# Date 2008-01-16 Time 01:40:02 PST -0800 (1200476402.58 s)
#phil __OFF__

Command line arguments: "../512.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 = 29198
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 512

-------------------------------------------------------------------------------
  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, 46.2261, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.97238
Completeness in resolution range: 0.959963
Completeness with d_max=infinity: 0.957008

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9592
                             d_min =   1.9724

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, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.97238
Completeness in resolution range: 0.959963
Completeness with d_max=infinity: 0.957008

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9596 -  4.2205 [2147/2171]  1929   218  10.2%
  bin  2:  4.2205 -  3.3625 [2049/2069]  1848   201   9.8%
  bin  3:  3.3625 -  2.9411 [2040/2059]  1834   206  10.1%
  bin  4:  2.9411 -  2.6739 [2005/2035]  1805   200  10.0%
  bin  5:  2.6739 -  2.4831 [2009/2028]  1811   198   9.9%
  bin  6:  2.4831 -  2.3373 [1979/2004]  1776   203  10.3%
  bin  7:  2.3373 -  2.2207 [1989/2017]  1790   199  10.0%
  bin  8:  2.2207 -  2.1243 [1975/2011]  1781   194   9.8%
  bin  9:  2.1243 -  2.0427 [1960/2002]  1766   194   9.9%
  bin 10:  2.0427 -  1.9724 [1436/2010]  1290   146  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_512/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:
        1.81 -     2.42: 30
        2.42 -     3.04: 2211
        3.04 -     3.66: 4747
        3.66 -     4.28: 9116
        4.28 -     4.90: 12385
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.953 3.040 -x+1/2,-y+1,z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.968 3.040 -x+1,y-1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  ... (remaining 28484 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_512/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_512/model_refine_001.geo

CPU time processing inputs: 9.48


============================ 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 46.22605 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4567   r_free= 0.4500   ksol= 0.00   Bsol= 0.00   scale= 0.812    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.259159                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7074 0.99   1394  154 0.3842 0.3701      6.5626      6.5542|
|  2:  4.7074 -  3.7559 0.99   1336  151 0.3616 0.3438      6.7201      6.6754|
|  3:  3.7559 -  3.2869 0.99   1310  143 0.3964 0.3603      6.6172      6.5935|
|  4:  3.2869 -  2.9889 0.99   1305  149 0.4402 0.4239      6.5044      6.4663|
|  5:  2.9889 -  2.7762 0.99   1301  145 0.4844 0.4677       6.348      6.3603|
|  6:  2.7762 -  2.6134 0.99   1296  141 0.4798 0.5430      6.2671      6.1977|
|  7:  2.6134 -  2.4831 0.99   1285  140 0.4961 0.4864      6.2221      6.2075|
|  8:  2.4831 -  2.3755 0.98   1273  145 0.5140 0.4743      6.1907      6.1733|
|  9:  2.3755 -  2.2844 0.98   1265  140 0.4902 0.5352      6.0907      6.1571|
| 10:  2.2844 -  2.2058 1.00   1296  144 0.5276 0.5045      6.1216      6.0719|
| 11:  2.2058 -  2.1370 0.97   1255  137 0.5112 0.4664      6.0259      6.0364|
| 12:  2.1370 -  2.0761 0.98   1249  144 0.5135 0.5198      5.9825       5.983|
| 13:  2.0761 -  2.0216 0.99   1303  135 0.5051 0.5205      5.8719      5.8417|
| 14:  2.0216 -  1.9724 0.60    762   91 0.5406 0.5424      5.8858        5.77|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7074  1394   154  0.71  33.70   0.80     0.75      68937.90|
|  2:  4.7074 -  3.7559  1336   151  0.75  30.82   0.89     0.82      85908.59|
|  3:  3.7559 -  3.2869  1310   143  0.67  37.99   0.88     0.78      90294.37|
|  4:  3.2869 -  2.9889  1305   149  0.59  44.92   0.82     0.67      83482.29|
|  5:  2.9889 -  2.7762  1301   145  0.47  53.97   0.77     0.56      73494.37|
|  6:  2.7762 -  2.6134  1296   141  0.44  56.99   0.74     0.49      67378.21|
|  7:  2.6134 -  2.4831  1285   140  0.39  60.83   0.75     0.45      64200.71|
|  8:  2.4831 -  2.3755  1273   145  0.37  61.86   0.74     0.44      58500.16|
|  9:  2.3755 -  2.2844  1265   140  0.40  59.69   0.75     0.47      51165.12|
| 10:  2.2844 -  2.2058  1296   144  0.43  57.93   0.76     0.50      43782.98|
| 11:  2.2058 -  2.1370  1255   137  0.42  58.75   0.77     0.52      42115.60|
| 12:  2.1370 -  2.0761  1249   144  0.37  62.06   0.79     0.46      40388.09|
| 13:  2.0761 -  2.0216  1303   135  0.34  64.93   0.73     0.41      36395.70|
| 14:  2.0216 -  1.9724   762    91  0.35  63.83   0.73     0.39      30214.65|
|alpha:            min =        0.39 max =            0.82 mean =         0.56|
|beta:             min =    30214.65 max =        90294.37 mean =     60874.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.98 mean =        52.90|
|phase err.(test): min =        0.00 max =           89.98 mean =        53.14|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.642917             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.428   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.014151              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.472   (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:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       31 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      696 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1514 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2647 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3995 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5090 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6615 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7767 |
