O   HOH Z  97 " =    2.457
peak=    3.812 closest distance to " OD1 ASN A  69 " =    2.566
peak=    3.809 closest distance to " O   HOH Z 369 " =    2.127
peak=    3.807 closest distance to " CB  VAL A 296 " =    0.997
peak=    3.807 closest distance to " O   HOH Z  54 " =    1.557
peak=    3.805 closest distance to " CD  ARG A 269 " =    1.033
peak=    3.804 closest distance to " O   HOH Z  43 " =    1.276
peak=    3.800 closest distance to " O   HOH Z  30 " =    1.270
peak=    3.797 closest distance to " OE1 GLU A   2 " =    2.112
peak=    3.791 closest distance to " O   HOH Z 295 " =    1.572
peak=    3.787 closest distance to " CB  SER A  62 " =    1.223
peak=    3.787 closest distance to " CA  ASP A 191 " =    0.970
peak=    3.784 closest distance to " CB  GLU A 128 " =    1.188
peak=    3.784 closest distance to " O   HOH Z 366 " =    2.859
peak=    3.765 closest distance to " O   HOH Z 298 " =    2.017
peak=    3.765 closest distance to " O   HOH Z  15 " =    2.238
peak=    3.764 closest distance to " O   HOH Z 303 " =    2.026
peak=    3.763 closest distance to " O   HOH Z 133 " =    1.525
peak=    3.760 closest distance to " O   HOH Z 209 " =    2.535
peak=    3.758 closest distance to " OD2 ASP A 286 " =    2.709
peak=    3.758 closest distance to " O   HOH Z 145 " =    2.282
peak=    3.747 closest distance to " O   HOH Z 368 " =    2.216
peak=    3.743 closest distance to " CB  GLU A 277 " =    3.592
peak=    3.741 closest distance to " O   HOH Z 283 " =    2.005
peak=    3.737 closest distance to " O   HOH Z  40 " =    1.559
peak=    3.735 closest distance to " CB  GLN A  88 " =    1.270
peak=    3.722 closest distance to " O   HOH Z  88 " =    3.138
peak=    3.719 closest distance to " O   HOH Z 345 " =    2.855
peak=    3.718 closest distance to " O   HOH Z 276 " =    1.347
peak=    3.713 closest distance to " CG1 ILE A  33 " =    1.298
peak=    3.712 closest distance to " CA  THR A 221 " =    0.909
peak=    3.705 closest distance to " O   HOH Z  67 " =    1.854
peak=    3.699 closest distance to " CB  VAL A 265 " =    1.202
peak=    3.690 closest distance to " O   HOH Z 130 " =    2.665
peak=    3.686 closest distance to " O   HOH Z 334 " =    1.647
peak=    3.683 closest distance to " NZ  LYS A 117 " =    3.089
peak=    3.683 closest distance to " O   HOH Z 402 " =    1.425
peak=    3.682 closest distance to " CB  VAL A 202 " =    1.583
peak=    3.674 closest distance to " O   HOH Z 128 " =    1.910
peak=    3.673 closest distance to " O   HOH Z 180 " =    2.144
peak=    3.670 closest distance to " NH1 ARG A  14 " =    1.052
peak=    3.665 closest distance to " O   HOH Z 406 " =    1.650
peak=    3.657 closest distance to " CB  SER A 141 " =    1.067
peak=    3.649 closest distance to " O   HOH Z 227 " =    1.851
peak=    3.642 closest distance to " CA  LYS A 117 " =    1.304
peak=    3.635 closest distance to " O   HOH Z  85 " =    1.421
peak=    3.632 closest distance to " O   HOH Z  21 " =    1.931
peak=    3.631 closest distance to " O   HOH Z 284 " =    1.390
peak=    3.619 closest distance to " O   HOH Z   4 " =    1.624
peak=    3.608 closest distance to " O   HOH Z 291 " =    1.547
peak=    3.602 closest distance to " O   HOH Z 118 " =    1.348
peak=    3.598 closest distance to " NZ  LYS A 119 " =    1.694
peak=    3.597 closest distance to " O   HOH Z 149 " =    2.246
peak=    3.592 closest distance to " CD2 HIS A  81 " =    1.285
peak=    3.591 closest distance to " O   HOH Z 261 " =    1.800
peak=    3.578 closest distance to " CB  ALA A   9 " =    1.495
peak=    3.577 closest distance to " O   HOH Z 214 " =    1.040
peak=    3.573 closest distance to " CB AVAL A  41 " =    1.247
peak=    3.571 closest distance to " O   HOH Z  48 " =    1.727
peak=    3.558 closest distance to " CB  ALA A 100 " =    1.284
peak=    3.557 closest distance to " OG  SER A  22 " =    2.716
peak=    3.556 closest distance to " CA  LEU A 282 " =    1.096
peak=    3.552 closest distance to " CD  LYS A 119 " =    1.589
peak=    3.551 closest distance to " CB  SER A  26 " =    1.673
peak=    3.547 closest distance to " CG  GLN A  58 " =    2.556
peak=    3.541 closest distance to " OG1 THR A 294 " =    2.289
peak=    3.534 closest distance to " CB  PRO A 198 " =    1.081
peak=    3.527 closest distance to " O   MET A 105 " =    1.862
peak=    3.527 closest distance to " CB  ALA A 291 " =    1.320
peak=    3.527 closest distance to " CA  GLY A 211 " =    1.156
peak=    3.526 closest distance to " CG  ARG A  66 " =    0.938
peak=    3.526 closest distance to " O   HOH Z 227 " =    1.550
peak=    3.519 closest distance to " O   HOH Z 327 " =    1.651
peak=    3.515 closest distance to " O   HOH Z 114 " =    1.192
peak=    3.514 closest distance to " O   HOH Z 163 " =    1.372
peak=    3.512 closest distance to " O   HOH Z 287 " =    1.741
peak=    3.506 closest distance to " O   HOH Z 273 " =    2.704
peak=    3.498 closest distance to " O   HOH Z 374 " =    2.455