|-----------------------------------------------------------------------------|
|-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 |       53.424 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.892 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.705)------------------------------------------|
|    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 = 11.705)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4652   r_free= 0.4525   ksol= 0.00   Bsol= 0.00   scale= 0.780    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.263057                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4488   r_free= 0.4347   ksol= 0.38   Bsol= 20.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.83,9.97,8.29,0.00,0.00,0.00); trace/3= 8.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.253701                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.869790              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.092   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.892944              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.816   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4488      final r-factor (work) = 0.3574          |
| start r-factor (free) = 0.4347      final r-factor (free) = 0.3762          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 81.1900 = 8.87 * 0.50 * 6.2609 + 1.00 * 53.4237                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.3763 = 8.87 * 0.50 * 6.1444 + 1.00 * 0.1265                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3574      final r-factor (work) = 0.3031          |
| start r-factor (free) = 0.3762      final r-factor (free) = 0.3501          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5010 = 0.89 * 1.00 * 6.1444 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3926 = 0.89 * 1.00 * 6.0230 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.705)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.03   12.31    None  None   None       |
|    all(noH): 2823   0      0.00    77.03   12.31    None  None   None       |
|    Sol.    : 438    0      0.00    77.03   26.37    None  None   None       |
|    Mac.    : 2385   0      0.00    68.54   9.73     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 -   7.703: 1243   |   5:    38.515 -  46.218:   59        |
|      1:     7.703 -  15.406:  772   |   6:    46.218 -  53.921:   28        |
|      2:    15.406 -  23.109:  385   |   7:    53.921 -  61.624:   12        |
|      3:    23.109 -  30.812:  189   |   8:    61.624 -  69.327:    4        |
|      4:    30.812 -  38.515:  130   |   9:    69.327 -  77.030:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3031 r_free = 0.3501             target_work(ml) = 5.993         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3027 r_free = 0.3495             target_work(ml) = 5.992         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3027   r_free= 0.3495   ksol= 0.38   Bsol= 20.00   scale= 1.110   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.83,9.97,8.29,0.00,0.00,0.00); trace/3= 8.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.991857                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2982   r_free= 0.3432   ksol= 0.35   Bsol= 36.03   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,5.67,5.06,0.00,0.00,0.00); trace/3= 4.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.991576                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.443703              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.662   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.414180              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.791  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2982      final r-factor (work) = 0.2059          |
| start r-factor (free) = 0.3432      final r-factor (free) = 0.2557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.5400 = 7.44 * 0.50 * 6.0221 + 1.00 * 0.1265                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7699 = 7.44 * 0.50 * 5.8256 + 1.00 * 0.0879                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2059      final r-factor (work) = 0.1772          |
| start r-factor (free) = 0.2557      final r-factor (free) = 0.2299          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4271 = 0.41 * 1.00 * 5.8256 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3215 = 0.41 * 1.00 * 5.5777 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.705)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.45   12.18    None  None   None       |
|    all(noH): 2823   0      0.00    81.45   12.18    None  None   None       |
|    Sol.    : 438    0      1.33    81.45   32.95    None  None   None       |
|    Mac.    : 2385   0      0.00    71.57   8.37     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 -   8.145: 1539   |   5:    40.724 -  48.869:   94        |
|      1:     8.145 -  16.290:  658   |   6:    48.869 -  57.014:   45        |
|      2:    16.290 -  24.435:  196   |   7:    57.014 -  65.159:   15        |
|      3:    24.435 -  32.580:  147   |   8:    65.159 -  73.304:    2        |
|      4:    32.580 -  40.724:  126   |   9:    73.304 -  81.449:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1772 r_free = 0.2299             target_work(ml) = 5.527         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1770 r_free = 0.2294             target_work(ml) = 5.526         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1770   r_free= 0.2294   ksol= 0.35   Bsol= 36.03   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,5.67,5.06,0.00,0.00,0.00); trace/3= 4.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.525693                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1746   r_free= 0.2271   ksol= 0.32   Bsol= 41.87   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.20,2.97,3.95,0.00,0.00,0.00); trace/3= 3.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.520537                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.826502              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.729   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.568968              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.614  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1746      final r-factor (work) = 0.1423          |
| start r-factor (free) = 0.2271      final r-factor (free) = 0.1894          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1924 = 1.83 * 0.50 * 5.5894 + 1.00 * 0.0879                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0138 = 1.83 * 0.50 * 5.4322 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1423      final r-factor (work) = 0.1344          |
| start r-factor (free) = 0.1894      final r-factor (free) = 0.1830          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1026 = 0.57 * 1.00 * 5.4322 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0496 = 0.57 * 1.00 * 5.3178 + 1.00 * 0.0239                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.705)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.58   12.79    None  None   None       |
|    all(noH): 2823   0      0.00    83.58   12.79    None  None   None       |
|    Sol.    : 438    0      1.45    83.58   36.71    None  None   None       |
|    Mac.    : 2385   0      0.00    82.41   8.39     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 -   8.358: 1615   |   5:    41.792 -  50.150:   89        |
|      1:     8.358 -  16.717:  600   |   6:    50.150 -  58.509:   70        |
|      2:    16.717 -  25.075:  173   |   7:    58.509 -  66.867:   27        |
|      3:    25.075 -  33.433:  108   |   8:    66.867 -  75.225:   16        |
|      4:    33.433 -  41.792:  121   |   9:    75.225 -  83.584:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1344 r_free = 0.1830             target_work(ml) = 5.301         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1343 r_free = 0.1830             target_work(ml) = 5.300         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1830   ksol= 0.32   Bsol= 41.87   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.20,2.97,3.95,0.00,0.00,0.00); trace/3= 3.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.299901                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1344   r_free= 0.1831   ksol= 0.32   Bsol= 46.06   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,2.43,3.81,0.00,0.00,0.00); trace/3= 2.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.299144                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.121699              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.186  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.285136              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.672   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1344      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1831      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6936 = 2.12 * 0.50 * 5.3173 + 1.00 * 0.0528                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6294 = 2.12 * 0.50 * 5.2519 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| 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) = 0.1188          |
| start r-factor (free) = 0.1678      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5167 = 0.29 * 1.00 * 5.2519 + 1.00 * 0.0192                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4944 = 0.29 * 1.00 * 5.2033 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.705)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.75   12.34    None  None   None       |
|    all(noH): 2823   0      0.00    83.75   12.34    None  None   None       |
|    Sol.    : 438    0      1.92    79.95   35.27    None  None   None       |
|    Mac.    : 2385   0      0.00    83.75   8.12     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 -   8.375: 1654   |   5:    41.875 -  50.250:   82        |
|      1:     8.375 -  16.750:  607   |   6:    50.250 -  58.625:   61        |
|      2:    16.750 -  25.125:  148   |   7:    58.625 -  67.001:   28        |
|      3:    25.125 -  33.500:  119   |   8:    67.001 -  75.376:    8        |
|      4:    33.500 -  41.875:  112   |   9:    75.376 -  83.751:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1634             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1187 r_free = 0.1632             target_work(ml) = 5.189         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1632   ksol= 0.32   Bsol= 46.06   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,2.43,3.81,0.00,0.00,0.00); trace/3= 2.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.189058                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1631   ksol= 0.32   Bsol= 44.70   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,2.32,3.83,0.00,0.00,0.00); trace/3= 2.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.188954                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.386047              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.026  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.631775              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 160.553  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2653 = 2.39 * 0.50 * 5.2030 + 1.00 * 0.0579                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2260 = 2.39 * 0.50 * 5.1682 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2758 = 0.63 * 1.00 * 5.1682 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2636 = 0.63 * 1.00 * 5.1471 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.705)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.69   12.33    None  None   None       |