peak=    3.496 closest distance to " NH2 ARG A 156 " =    1.095
peak=    3.495 closest distance to " O   HOH Z 422 " =    2.580
peak=    3.491 closest distance to " ND2 ASN A 187 " =    1.712
peak=    3.489 closest distance to " O   HOH Z 193 " =    2.159
peak=    3.483 closest distance to " O   HOH Z  63 " =    1.406
peak=    3.482 closest distance to " CZ AARG A 102 " =    1.813
peak=    3.479 closest distance to " O   HOH Z 344 " =    1.632
peak=    3.477 closest distance to " CG  MET A 188 " =    1.406
peak=    3.477 closest distance to " CB  ARG A 139 " =    1.001
peak=    3.472 closest distance to " CA  VAL A 126 " =    1.003
peak=    3.472 closest distance to " O   HOH Z 102 " =    1.196
peak=    3.464 closest distance to " O   HOH Z 313 " =    1.740
peak=    3.463 closest distance to " O   ALA A 158 " =    1.281
peak=    3.463 closest distance to " O   HOH Z 261 " =    1.659
peak=    3.461 closest distance to " O   HOH Z 280 " =    1.948
peak=    3.457 closest distance to " O   HOH Z  71 " =    1.324
peak=    3.454 closest distance to " C   ALA A 299 " =    0.972
peak=    3.452 closest distance to " O   HOH Z 132 " =    3.461
peak=    3.445 closest distance to " O   HOH Z 155 " =    2.486
peak=    3.442 closest distance to " O   HOH Z 392 " =    2.475
peak=    3.441 closest distance to " CA  ARG A  36 " =    1.033
peak=    3.434 closest distance to " CD1 ILE A  33 " =    1.662
peak=    3.427 closest distance to " O   TRP A 274 " =    1.826
peak=    3.426 closest distance to " N   ASN A  39 " =    1.177
peak=    3.419 closest distance to " CD2 LEU A 255 " =    1.103
peak=    3.415 closest distance to " O   HOH Z 245 " =    1.343
peak=    3.414 closest distance to " CD  LYS A 166 " =    1.405
peak=    3.413 closest distance to " OG BSER A 164 " =    2.252
peak=    3.411 closest distance to " O   HOH Z  48 " =    2.163
peak=    3.410 closest distance to " O   HOH Z 215 " =    1.500
peak=    3.401 closest distance to " O   HOH Z 329 " =    3.328
peak=    3.392 closest distance to " CB  ARG A 102 " =    0.813
peak=    3.391 closest distance to " O   HOH Z 420 " =    2.291
peak=    3.388 closest distance to " O   HOH Z 395 " =    1.351
peak=    3.384 closest distance to " O   HOH Z 171 " =    2.649
peak=    3.384 closest distance to " CG  PRO A 243 " =    1.245
peak=    3.379 closest distance to " O   HOH Z 130 " =    1.182
peak=    3.376 closest distance to " CB  ARG A 190 " =    1.742
peak=    3.374 closest distance to " NZ  LYS A 166 " =    3.003
peak=    3.372 closest distance to " CB  ILE A 199 " =    1.031
peak=    3.369 closest distance to " CD1 LEU A 300 " =    1.037
peak=    3.369 closest distance to " CB  SER A 273 " =    0.844
peak=    3.365 closest distance to " NH2BARG A 145 " =    2.251
peak=    3.363 closest distance to " CA  MET A  40 " =    0.992
peak=    3.357 closest distance to " CA  ALA A 295 " =    1.102
peak=    3.357 closest distance to " O   HOH Z 407 " =    2.840
peak=    3.355 closest distance to " O   HOH Z 419 " =    1.486
peak=    3.353 closest distance to " O   HOH Z 209 " =    2.310
peak=    3.352 closest distance to " CA  GLN A 194 " =    1.157
peak=    3.348 closest distance to " O   HOH Z 345 " =    1.857
peak=    3.346 closest distance to " CG  GLN A  77 " =    2.217
peak=    3.339 closest distance to " O   HOH Z 383 " =    1.839
peak=    3.335 closest distance to " O   HOH Z 141 " =    1.571
peak=    3.334 closest distance to " OD1 ASN A  60 " =    1.490
peak=    3.332 closest distance to " C   GLY A  80 " =    1.124
peak=    3.331 closest distance to " O   HOH Z 108 " =    1.917
peak=    3.330 closest distance to " CB  ALA A 248 " =    1.359
peak=    3.326 closest distance to " O   SER A  26 " =    1.619
peak=    3.323 closest distance to " O   HOH Z 355 " =    1.731
peak=    3.323 closest distance to " O   HOH Z 332 " =    1.540
peak=    3.319 closest distance to " O   THR A  31 " =    1.543
peak=    3.315 closest distance to " CD BLYS A 290 " =    1.066
peak=    3.313 closest distance to " O   HOH Z  90 " =    3.227
peak=    3.313 closest distance to " O   HOH Z 367 " =    3.510
peak=    3.310 closest distance to " O   HOH Z 352 " =    1.265
peak=    3.310 closest distance to " CA  ASN A 176 " =    1.132
peak=    3.305 closest distance to " OG  SER A  97 " =    2.465
peak=    3.293 closest distance to " O   HOH Z  19 " =    1.817
peak=    3.289 closest distance to " CD2 LEU A  83 " =    1.563
peak=    3.287 closest distance to " O   HOH Z 411 " =    1.768
peak=    3.284 closest distance to " CD2 HIS A 115 " =    0.871
peak=    3.283 closest distance to " CD  LYS A  76 " =    1.841
peak=    3.281 closest distance to " O   HOH Z  63 " =    1.864
peak=    3.280 closest distance to " O   HOH Z 403 " =    1.372
peak=    3.275 closest distance to " CA  THR A 264 " =    0.815
peak=    3.274 closest distance to " NH1 ARG A 269 " =    0.845
peak=    3.271 closest distance to " O   HOH Z 408 " =    1.533
peak=    3.269 closest distance to " O   HOH Z 248 " =    1.761
peak=    3.268 closest distance to " OD2 ASP A 298 " =    3.973
peak=    3.264 closest distance to " O   HOH Z  98 " =    2.028
peak=    3.261 closest distance to " O   HOH Z 217 " =    2.193
peak=    3.258 closest distance to " NE2 GLN A  58 " =    4.241
peak=    3.255 closest distance to " O   HOH Z  10 " =    1.797
peak=    3.250 closest distance to " CG  GLN A  88 " =    1.059
peak=    3.250 closest distance to " O   GLY A  91 " =    1.644
peak=    3.250 closest distance to " O   GLY A  23 " =    2.330
peak=    3.249 closest distance to " CD2 TRP A 179 " =    1.360
peak=    3.245 closest distance to " O   HOH Z  63 " =    2.583
peak=    3.240 closest distance to " O   HOH Z 279 " =    2.202
peak=    3.238 closest distance to " O   HOH Z 150 " =    1.673
peak=    3.237 closest distance to " CG  ARG A 269 " =    1.062
peak=    3.237 closest distance to " O   HOH Z 151 " =    1.718
peak=    3.228 closest distance to " O   HOH Z 322 " =    2.093
peak=    3.227 closest distance to " O   HOH Z 277 " =    2.324
peak=    3.226 closest distance to " O   HOH Z 359 " =    2.093
peak=    3.226 closest distance to " CB  MET A  47 " =    1.482
peak=    3.226 closest distance to " CB  GLN A 278 " =    0.915
peak=    3.225 closest distance to " NZ  LYS A  76 " =    1.370
peak=    3.224 closest distance to " CB  ALA A  71 " =    1.242
peak=    3.218 closest distance to " CA  THR A 246 " =    1.166
peak=    3.217 closest distance to " C   SER A  32 " =    1.131
peak=    3.215 closest distance to " O   ASN A 217 " =    1.364
peak=    3.211 closest distance to " CD AARG A 102 " =    2.329
peak=    3.211 closest distance to " CG1 VAL A 153 " =    0.997
peak=    3.207 closest distance to " CA  ASN A  74 " =    1.253
peak=    3.205 closest distance to " O   HOH Z 143 " =    1.134
peak=    3.205 closest distance to " O   HOH Z 331 " =    1.313
peak=    3.202 closest distance to " CB  ARG A  79 " =    1.297
peak=    3.201 closest distance to " C   ALA A   1 " =    1.701
peak=    3.200 closest distance to " O   HOH Z 425 " =    1.355
peak=    3.199 closest distance to " O   HOH Z 211 " =    2.276
peak=    3.198 closest distance to " CG  MET A  93 " =    1.053
peak=    3.195 closest distance to " CD2 TYR A 186 " =    1.058
peak=    3.194 closest distance to " CE1 TYR A 186 " =    1.203
peak=    3.193 closest distance to " O   HOH Z 116 " =    1.686
peak=    3.190 closest distance to " CG1BVAL A 121 " =    1.178
peak=    3.190 closest distance to " CE  LYS A 119 " =    1.101
peak=    3.188 closest distance to " CB  ASN A 148 " =    1.940
peak=    3.188 closest distance to " O   HOH Z 175 " =    3.537
peak=    3.187 closest distance to " CB  LEU A 237 " =    0.906
peak=    3.186 closest distance to " O   HOH Z 414 " =    1.437
peak=    3.183 closest distance to " CB  TYR A  30 " =    1.505
peak=    3.183 closest distance to " O   HOH Z 287 " =    1.762
peak=    3.183 closest distance to " CD2 TYR A  30 " =    0.855
peak=    3.181 closest distance to " CG  MET A 185 " =    1.315
peak=    3.179 closest distance to " CB  LEU A 255 " =    0.785
peak=    3.178 closest distance to " CE2 TRP A 179 " =    1.684
peak=    3.172 closest distance to " C   LYS A 290 " =    1.258
peak=    3.172 closest distance to " OH  TYR A 116 " =    1.187
peak=    3.171 closest distance to " CB  ALA A  84 " =    1.214
peak=    3.171 closest distance to " CA  ALA A  51 " =    0.990
peak=    3.169 closest distance to " O   HOH Z 155 " =    1.620
peak=    3.169 closest distance to " O   HOH Z  54 " =    2.542
peak=    3.167 closest distance to " O   HOH Z 215 " =    1.493
peak=    3.163 closest distance to " N   ARG A 156 " =    1.330
peak=    3.163 closest distance to " O   HOH Z  35 " =    2.309
peak=    3.161 closest distance to " CB  ALA A 137 " =    1.250
peak=    3.160 closest distance to " CD  ARG A 195 " =    3.363
peak=    3.155 closest distance to " CA  ASP A 140 " =    1.227
peak=    3.154 closest distance to " NH2BARG A 190 " =    1.843
peak=    3.153 closest distance to " CA  ARG A  56 " =    1.438
peak=    3.152 closest distance to " O   GLN A 278 " =    1.349
peak=    3.151 closest distance to " CB  ARG A 259 " =    1.889
peak=    3.150 closest distance to " OD1 ASP A 286 " =    1.696
peak=    3.148 closest distance to " O   HOH Z 139 " =    5.145
peak=    3.147 closest distance to " NZ  LYS A 117 " =    1.167
peak=    3.141 closest distance to " O   HOH Z 251 " =    1.693
peak=    3.141 closest distance to " CG2 ILE A 120 " =    1.322
peak=    3.141 closest distance to " CD  ARG A 159 " =    0.741
peak=    3.141 closest distance to " CD1 LEU A  96 " =    0.804
peak=    3.140 closest distance to " O   HOH Z  96 " =    2.120
peak=    3.136 closest distance to " O   HOH Z 106 " =    2.375
peak=    3.125 closest distance to " O   HOH Z   3 " =    1.449
peak=    3.117 closest distance to " CD2 LEU A 282 " =    1.966
peak=    3.115 closest distance to " O   HOH Z 133 " =    2.184