|    all(noH): 2823   0      0.00    85.69   12.33    None  None   None       |
|    Sol.    : 438    0      1.69    80.32   35.58    None  None   None       |
|    Mac.    : 2385   0      0.00    85.69   8.06     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 -   8.569: 1684   |   5:    42.847 -  51.416:   81        |
|      1:     8.569 -  17.139:  580   |   6:    51.416 -  59.985:   58        |
|      2:    17.139 -  25.708:  146   |   7:    59.985 -  68.555:   28        |
|      3:    25.708 -  34.277:  132   |   8:    68.555 -  77.124:    7        |
|      4:    34.277 -  42.847:  103   |   9:    77.124 -  85.693:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1579             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1120 r_free = 0.1579             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1579   ksol= 0.32   Bsol= 44.70   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,2.32,3.83,0.00,0.00,0.00); trace/3= 2.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148924                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7074 0.99   1394  154 0.1016 0.1259      5.3955      5.5416|
|  2:  4.7074 -  3.7559 0.99   1336  151 0.0860 0.1151      5.4429      5.6295|
|  3:  3.7559 -  3.2869 0.99   1310  143 0.1075 0.1463       5.485      5.8471|
|  4:  3.2869 -  2.9889 0.99   1305  149 0.1223 0.1713      5.4524      5.6055|
|  5:  2.9889 -  2.7762 0.99   1301  145 0.1318 0.1661      5.3289      5.5577|
|  6:  2.7762 -  2.6134 0.99   1296  141 0.1171 0.1970      5.1852      5.4734|
|  7:  2.6134 -  2.4831 0.99   1285  140 0.1277 0.1562       5.169      5.3244|
|  8:  2.4831 -  2.3755 0.98   1273  145 0.1151 0.1692      5.0732        5.33|
|  9:  2.3755 -  2.2844 0.98   1265  140 0.1201 0.1755      5.0546       5.298|
| 10:  2.2844 -  2.2058 1.00   1296  144 0.1126 0.1707      4.9726      5.2186|
| 11:  2.2058 -  2.1370 0.97   1255  137 0.1155 0.1823      4.9597       5.325|
| 12:  2.1370 -  2.0761 0.98   1249  144 0.1118 0.1757      4.8861      5.2078|
| 13:  2.0761 -  2.0216 0.99   1303  135 0.1101 0.1667       4.776      5.0284|
| 14:  2.0216 -  1.9724 0.60    762   91 0.0951 0.1569      4.6452      4.8495|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7074  1394   154  0.94   9.30   0.98     0.96       7228.90|
|  2:  4.7074 -  3.7559  1336   151  0.95   7.84   1.02     1.01       9098.45|
|  3:  3.7559 -  3.2869  1310   143  0.93  11.34   1.03     1.03      10388.34|
|  4:  3.2869 -  2.9889  1305   149  0.92  13.53   1.01     0.99      10184.75|
|  5:  2.9889 -  2.7762  1301   145  0.90  15.60   1.00     0.98       8282.21|
|  6:  2.7762 -  2.6134  1296   141  0.90  15.61   0.98     0.96       6709.21|
|  7:  2.6134 -  2.4831  1285   140  0.91  15.55   0.99     0.96       6078.72|
|  8:  2.4831 -  2.3755  1273   145  0.91  15.17   1.00     0.97       5331.66|
|  9:  2.3755 -  2.2844  1265   140  0.91  15.46   1.01     0.98       5259.11|
| 10:  2.2844 -  2.2058  1296   144  0.90  16.30   1.00     0.96       4620.86|
| 11:  2.2058 -  2.1370  1255   137  0.89  16.82   1.00     0.96       4605.83|
| 12:  2.1370 -  2.0761  1249   144  0.91  15.75   1.01     1.01       4073.06|
| 13:  2.0761 -  2.0216  1303   135  0.90  16.19   1.01     0.99       3312.77|
| 14:  2.0216 -  1.9724   762    91  0.93  13.32   0.99     0.96       2500.00|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2500.00 max =        10388.34 mean =      6405.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.09|
|phase err.(test): min =        0.00 max =           88.33 mean =        13.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1579   ksol= 0.32   Bsol= 47.53   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.48,1.08,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148904                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1579   ksol= 0.32   Bsol= 47.53   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.48,1.08,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148904                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7074 0.99   1394  154 0.1016 0.1259      5.3959      5.5422|
|  2:  4.7074 -  3.7559 0.99   1336  151 0.0860 0.1151      5.4432      5.6296|
|  3:  3.7559 -  3.2869 0.99   1310  143 0.1075 0.1463       5.485      5.8473|
|  4:  3.2869 -  2.9889 0.99   1305  149 0.1223 0.1712      5.4524      5.6054|
|  5:  2.9889 -  2.7762 0.99   1301  145 0.1318 0.1661      5.3287      5.5574|
|  6:  2.7762 -  2.6134 0.99   1296  141 0.1170 0.1969       5.185      5.4729|
|  7:  2.6134 -  2.4831 0.99   1285  140 0.1277 0.1564       5.169      5.3248|
|  8:  2.4831 -  2.3755 0.98   1273  145 0.1151 0.1691      5.0732      5.3298|
|  9:  2.3755 -  2.2844 0.98   1265  140 0.1201 0.1753      5.0546      5.2976|
| 10:  2.2844 -  2.2058 1.00   1296  144 0.1125 0.1709      4.9725      5.2194|
| 11:  2.2058 -  2.1370 0.97   1255  137 0.1155 0.1823      4.9599      5.3249|
| 12:  2.1370 -  2.0761 0.98   1249  144 0.1117 0.1757      4.8861       5.208|
| 13:  2.0761 -  2.0216 0.99   1303  135 0.1102 0.1665      4.7757      5.0276|
| 14:  2.0216 -  1.9724 0.60    762   91 0.0951 0.1567      4.6445      4.8489|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7074  1394   154  0.94   9.30   0.98     0.96       7235.54|
|  2:  4.7074 -  3.7559  1336   151  0.95   7.85   1.02     1.01       9103.91|
|  3:  3.7559 -  3.2869  1310   143  0.93  11.34   1.03     1.03      10390.73|
|  4:  3.2869 -  2.9889  1305   149  0.92  13.53   1.01     0.99      10182.72|
|  5:  2.9889 -  2.7762  1301   145  0.90  15.59   1.00     0.99       8276.45|
|  6:  2.7762 -  2.6134  1296   141  0.90  15.61   0.98     0.96       6707.11|
|  7:  2.6134 -  2.4831  1285   140  0.91  15.55   0.99     0.96       6078.08|