peak=    3.098 closest distance to " CD1 ILE A 199 " =    0.992
peak=    3.094 closest distance to " CG2 VAL A 174 " =    1.277
peak=    3.092 closest distance to " O   HOH Z 277 " =    1.016
peak=    3.092 closest distance to " CB  TRP A 266 " =    0.979
peak=    3.091 closest distance to " O   HOH Z 148 " =    2.877
peak=    3.083 closest distance to " CA  ARG A 195 " =    1.104
peak=    3.082 closest distance to " OD1 ASN A  45 " =    1.362
peak=    3.082 closest distance to " CD1 LEU A 228 " =    1.394
peak=    3.079 closest distance to " O   HOH Z 380 " =    2.127
peak=    3.074 closest distance to " CD1 TRP A 266 " =    1.230
peak=    3.066 closest distance to " CB  THR A  31 " =    1.728
peak=    3.063 closest distance to " O   HOH Z  59 " =    2.108
peak=    3.059 closest distance to " O   HOH Z 407 " =    3.781
peak=    3.049 closest distance to " CB  ALA A 256 " =    1.128
peak=    3.045 closest distance to " CA  ALA A 158 " =    1.083
peak=    3.043 closest distance to " O   HOH Z  87 " =    2.360
peak=    3.040 closest distance to " CG2 VAL A 268 " =    0.915
peak=    3.035 closest distance to " O   HOH Z  71 " =    1.570
peak=    3.023 closest distance to " O   HOH Z   1 " =    1.961
peak=    3.021 closest distance to " CB  ALA A 248 " =    0.955

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.777 - 5.150
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 199
   mapped sites are within: 0.777 - 5.150

peak=   -5.094 closest distance to " CG2 VAL A 230 " =    0.847
peak=   -4.480 closest distance to " O   HOH Z  13 " =    1.210
peak=   -4.393 closest distance to " OG ASER A 134 " =    1.205
peak=   -4.373 closest distance to " O   HOH Z 210 " =    0.781
peak=   -4.192 closest distance to " CA  SER A 164 " =    2.033
peak=   -4.169 closest distance to " O   HOH Z 266 " =    4.318
peak=   -4.151 closest distance to " CB  ALA A 161 " =    2.608
peak=   -4.149 closest distance to " CD1 LEU A 101 " =    2.533
peak=   -4.129 closest distance to " OXT GLY A 302 " =    2.786
peak=   -4.120 closest distance to " O   HOH Z  92 " =    1.212
peak=   -4.034 closest distance to " CG  ASP A  50 " =    2.294
peak=   -4.027 closest distance to " CD  ARG A 156 " =    1.991
peak=   -3.999 closest distance to " O   HOH Z 166 " =    1.849
peak=   -3.990 closest distance to " CG2 THR A   4 " =    1.872
peak=   -3.980 closest distance to " O   VAL A  67 " =    2.477
peak=   -3.963 closest distance to " NH2 ARG A  79 " =    1.837
peak=   -3.948 closest distance to " SG  CYS A 254 " =    3.161
peak=   -3.931 closest distance to " O   ALA A 161 " =    1.344
peak=   -3.895 closest distance to " N   GLN A  58 " =    1.815
peak=   -3.883 closest distance to " CE2 TYR A  30 " =    2.810
peak=   -3.868 closest distance to " CZ  TYR A 169 " =    1.900
peak=   -3.834 closest distance to " O   HOH Z  11 " =    1.534
peak=   -3.830 closest distance to " C   ALA A 158 " =    1.200
peak=   -3.822 closest distance to " CH2 TRP A 179 " =    1.303
peak=   -3.814 closest distance to " O   HOH Z 290 " =    1.000
peak=   -3.805 closest distance to " O   HOH Z 292 " =    4.278
peak=   -3.803 closest distance to " O   ASN A 187 " =    1.395
peak=   -3.799 closest distance to " O   HOH Z 165 " =    2.127
peak=   -3.791 closest distance to " O   HOH Z 231 " =    1.844
peak=   -3.790 closest distance to " CD1 PHE A  59 " =    1.828
peak=   -3.790 closest distance to " N   SER A 276 " =    1.336
peak=   -3.772 closest distance to " ND2 ASN A  45 " =    1.041
peak=   -3.762 closest distance to " OG BSER A 134 " =    1.705
peak=   -3.756 closest distance to " O   HOH Z 138 " =    1.020
peak=   -3.754 closest distance to " O   HOH Z 423 " =    2.311
peak=   -3.744 closest distance to " CD2 LEU A 300 " =    2.779
peak=   -3.742 closest distance to " NH2 ARG A  66 " =    1.402
peak=   -3.717 closest distance to " CD  ARG A 139 " =    1.641
peak=   -3.712 closest distance to " O   PRO A 198 " =    1.348
peak=   -3.708 closest distance to " CB  CYS A 254 " =    2.573
peak=   -3.699 closest distance to " CG  LYS A 193 " =    2.232
peak=   -3.689 closest distance to " N   ALA A 226 " =    2.052
peak=   -3.680 closest distance to " O   HOH Z  56 " =    2.203
peak=   -3.666 closest distance to " CG  GLU A  53 " =    1.501
peak=   -3.655 closest distance to " O   ALA A  51 " =    1.441
peak=   -3.649 closest distance to " OG  SER A  62 " =    1.407
peak=   -3.648 closest distance to " O   HOH Z 126 " =    1.879
peak=   -3.647 closest distance to " OE2 GLU A   2 " =    1.824
peak=   -3.644 closest distance to " O   HOH Z  43 " =    1.714
peak=   -3.635 closest distance to " C   HIS A 108 " =    1.169
peak=   -3.630 closest distance to " O   HOH Z 103 " =    1.874
peak=   -3.626 closest distance to " CD  GLN A  88 " =    2.248
peak=   -3.623 closest distance to " CG  ASP A 231 " =    0.835
peak=   -3.621 closest distance to " CB  ALA A 248 " =    1.941
peak=   -3.615 closest distance to " O   LEU A 228 " =    2.315
peak=   -3.611 closest distance to " C   ASN A 285 " =    2.244
peak=   -3.607 closest distance to " O   HOH Z 407 " =    2.950
peak=   -3.605 closest distance to " CA  ASP A 298 " =    1.053
peak=   -3.604 closest distance to " OG BSER A 134 " =    1.205
peak=   -3.594 closest distance to " CD  LYS A 289 " =    2.473
peak=   -3.574 closest distance to " O   MET A  40 " =    2.650
peak=   -3.563 closest distance to " OD1 ASP A 200 " =    1.204
peak=   -3.533 closest distance to " O   ALA A   1 " =    1.914
peak=   -3.532 closest distance to " O   HOH Z 266 " =    4.392
peak=   -3.529 closest distance to " CG2 VAL A 112 " =    2.554
peak=   -3.529 closest distance to " O   ASP A 191 " =    1.237
peak=   -3.526 closest distance to " O   HOH Z 221 " =    1.237
peak=   -3.523 closest distance to " OXT GLY A 302 " =    3.392
peak=   -3.516 closest distance to " ND2 ASN A  39 " =    1.231
peak=   -3.516 closest distance to " N   HIS A 115 " =    2.003
peak=   -3.515 closest distance to " O   HOH Z  71 " =    1.152
peak=   -3.515 closest distance to " O   VAL A  67 " =    2.687
peak=   -3.510 closest distance to " ND2 ASN A  60 " =    1.333
peak=   -3.506 closest distance to " CE3 TRP A 150 " =    1.961
peak=   -3.500 closest distance to " O   HOH Z  98 " =    1.587
peak=   -3.499 closest distance to " CB  ALA A  51 " =    1.845
peak=   -3.494 closest distance to " NH2AARG A 275 " =    5.090
peak=   -3.491 closest distance to " N   GLN A 122 " =    1.592
peak=   -3.487 closest distance to " O   HOH Z 151 " =    1.433
peak=   -3.485 closest distance to " CG  ARG A 219 " =    2.468
peak=   -3.470 closest distance to " CE  MET A 105 " =    2.119
peak=   -3.467 closest distance to " CB  TYR A  15 " =    2.188
peak=   -3.463 closest distance to " O   TRP A  92 " =    1.893
peak=   -3.462 closest distance to " CD2 LEU A 237 " =    2.557
peak=   -3.461 closest distance to " O   HOH Z  97 " =    1.389
peak=   -3.459 closest distance to " N   GLY A 133 " =    1.840
peak=   -3.458 closest distance to " O   HOH Z 426 " =    2.276
peak=   -3.456 closest distance to " ND2 ASN A 187 " =    1.748
peak=   -3.456 closest distance to " CD1 LEU A 228 " =    2.341
peak=   -3.453 closest distance to " O   HOH Z 377 " =    1.705
peak=   -3.441 closest distance to " O   HOH Z  52 " =    1.757
peak=   -3.433 closest distance to " CE BMET A  47 " =    1.528
peak=   -3.430 closest distance to " OG  SER A  97 " =    2.234
peak=   -3.427 closest distance to " CB  ALA A 227 " =    2.334
peak=   -3.420 closest distance to " CD2 LEU A 167 " =    1.762
peak=   -3.416 closest distance to " CD1 LEU A 255 " =    2.701
peak=   -3.396 closest distance to " CD1 TRP A 179 " =    1.165
peak=   -3.388 closest distance to " O   HOH Z 208 " =    1.159
peak=   -3.386 closest distance to " O   HOH Z  60 " =    2.229
peak=   -3.386 closest distance to " O   HOH Z 431 " =    1.958
peak=   -3.374 closest distance to " O   HOH Z 265 " =    1.769
peak=   -3.371 closest distance to " O   HOH Z 310 " =    1.556
peak=   -3.367 closest distance to " O   PHE A 218 " =    1.636
peak=   -3.366 closest distance to " O   HOH Z 292 " =    2.701
peak=   -3.362 closest distance to " O   HOH Z 198 " =    2.163
peak=   -3.362 closest distance to " O   ALA A 256 " =    1.381
peak=   -3.361 closest distance to " OD1 ASN A 249 " =    1.096
peak=   -3.356 closest distance to " N   GLY A  17 " =    1.450
peak=   -3.340 closest distance to " O  BHOH Z 338 " =    1.522
peak=   -3.339 closest distance to " O   LEU A 300 " =    2.606
peak=   -3.331 closest distance to " CB  SER A 245 " =    2.442
peak=   -3.331 closest distance to " O   ALA A 160 " =    1.263
peak=   -3.327 closest distance to " O   HOH Z  48 " =    1.228
peak=   -3.327 closest distance to " N   THR A 235 " =    1.272
peak=   -3.322 closest distance to " O   HOH Z 297 " =    2.852
peak=   -3.312 closest distance to " O   HOH Z 250 " =    1.346
peak=   -3.312 closest distance to " O   ALA A 161 " =    2.715
peak=   -3.310 closest distance to " O   HOH Z 193 " =    1.764
peak=   -3.308 closest distance to " O   SER A 273 " =    1.376
peak=   -3.307 closest distance to " O   ASP A 270 " =    1.811
peak=   -3.305 closest distance to " O   HOH Z 388 " =    2.068
peak=   -3.299 closest distance to " O   HOH Z 138 " =    1.197
peak=   -3.296 closest distance to " O   HOH Z  10 " =    1.453
peak=   -3.294 closest distance to " O   HOH Z 147 " =    1.958
peak=   -3.292 closest distance to " O   GLY A 196 " =    0.946
peak=   -3.286 closest distance to " O   HOH Z 360 " =    2.479
peak=   -3.280 closest distance to " CG  GLU A 277 " =    1.103
peak=   -3.278 closest distance to " O   SER A  95 " =    1.448
peak=   -3.278 closest distance to " N   ALA A 248 " =    1.679
peak=   -3.277 closest distance to " O   HOH Z 427 " =    1.402
peak=   -3.277 closest distance to " NE2 GLN A  58 " =    1.108
peak=   -3.266 closest distance to " O   HOH Z 125 " =    2.942