|  8:  2.4831 -  2.3755  1273   145  0.91  15.17   1.00     0.98       5331.07|
|  9:  2.3755 -  2.2844  1265   140  0.91  15.47   1.01     0.98       5259.18|
| 10:  2.2844 -  2.2058  1296   144  0.90  16.30   1.01     0.97       4621.80|
| 11:  2.2058 -  2.1370  1255   137  0.89  16.82   1.00     0.96       4607.94|
| 12:  2.1370 -  2.0761  1249   144  0.91  15.75   1.02     1.01       4074.14|
| 13:  2.0761 -  2.0216  1303   135  0.90  16.18   1.01     0.99       3310.27|
| 14:  2.0216 -  1.9724   762    91  0.93  13.31   1.00     0.97       2495.15|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2495.15 max =        10390.73 mean =      6405.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.09|
|phase err.(test): min =        0.00 max =           88.33 mean =        13.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.705)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.83    88.52   15.16    None  None   None       |
|    all(noH): 2823   0      2.83    88.52   15.16    None  None   None       |
|    Sol.    : 438    0      4.52    83.14   38.40    None  None   None       |
|    Mac.    : 2385   0      2.83    88.52   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:     2.827 -  11.396: 1684   |   5:    45.674 -  54.243:   81        |
|      1:    11.396 -  19.966:  580   |   6:    54.243 -  62.812:   58        |
|      2:    19.966 -  28.535:  146   |   7:    62.812 -  71.382:   28        |
|      3:    28.535 -  37.104:  132   |   8:    71.382 -  79.951:    7        |
|      4:    37.104 -  45.674:  103   |   9:    79.951 -  88.521:    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)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.295 - 4.719
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 297
   mapped sites are within: 0.721 - 4.719

peak=   11.183 closest distance to " CB  VAL A 230 " =    1.463
peak=   10.041 closest distance to " CG2 VAL A 296 " =    1.574
peak=    6.903 closest distance to " O   HOH Z 130 " =    1.267
peak=    6.197 closest distance to " NE2 GLN A  11 " =    1.177
peak=    6.143 closest distance to " CD2 LEU A   5 " =    1.230
peak=    6.014 closest distance to " CG  LEU A   5 " =    1.161
peak=    5.780 closest distance to " O   HOH Z   9 " =    1.883
peak=    5.629 closest distance to " O   HOH Z 142 " =    2.003
peak=    5.580 closest distance to " NH2 ARG A  56 " =    2.064
peak=    5.494 closest distance to " CG  LEU A 228 " =    1.120
peak=    5.460 closest distance to " CG  PRO A  54 " =    1.365
peak=    5.329 closest distance to " O   HOH Z 427 " =    2.468
peak=    5.125 closest distance to " O   HOH Z 232 " =    2.352
peak=    4.991 closest distance to " CB  PRO A  54 " =    1.018
peak=    4.745 closest distance to " O   HOH Z  65 " =    1.036
peak=    4.657 closest distance to " CB  GLN A 223 " =    1.458
peak=    4.603 closest distance to " O   HOH Z 126 " =    2.103
peak=    4.595 closest distance to " CB  ARG A 275 " =    0.940
peak=    4.587 closest distance to " CB  VAL A 230 " =    1.143
peak=    4.586 closest distance to " O   HOH Z  78 " =    1.628
peak=    4.562 closest distance to " CB  SER A  63 " =    1.288
peak=    4.550 closest distance to " CB  SER A   3 " =    1.336
peak=    4.538 closest distance to " O   HOH Z 209 " =    2.320
peak=    4.519 closest distance to " CB  GLN A 183 " =    1.221
peak=    4.448 closest distance to " O   HOH Z 425 " =    1.468
peak=    4.412 closest distance to " CB AVAL A  41 " =    1.288
peak=    4.384 closest distance to " CB  ASN A 148 " =    1.379
peak=    4.384 closest distance to " O   HOH Z 346 " =    1.564
peak=    4.361 closest distance to " ND2 ASN A 187 " =    1.641
peak=    4.340 closest distance to " O   HOH Z   2 " =    1.645
peak=    4.301 closest distance to " O   HOH Z 298 " =    1.776
peak=    4.232 closest distance to " CB  TRP A 266 " =    1.036
peak=    4.212 closest distance to " O   HOH Z 287 " =    1.842
peak=    4.201 closest distance to " O   SER A  87 " =    2.363
peak=    4.191 closest distance to " O   HOH Z 380 " =    1.835
peak=    4.188 closest distance to " OG ASER A 258 " =    2.968
peak=    4.181 closest distance to " CG  PRO A 213 " =    1.210
peak=    4.165 closest distance to " CB  ARG A  79 " =    1.431
peak=    4.154 closest distance to " O   HOH Z 193 " =    1.727
peak=    4.153 closest distance to " O   HOH Z  55 " =    2.194
peak=    4.143 closest distance to " CB  GLU A 152 " =    1.223
peak=    4.143 closest distance to " O   HOH Z 422 " =    2.584
peak=    4.137 closest distance to " O   HOH Z 423 " =    1.535
peak=    4.120 closest distance to " CG  LEU A 167 " =    1.231
peak=    4.105 closest distance to " CG  PRO A 198 " =    1.218
peak=    4.096 closest distance to " CB  VAL A 265 " =    1.312
peak=    4.089 closest distance to " CG  PRO A 243 " =    1.102
peak=    4.058 closest distance to " O   HOH Z 369 " =    2.203
peak=    4.055 closest distance to " NH2AARG A 190 " =    1.800
peak=    4.045 closest distance to " O   HOH Z 234 " =    3.621
peak=    4.043 closest distance to " O   HOH Z 272 " =    1.801
peak=    4.039 closest distance to " O   HOH Z 130 " =    2.624
peak=    4.031 closest distance to " O   HOH Z   1 " =    1.731
peak=    4.028 closest distance to " O   HOH Z 112 " =    1.015
peak=    4.021 closest distance to " O   HOH Z 425 " =    2.128
peak=    4.019 closest distance to " CD2 LEU A 228 " =    1.167
peak=    4.008 closest distance to " O   HOH Z  30 " =    1.608
peak=    4.007 closest distance to " O   PRO A 198 " =    1.568
peak=    4.000 closest distance to " CB  VAL A 202 " =    1.675
peak=    3.990 closest distance to " O   HOH Z 214 " =    2.267
peak=    3.913 closest distance to " CB  ASN A 142 " =    1.001
peak=    3.906 closest distance to " OG BSER A 164 " =    2.097
peak=    3.906 closest distance to " CB  ASN A  39 " =    0.960