peak=   -3.264 closest distance to " O   HOH Z 234 " =    4.258
peak=   -3.264 closest distance to " CE  LYS A 166 " =    3.031
peak=   -3.262 closest distance to " N   LEU A 281 " =    1.790
peak=   -3.259 closest distance to " O   SER A 146 " =    0.793
peak=   -3.258 closest distance to " CD  GLN A  88 " =    0.865
peak=   -3.252 closest distance to " OG1 THR A  82 " =    1.394
peak=   -3.249 closest distance to " NH2 ARG A  66 " =    4.566
peak=   -3.244 closest distance to " O   HOH Z 423 " =    1.178
peak=   -3.240 closest distance to " CD2 TYR A 293 " =    2.164
peak=   -3.233 closest distance to " CG  LEU A 228 " =    1.032
peak=   -3.223 closest distance to " CB  PRO A 243 " =    2.681
peak=   -3.222 closest distance to " CA  ARG A  66 " =    1.798
peak=   -3.221 closest distance to " O   HOH Z 295 " =    1.374
peak=   -3.216 closest distance to " CA  GLY A  98 " =    2.097
peak=   -3.215 closest distance to " O   HOH Z  93 " =    1.221
peak=   -3.213 closest distance to " O   HOH Z 313 " =    1.192
peak=   -3.207 closest distance to " O   ALA A   8 " =    1.878
peak=   -3.200 closest distance to " O   HOH Z  17 " =    1.308
peak=   -3.198 closest distance to " OD2 ASP A 286 " =    2.479
peak=   -3.198 closest distance to " CG  ASN A  45 " =    1.670
peak=   -3.194 closest distance to " N   THR A 157 " =    1.561
peak=   -3.188 closest distance to " O   HOH Z 419 " =    1.060
peak=   -3.188 closest distance to " O   HOH Z 281 " =    2.802
peak=   -3.188 closest distance to " N   ALA A  43 " =    2.613
peak=   -3.185 closest distance to " CG  GLU A 152 " =    2.382
peak=   -3.183 closest distance to " O   HOH Z   9 " =    2.035
peak=   -3.183 closest distance to " O   HOH Z 150 " =    1.369
peak=   -3.182 closest distance to " CG  PHE A  59 " =    2.189
peak=   -3.176 closest distance to " NH1 ARG A  56 " =    2.588
peak=   -3.175 closest distance to " CG  GLN A  58 " =    1.270
peak=   -3.175 closest distance to " O   HOH Z  63 " =    0.777
peak=   -3.174 closest distance to " O   HOH Z 191 " =    5.150
peak=   -3.174 closest distance to " O   HOH Z 134 " =    2.551
peak=   -3.169 closest distance to " OG1 THR A 178 " =    1.209
peak=   -3.163 closest distance to " ND2 ASN A 252 " =    1.661
peak=   -3.160 closest distance to " CG  TRP A 266 " =    1.543
peak=   -3.159 closest distance to " O   GLY A  80 " =    2.583
peak=   -3.149 closest distance to " O   HOH Z 130 " =    2.394
peak=   -3.147 closest distance to " CG  ASN A 110 " =    1.180
peak=   -3.139 closest distance to " O   ASN A 301 " =    1.402
peak=   -3.133 closest distance to " OD1 ASN A 148 " =    1.657
peak=   -3.130 closest distance to " O   HOH Z  12 " =    3.486
peak=   -3.130 closest distance to " OD1 ASP A 191 " =    1.590
peak=   -3.129 closest distance to " O   HOH Z 166 " =    1.564
peak=   -3.124 closest distance to " NE1 TRP A 266 " =    2.294
peak=   -3.121 closest distance to " O   HOH Z 108 " =    2.179
peak=   -3.118 closest distance to " CG  PRO A 280 " =    2.175
peak=   -3.117 closest distance to " O   HOH Z 313 " =    2.071
peak=   -3.116 closest distance to " CD1 LEU A  96 " =    2.377
peak=   -3.111 closest distance to " C   LEU A 143 " =    1.232
peak=   -3.110 closest distance to " O   ALA A 114 " =    1.398
peak=   -3.110 closest distance to " O   SER A 271 " =    2.165
peak=   -3.102 closest distance to " OG BSER A 210 " =    2.141
peak=   -3.100 closest distance to " CB  PHE A 208 " =    2.230
peak=   -3.094 closest distance to " CD1 TYR A 247 " =    2.324
peak=   -3.093 closest distance to " O   HOH Z  70 " =    1.483
peak=   -3.084 closest distance to " NH1BARG A 190 " =    2.244
peak=   -3.081 closest distance to " O   SER A 258 " =    1.893
peak=   -3.079 closest distance to " OH  TYR A 169 " =    1.007
peak=   -3.067 closest distance to " O   HOH Z 389 " =    4.641
peak=   -3.065 closest distance to " CG  ARG A 269 " =    2.221
peak=   -3.063 closest distance to " CB  ASP A 124 " =    2.057
peak=   -3.055 closest distance to " CD2 PHE A  61 " =    1.837
peak=   -3.053 closest distance to " CG1 VAL A 112 " =    2.642
peak=   -3.002 closest distance to " ND2 ASN A  60 " =    1.717

================= 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    :  0.4793 0.4848   6.282438e+00   6.277537e+00
   1_bss:  0.4711 0.4749   6.280783e+00   6.268174e+00
   1_xyz:  0.4017 0.4212   6.182348e+00   6.218030e+00
   1_adp:  0.3584 0.4040   6.115065e+00   6.195355e+00
   1_occ:  0.3578 0.4038   6.114837e+00   6.195171e+00
   2_bss:  0.3548 0.4014   6.115659e+00   6.193556e+00
   2_xyz:  0.2627 0.3209   5.873865e+00   6.023548e+00
   2_adp:  0.2365 0.2940   5.788779e+00   5.956554e+00
   2_occ:  0.2363 0.2942   5.788080e+00   5.956611e+00
   3_bss:  0.2338 0.2916   5.785091e+00   5.952994e+00
   3_xyz:  0.1742 0.2305   5.533606e+00   5.747095e+00
   3_adp:  0.1598 0.2148   5.453223e+00   5.671858e+00
   3_occ:  0.1596 0.2147   5.452965e+00   5.671943e+00