peak=    3.902 closest distance to " O   HOH Z 261 " =    2.214
peak=    3.899 closest distance to " O   HOH Z 124 " =    1.312
peak=    3.886 closest distance to " O   HOH Z 371 " =    2.790
peak=    3.879 closest distance to " CB  GLU A 277 " =    3.485
peak=    3.873 closest distance to " N   PHE A 130 " =    1.290
peak=    3.845 closest distance to " CB  SER A 216 " =    0.791
peak=    3.823 closest distance to " O   HOH Z  61 " =    1.539
peak=    3.819 closest distance to " O   HOH Z 411 " =    3.642
peak=    3.818 closest distance to " O   HOH Z  97 " =    2.072
peak=    3.815 closest distance to " O   HOH Z 359 " =    1.361
peak=    3.814 closest distance to " CB  ASN A 187 " =    1.114
peak=    3.809 closest distance to " CB  TRP A 179 " =    1.400
peak=    3.809 closest distance to " CA  TYR A  30 " =    0.988
peak=    3.807 closest distance to " O   HOH Z 419 " =    2.029
peak=    3.805 closest distance to " O   HOH Z 203 " =    1.673
peak=    3.802 closest distance to " OG  SER A  97 " =    2.916
peak=    3.788 closest distance to " O   HOH Z 222 " =    2.412
peak=    3.778 closest distance to " O   HOH Z 303 " =    2.166
peak=    3.778 closest distance to " CG2 VAL A 257 " =    0.845
peak=    3.774 closest distance to " O   HOH Z  10 " =    1.788
peak=    3.760 closest distance to " OD1 ASN A  69 " =    2.444
peak=    3.758 closest distance to " O   HOH Z  63 " =    1.298
peak=    3.756 closest distance to " CB  GLU A 128 " =    1.049
peak=    3.747 closest distance to " O   HOH Z 368 " =    2.029
peak=    3.747 closest distance to " O   HOH Z  68 " =    2.158
peak=    3.737 closest distance to " CB  GLN A  88 " =    1.246
peak=    3.729 closest distance to " NZ  LYS A 117 " =    3.069
peak=    3.721 closest distance to " O   HOH Z  43 " =    1.892
peak=    3.720 closest distance to " CA  ASN A 215 " =    1.055
peak=    3.699 closest distance to " O   HOH Z  59 " =    1.701
peak=    3.697 closest distance to " O   HOH Z 193 " =    1.931
peak=    3.686 closest distance to " CB  ARG A 190 " =    1.662
peak=    3.686 closest distance to " O   HOH Z  61 " =    1.533
peak=    3.683 closest distance to " O   HOH Z 417 " =    1.266
peak=    3.681 closest distance to " O   HOH Z  44 " =    1.680
peak=    3.678 closest distance to " O   HOH Z 405 " =    1.376
peak=    3.675 closest distance to " OG  SER A  62 " =    2.708
peak=    3.653 closest distance to " O   HOH Z  88 " =    2.901
peak=    3.638 closest distance to " O   HOH Z 403 " =    1.627
peak=    3.638 closest distance to " CD1AILE A 234 " =    0.912
peak=    3.637 closest distance to " CG1BVAL A  72 " =    1.435
peak=    3.636 closest distance to " CA  LYS A 117 " =    1.195
peak=    3.629 closest distance to " O   HOH Z   3 " =    2.005
peak=    3.611 closest distance to " CB  LYS A 117 " =    1.234
peak=    3.609 closest distance to " O   HOH Z 193 " =    1.648
peak=    3.609 closest distance to " O   HOH Z   7 " =    1.371
peak=    3.605 closest distance to " O   HOH Z 146 " =    1.425
peak=    3.605 closest distance to " CA  ALA A 299 " =    0.943
peak=    3.602 closest distance to " CG  GLN A  88 " =    1.108
peak=    3.599 closest distance to " O   HOH Z 353 " =    2.507
peak=    3.597 closest distance to " O   HOH Z  22 " =    2.091
peak=    3.593 closest distance to " O   HOH Z 366 " =    2.842
peak=    3.581 closest distance to " CA  PHE A 283 " =    1.337
peak=    3.581 closest distance to " O   HOH Z 213 " =    2.105
peak=    3.580 closest distance to " O   HOH Z 424 " =    2.305
peak=    3.577 closest distance to " CG BARG A 102 " =    1.871
peak=    3.576 closest distance to " O   HOH Z 263 " =    1.648
peak=    3.570 closest distance to " CB  ARG A  79 " =    0.874
peak=    3.561 closest distance to " O   HOH Z 128 " =    2.116
peak=    3.547 closest distance to " O   HOH Z 371 " =    1.692
peak=    3.543 closest distance to " CD1 ILE A  33 " =    1.720
peak=    3.533 closest distance to " CB  SER A  26 " =    1.626
peak=    3.531 closest distance to " NH1AARG A 145 " =    1.209
peak=    3.524 closest distance to " CB  ARG A 139 " =    1.001
peak=    3.514 closest distance to " O   HOH Z 389 " =    1.751
peak=    3.510 closest distance to " O   HOH Z 128 " =    1.923
peak=    3.505 closest distance to " CG  ARG A 138 " =    1.228
peak=    3.501 closest distance to " CB  HIS A 108 " =    0.861
peak=    3.499 closest distance to " CB  THR A 157 " =    1.140
peak=    3.492 closest distance to " N   ARG A 156 " =    1.267
peak=    3.485 closest distance to " O   HOH Z 305 " =    3.441
peak=    3.484 closest distance to " CZ  PHE A 218 " =    1.145
peak=    3.477 closest distance to " CB  ASN A 148 " =    1.937
peak=    3.471 closest distance to " O   HOH Z  97 " =    2.559
peak=    3.468 closest distance to " CB  ASP A 124 " =    0.784
peak=    3.467 closest distance to " ND1 HIS A  86 " =    1.820
peak=    3.466 closest distance to " CG1 ILE A  33 " =    1.343
peak=    3.465 closest distance to " O   HOH Z 145 " =    3.709
peak=    3.463 closest distance to " CA  SER A  87 " =    0.969
peak=    3.463 closest distance to " O   HOH Z 145 " =    1.956
peak=    3.460 closest distance to " O   HOH Z 222 " =    2.255
peak=    3.457 closest distance to " O   HOH Z 329 " =    3.949
peak=    3.454 closest distance to " O   HOH Z 236 " =    1.508
peak=    3.453 closest distance to " O   HOH Z 368 " =    3.542
peak=    3.452 closest distance to " O   HOH Z 250 " =    1.354
peak=    3.451 closest distance to " O   HOH Z 273 " =    2.915
peak=    3.442 closest distance to " OG BSER A  99 " =    2.186
peak=    3.434 closest distance to " O   PRO A 198 " =    1.252
peak=    3.434 closest distance to " O   HOH Z 392 " =    1.285
peak=    3.431 closest distance to " O   HOH Z 327 " =    1.536
peak=    3.428 closest distance to " CB  ASN A 215 " =    1.150
peak=    3.428 closest distance to " O   HOH Z  88 " =    3.167