   4_bss:  0.1592 0.2139   5.452728e+00   5.671652e+00
   4_xyz:  0.1366 0.1833   5.308896e+00   5.525576e+00
   4_adp:  0.1319 0.1774   5.277001e+00   5.493659e+00
   4_occ:  0.1316 0.1771   5.275889e+00   5.492800e+00
   5_bss:  0.1320 0.1772   5.278046e+00   5.494577e+00
   5_xyz:  0.1203 0.1660   5.207934e+00   5.436169e+00
   5_adp:  0.1179 0.1657   5.197214e+00   5.433124e+00
   5_occ:  0.1176 0.1656   5.195858e+00   5.432421e+00
   5_bss:  0.1176 0.1657   5.195869e+00   5.432485e+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:  0.358  17.395   6.456   8.718   9.239   0.000   0.000   0.000
   1_xyz:  0.358  17.395   6.456   8.718   9.239   0.000   0.000   0.000
   1_adp:  0.358  17.395   6.456   8.718   9.239   0.000   0.000   0.000
   1_occ:  0.358  17.395   6.456   8.718   9.239   0.000   0.000   0.000
   2_bss:  0.337  35.997   2.806   5.013   6.053   0.000   0.000   0.000
   2_xyz:  0.337  35.997   2.806   5.013   6.053   0.000   0.000   0.000
   2_adp:  0.337  35.997   2.806   5.013   6.053   0.000   0.000   0.000
   2_occ:  0.337  35.997   2.806   5.013   6.053   0.000   0.000   0.000
   3_bss:  0.316  39.238   1.537   2.860   3.279   0.000   0.000   0.000
   3_xyz:  0.316  39.238   1.537   2.860   3.279   0.000   0.000   0.000
   3_adp:  0.316  39.238   1.537   2.860   3.279   0.000   0.000   0.000
   3_occ:  0.316  39.238   1.537   2.860   3.279   0.000   0.000   0.000
   4_bss:  0.316  37.663   0.846   1.875   1.984   0.000   0.000   0.000
   4_xyz:  0.316  37.663   0.846   1.875   1.984   0.000   0.000   0.000
   4_adp:  0.316  37.663   0.846   1.875   1.984   0.000   0.000   0.000
   4_occ:  0.316  37.663   0.846   1.875   1.984   0.000   0.000   0.000
   5_bss:  0.317  38.853   0.756   1.622   1.633   0.000   0.000   0.000
   5_xyz:  0.317  38.853   0.756   1.622   1.633   0.000   0.000   0.000
   5_adp:  0.317  38.853   0.756   1.622   1.633   0.000   0.000   0.000
   5_occ:  0.317  38.853   0.756   1.622   1.633   0.000   0.000   0.000
   5_bss:  0.320  41.955  -0.581   0.285   0.296   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.732 0.3967  0.4683    72813.288
   1_bss:  59.503 0.3970  0.5834    69206.485
   1_xyz:  51.255 0.5018  0.7324    54235.153
   1_adp:  47.594 0.5484  0.8485    49259.139
   1_occ:  47.622 0.5481  0.8478    49343.790
   2_bss:  47.367 0.5513  0.7573    49110.674
   2_xyz:  34.176 0.7099  0.9576    28086.098
   2_adp:  30.540 0.7515  1.0039    23431.339
   2_occ:  30.552 0.7514  1.0031    23430.927
   3_bss:  30.318 0.7537  0.9337    23116.769
   3_xyz:  22.780 0.8337  0.9927    13779.700
   3_adp:  20.513 0.8568  1.0045    11756.868
   3_occ:  20.524 0.8567  1.0042    11763.273
   4_bss:  20.463 0.8572  0.9688    11708.731
   4_xyz:  17.144 0.8879  0.9837     8533.490
   4_adp:  16.354 0.8953  0.9867     7998.556
   4_occ:  16.328 0.8955  0.9867     7980.459
   5_bss:  16.366 0.8953  0.9781     8038.461
   5_xyz:  15.199 0.9051  0.9826     7130.725
   5_adp:  15.057 0.9065  0.9821     7068.513
   5_occ:  15.039 0.9067  0.9819     7062.626
   5_bss:  15.040 0.9067  0.9819     7067.090
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3266e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3266e+01
   1_xyz:   1.695  0.013  0.108 18.231  0.007  4.109   1.4235e-01
   1_adp:   1.695  0.013  0.108 18.231  0.007  4.109   1.4235e-01
   1_occ:   1.695  0.013  0.108 18.231  0.007  4.109   1.4235e-01
   2_bss:   1.695  0.013  0.108 18.231  0.007  4.109   1.4235e-01
   2_xyz:   1.270  0.010  0.084 16.367  0.005  4.115   9.7071e-02
   2_adp:   1.270  0.010  0.084 16.367  0.005  4.115   9.7071e-02
   2_occ:   1.270  0.010  0.084 16.367  0.005  4.115   9.7071e-02
   3_bss:   1.270  0.010  0.084 16.367  0.005  4.115   9.7071e-02
   3_xyz:   1.053  0.007  0.074 15.496  0.004  4.110   6.5162e-02
   3_adp:   1.053  0.007  0.074 15.496  0.004  4.110   6.5162e-02
   3_occ:   1.053  0.007  0.074 15.496  0.004  4.110   6.5162e-02
   4_bss:   1.053  0.007  0.074 15.496  0.004  4.110   6.5162e-02
   4_xyz:   0.924  0.005  0.069 15.101  0.003  4.114   5.3692e-02
   4_adp:   0.924  0.005  0.069 15.101  0.003  4.114   5.3692e-02
   4_occ:   0.924  0.005  0.069 15.101  0.003  4.114   5.3692e-02
   5_bss:   0.924  0.005  0.069 15.101  0.003  4.114   5.3692e-02
   5_xyz:   1.024  0.006  0.077 15.299  0.004  4.116   6.1057e-02
   5_adp:   1.024  0.006  0.077 15.299  0.004  4.116   6.1057e-02
   5_occ:   1.024  0.006  0.077 15.299  0.004  4.116   6.1057e-02
   5_bss:   1.024  0.006  0.077 15.299  0.004  4.116   6.1057e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9026e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9026e+00
   1_xyz:  14.742  0.170  0.475 88.295  0.057  2.205   9.8473e-02
   1_adp:  14.742  0.170  0.475 88.295  0.057  2.205   9.8473e-02
   1_occ:  14.742  0.170  0.475 88.295  0.057  2.205   9.8473e-02
   2_bss:  14.742  0.170  0.475 88.295  0.057  2.205   9.8473e-02
   2_xyz:   7.671  0.114  0.264 86.253  0.041  2.179   1.3045e-01
   2_adp:   7.671  0.114  0.264 86.253  0.041  2.179   1.3045e-01
   2_occ:   7.671  0.114  0.264 86.253  0.041  2.179   1.3045e-01
   3_bss:   7.671  0.114  0.264 86.253  0.041  2.179   1.3045e-01
   3_xyz:   6.698  0.041  0.333 88.661  0.036  2.347   6.0918e-02
   3_adp:   6.698  0.041  0.333 88.661  0.036  2.347   6.0918e-02
   3_occ:   6.698  0.041  0.333 88.661  0.036  2.347   6.0918e-02
   4_bss:   6.698  0.041  0.333 88.661  0.036  2.347   6.0918e-02
   4_xyz:   6.239  0.039  0.361 78.567  0.024  2.392   3.3979e-02
   4_adp:   6.239  0.039  0.361 78.567  0.024  2.392   3.3979e-02
   4_occ:   6.239  0.039  0.361 78.567  0.024  2.392   3.3979e-02
   5_bss:   6.239  0.039  0.361 78.567  0.024  2.392   3.3979e-02
   5_xyz:   6.706  0.035  0.480 83.369  0.026  2.353   4.1525e-02
   5_adp:   6.706  0.035  0.480 83.369  0.026  2.353   4.1525e-02
   5_occ:   6.706  0.035  0.480 83.369  0.026  2.353   4.1525e-02
   5_bss:   6.706  0.035  0.480 83.369  0.026  2.353   4.1525e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  74.64   0.00  13.52  70.70   0.00  11.14  74.64   0.00  26.46
   1_occ:  74.64   0.00  13.52  70.70   0.00  11.14  74.64   0.00  26.46
   2_bss:  74.64   0.00  13.52  70.70   0.00  11.14  74.64   0.00  26.46
   2_xyz:  74.64   0.00  13.52  70.70   0.00  11.14  74.64   0.00  26.46
   2_adp:  69.59   0.00  13.87  69.59   0.00  10.39  68.07   1.10  32.84
   2_occ:  69.59   0.00  13.87  69.59   0.00  10.39  68.07   1.10  32.84
   3_bss:  69.59   0.00  13.87  69.59   0.00  10.39  68.07   1.10  32.84
   3_xyz:  69.59   0.00  13.87  69.59   0.00  10.39  68.07   1.10  32.84
   3_adp:  76.43   0.00  13.96  76.43   0.00   9.79  69.45   3.45  36.68
   3_occ:  76.43   0.00  13.96  76.43   0.00   9.79  69.45   3.45  36.68
   4_bss:  76.43   0.00  13.96  76.43   0.00   9.79  69.45   3.45  36.68
   4_xyz:  76.43   0.00  13.96  76.43   0.00   9.79  69.45   3.45  36.68
   4_adp:  78.54   0.00  13.85  78.54   0.00   9.60  70.37   2.61  36.96
   4_occ:  78.54   0.00  13.85  78.54   0.00   9.60  70.37   2.61  36.96
   5_bss:  78.54   0.00  13.85  78.54   0.00   9.60  70.37   2.61  36.96
   5_xyz:  78.54   0.00  13.85  78.54   0.00   9.60  70.37   2.61  36.96
   5_adp:  88.16   0.00  13.89  88.16   0.00   9.55  75.13   1.75  37.53
   5_occ:  88.16   0.00  13.89  88.16   0.00   9.55  75.13   1.75  37.53
   5_bss:  89.49   1.34  15.23  89.49   1.34  10.89  76.46   3.09  38.87
------------------------------------------------------------------------
 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:    1.210    0.017    0.410
   1_adp:    1.210    0.017    0.410
   1_occ:    1.210    0.017    0.410
   2_bss:    1.210    0.017    0.410
   2_xyz:    1.631    0.028    0.609
   2_adp:    1.631    0.028    0.609
   2_occ:    1.631    0.028    0.609
   3_bss:    1.631    0.028    0.609
   3_xyz:    1.610    0.048    0.676
   3_adp:    1.610    0.048    0.676
   3_occ:    1.610    0.048    0.676
   4_bss:    1.610    0.048    0.676
   4_xyz:    1.791    0.018    0.732
   4_adp:    1.791    0.018    0.732
   4_occ:    1.791    0.018    0.732
   5_bss:    1.791    0.018    0.732
   5_xyz:    1.803    0.070    0.747
   5_adp:    1.803    0.070    0.747
   5_occ:    1.803    0.070    0.747
   5_bss:    1.803    0.070    0.747
------------------------------------------------------------------------

CPU time actual refinement: 346.11


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_561/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_561/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_561/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_561/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_561/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.96 
  Macro-tasks:
    bulk solvent and scale       = 42.82  
    individual site refinement   = 139.77 
    weights calculation          = 32.43  
    collect and process          = 6.53   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 221.69 
  Micro-tasks:
    mask                            = 2.58   
    f_calc                          = 108.32 
    alpha_beta                      = 8.29   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 117.51 
    fmodel                         = 7.17   
    r_factors                      = 0.23   
    phase_errors                   = 10.12  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 255.66 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.917 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    642 calls, 107.91 s
gradients_fft:          587 calls, 104.76 s

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

# Date 2008-01-16 Time 01:52:30 PST -0800 (1200477150.61 s)
Start R-work = 0.4793, R-free = 0.4848 (no bulk solvent and anisotropic scale)
Final R-work = 0.1346, R-free = 0.1838 (no bulk solvent and anisotropic scale)

Start R-work = 0.4711, R-free = 0.4749
Final R-work = 0.1176, R-free = 0.1657