peak=    3.427 closest distance to " O   HOH Z  40 " =    1.961
peak=    3.426 closest distance to " O   HOH Z 175 " =    2.022
peak=    3.425 closest distance to " ND2 ASN A 249 " =    0.816
peak=    3.421 closest distance to " CA  ALA A  51 " =    1.013
peak=    3.421 closest distance to " CB  ASP A 140 " =    0.876
peak=    3.419 closest distance to " O   HOH Z   1 " =    1.747
peak=    3.418 closest distance to " CG2 ILE A  20 " =    1.583
peak=    3.417 closest distance to " OE2 GLU A   2 " =    1.901
peak=    3.414 closest distance to " CG1 ILE A  49 " =    1.433
peak=    3.411 closest distance to " CG AARG A 275 " =    1.092
peak=    3.409 closest distance to " N   ASN A 127 " =    1.324
peak=    3.407 closest distance to " O   HOH Z 423 " =    1.652
peak=    3.401 closest distance to " CD2 TRP A 179 " =    1.296
peak=    3.400 closest distance to " O   HOH Z 158 " =    3.199
peak=    3.394 closest distance to " OG  SER A  62 " =    2.924
peak=    3.387 closest distance to " NE  ARG A  56 " =    3.469
peak=    3.383 closest distance to " NH2BARG A 145 " =    1.999
peak=    3.383 closest distance to " CH2 TRP A 266 " =    1.067
peak=    3.380 closest distance to " O   HOH Z 437 " =    2.091
peak=    3.378 closest distance to " CG1 ILE A 151 " =    1.167
peak=    3.372 closest distance to " CB  ASN A 110 " =    1.034
peak=    3.364 closest distance to " O   HOH Z 389 " =    3.226
peak=    3.363 closest distance to " N   SER A 135 " =    1.276
peak=    3.361 closest distance to " CA  ARG A  36 " =    1.010
peak=    3.360 closest distance to " O   HOH Z 260 " =    1.495
peak=    3.358 closest distance to " OE2 GLU A  53 " =    1.885
peak=    3.353 closest distance to " CB  VAL A 250 " =    1.072
peak=    3.348 closest distance to " N   GLN A 278 " =    1.270
peak=    3.347 closest distance to " O   HOH Z 248 " =    1.600
peak=    3.344 closest distance to " O  BHOH Z 338 " =    2.462
peak=    3.337 closest distance to " CB  ASN A 224 " =    1.036
peak=    3.337 closest distance to " O   HOH Z 133 " =    2.557
peak=    3.334 closest distance to " CG  MET A 185 " =    1.228
peak=    3.330 closest distance to " O   HOH Z   9 " =    1.704
peak=    3.322 closest distance to " CB  SER A 276 " =    1.171
peak=    3.320 closest distance to " CB  SER A  62 " =    1.237
peak=    3.318 closest distance to " N   ASN A  39 " =    1.156
peak=    3.315 closest distance to " CB  VAL A 296 " =    1.077
peak=    3.309 closest distance to " CG2 THR A 221 " =    1.172
peak=    3.308 closest distance to " NZ  LYS A  48 " =    1.215
peak=    3.307 closest distance to " CE  LYS A  76 " =    0.895
peak=    3.307 closest distance to " O   HOH Z 423 " =    2.141
peak=    3.298 closest distance to " CE3 TRP A 150 " =    0.949
peak=    3.285 closest distance to " CD  LYS A 166 " =    1.378
peak=    3.282 closest distance to " N   ASP A 162 " =    1.129
peak=    3.279 closest distance to " CB  ALA A 291 " =    1.343
peak=    3.278 closest distance to " CA  GLY A 267 " =    0.987
peak=    3.275 closest distance to " OD2 ASP A 286 " =    2.663
peak=    3.275 closest distance to " O   HOH Z   6 " =    2.103
peak=    3.271 closest distance to " CG2 VAL A 197 " =    1.017
peak=    3.268 closest distance to " O   HOH Z 130 " =    1.837
peak=    3.267 closest distance to " O   HOH Z 343 " =    3.257
peak=    3.264 closest distance to " CD2 LEU A 255 " =    1.548
peak=    3.256 closest distance to " CD  LYS A  76 " =    1.766
peak=    3.253 closest distance to " CD  ARG A 138 " =    0.916
peak=    3.252 closest distance to " O   HOH Z 426 " =    1.925
peak=    3.251 closest distance to " CA  ASN A 217 " =    1.215
peak=    3.247 closest distance to " CD1 ILE A 263 " =    1.317
peak=    3.242 closest distance to " CD2 TYR A 186 " =    1.030
peak=    3.240 closest distance to " CB  GLN A 278 " =    0.887
peak=    3.237 closest distance to " CA  ALA A 158 " =    1.271
peak=    3.236 closest distance to " CB  MET A  40 " =    0.832
peak=    3.231 closest distance to " ND2 ASN A 110 " =    1.670
peak=    3.230 closest distance to " CA  LYS A 290 " =    1.275
peak=    3.229 closest distance to " O   HOH Z 119 " =    1.678
peak=    3.229 closest distance to " O   HOH Z 116 " =    2.914
peak=    3.228 closest distance to " CG  LEU A 281 " =    1.028
peak=    3.228 closest distance to " NH1BARG A 145 " =    1.246
peak=    3.228 closest distance to " O   HOH Z 284 " =    2.990
peak=    3.227 closest distance to " CD1 LEU A 228 " =    1.990
peak=    3.226 closest distance to " O   HOH Z 135 " =    1.942
peak=    3.226 closest distance to " CB  ALA A 114 " =    1.426
peak=    3.224 closest distance to " O   HOH Z 234 " =    1.961
peak=    3.224 closest distance to " O   HOH Z 148 " =    2.259
peak=    3.224 closest distance to " NE2 GLN A 278 " =    3.446
peak=    3.222 closest distance to " CA  ASP A 162 " =    1.006
peak=    3.218 closest distance to " O   HOH Z 145 " =    1.459
peak=    3.218 closest distance to " NH2BARG A 190 " =    1.541
peak=    3.216 closest distance to " CB  ARG A 138 " =    0.880
peak=    3.214 closest distance to " O   HOH Z 427 " =    1.424
peak=    3.213 closest distance to " CG1 VAL A 153 " =    0.901
peak=    3.205 closest distance to " CA  ALA A  84 " =    1.435
peak=    3.203 closest distance to " O   TYR A 116 " =    1.284
peak=    3.202 closest distance to " CB  SER A 212 " =    1.263
peak=    3.201 closest distance to " CA  THR A 264 " =    0.721
peak=    3.196 closest distance to " O   LEU A 228 " =    1.987
peak=    3.195 closest distance to " O   HOH Z 153 " =    3.736
peak=    3.194 closest distance to " O   HOH Z 303 " =    3.012
peak=    3.189 closest distance to " O   HOH Z 344 " =    2.945
peak=    3.188 closest distance to " O   HOH Z  58 " =    1.726
peak=    3.186 closest distance to " O   HOH Z 411 " =    3.955
peak=    3.184 closest distance to " CG  GLN A  89 " =    1.426
peak=    3.184 closest distance to " CA  ALA A 233 " =    0.954
peak=    3.181 closest distance to " CA  ALA A  21 " =    1.204
peak=    3.181 closest distance to " O   HOH Z  85 " =    2.115
peak=    3.173 closest distance to " CA  ASN A 127 " =    1.008
peak=    3.172 closest distance to " CA  ILE A 234 " =    1.011
peak=    3.171 closest distance to " CB  TRP A 150 " =    1.366
peak=    3.167 closest distance to " CA  ALA A 291 " =    0.867
peak=    3.167 closest distance to " O   HOH Z 180 " =    2.050
peak=    3.163 closest distance to " CD1 ILE A 106 " =    1.119
peak=    3.159 closest distance to " O   HOH Z 390 " =    2.382
peak=    3.157 closest distance to " CA  MET A 105 " =    0.936
peak=    3.154 closest distance to " N   ALA A   1 " =    1.893
peak=    3.153 closest distance to " CG2 ILE A 234 " =    0.915
peak=    3.147 closest distance to " CA  SER A 146 " =    1.765
peak=    3.145 closest distance to " CG1 ILE A 263 " =    1.258
peak=    3.145 closest distance to " O   PRO A  90 " =    1.683
peak=    3.141 closest distance to " CG2 ILE A 120 " =    1.217
peak=    3.140 closest distance to " CA  ARG A 102 " =    1.150
peak=    3.137 closest distance to " O   HOH Z 238 " =    3.726
peak=    3.128 closest distance to " NE2 HIS A 207 " =    1.321
peak=    3.125 closest distance to " O   PHE A 192 " =    1.368
peak=    3.124 closest distance to " NE2 GLN A  58 " =    3.919
peak=    3.120 closest distance to " CB  THR A  52 " =    1.216
peak=    3.119 closest distance to " O   HOH Z 105 " =    1.598
peak=    3.116 closest distance to " CA  ALA A 154 " =    0.996
peak=    3.106 closest distance to " CG1 ILE A 120 " =    1.396
peak=    3.105 closest distance to " O   HOH Z 291 " =    1.700
peak=    3.104 closest distance to " CA  GLY A 136 " =    1.110
peak=    3.103 closest distance to " CB  TYR A  30 " =    1.723
peak=    3.098 closest distance to " CG  GLN A 278 " =    1.307
peak=    3.092 closest distance to " CA  ILE A 106 " =    0.732
peak=    3.091 closest distance to " O   HOH Z 259 " =    2.236
peak=    3.088 closest distance to " CA  ARG A 195 " =    1.156
peak=    3.088 closest distance to " O   HOH Z  80 " =    2.324
peak=    3.085 closest distance to " O   HOH Z 438 " =    2.693
peak=    3.082 closest distance to " O   HOH Z 172 " =    3.034
peak=    3.078 closest distance to " CB  PHE A 204 " =    0.913
peak=    3.078 closest distance to " CB  ILE A  20 " =    1.420
peak=    3.069 closest distance to " O   HOH Z 325 " =    2.116
peak=    3.065 closest distance to " O   HOH Z 227 " =    2.106
peak=    3.058 closest distance to " O   HOH Z 251 " =    1.503
peak=    3.057 closest distance to " O   HOH Z 383 " =    2.239
peak=    3.053 closest distance to " CB  ALA A   1 " =    4.719
peak=    3.032 closest distance to " O   HOH Z  59 " =    2.156
peak=    3.012 closest distance to " CB  LEU A 300 " =    0.868

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.724 - 5.443
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 203
   mapped sites are within: 0.724 - 5.443

peak=   -4.980 closest distance to " CG2 VAL A 230 " =    0.724
peak=   -4.491 closest distance to " CD  ARG A 156 " =    2.023
peak=   -4.350 closest distance to " CB  PRO A 243 " =    2.617
peak=   -4.338 closest distance to " CD1 LEU A 255 " =    2.780
peak=   -4.281 closest distance to " OG BSER A 134 " =    1.276
peak=   -4.250 closest distance to " O   HOH Z 266 " =    5.058
peak=   -4.172 closest distance to " CD  ARG A  14 " =    3.191
peak=   -4.149 closest distance to " CG  GLN A  58 " =    0.999
peak=   -4.015 closest distance to " O   HOH Z 185 " =    2.125
peak=   -4.000 closest distance to " C   HIS A 108 " =    1.220
peak=   -3.997 closest distance to " CB  ALA A  43 " =    2.421
peak=   -3.964 closest distance to " O   HOH Z 231 " =    1.903
peak=   -3.945 closest distance to " O   HOH Z  43 " =    1.848
peak=   -3.945 closest distance to " O   HOH Z 351 " =    1.489
peak=   -3.927 closest distance to " O   VAL A  67 " =    2.521
peak=   -3.909 closest distance to " O   HOH Z 290 " =    1.136
peak=   -3.903 closest distance to " O   HOH Z 191 " =    5.443
peak=   -3.838 closest distance to " CE2 PHE A 218 " =    2.485
peak=   -3.832 closest distance to " N   ALA A  43 " =    2.518
peak=   -3.827 closest distance to " O   HOH Z  52 " =    1.349
peak=   -3.806 closest distance to " O   HOH Z 114 " =    2.974
peak=   -3.796 closest distance to " O   HOH Z 429 " =    2.076
peak=   -3.795 closest distance to " CG  GLN A 223 " =    2.053
peak=   -3.782 closest distance to " CG2 VAL A 296 " =    1.880
peak=   -3.775 closest distance to " CD2 LEU A 237 " =    2.769
peak=   -3.768 closest distance to " NH2 ARG A  79 " =    1.985
peak=   -3.759 closest distance to " N   THR A 157 " =    1.392
peak=   -3.755 closest distance to " O   HOH Z 359 " =    1.607
peak=   -3.742 closest distance to " O   PRO A 198 " =    1.192
peak=   -3.734 closest distance to " C   MET A 188 " =    1.427
peak=   -3.733 closest distance to " CB  PHE A 192 " =    1.808
peak=   -3.722 closest distance to " CA  VAL A  67 " =    2.921
peak=   -3.720 closest distance to " O   HOH Z  11 " =    1.830
peak=   -3.714 closest distance to " O   HOH Z 140 " =    1.526
peak=   -3.709 closest distance to " O   HOH Z 359 " =    3.313
peak=   -3.693 closest distance to " CA  GLY A 203 " =    2.393
peak=   -3.691 closest distance to " O   SER A 135 " =    1.439
peak=   -3.683 closest distance to " C   ILE A 239 " =    2.173
peak=   -3.680 closest distance to " OG  SER A   3 " =    1.627
peak=   -3.675 closest distance to " CZ2 TRP A 274 " =    0.898
peak=   -3.650 closest distance to " O   HOH Z  65 " =    1.131
peak=   -3.634 closest distance to " CZ3 TRP A 179 " =    1.261
peak=   -3.628 closest distance to " O   ARG A 145 " =    1.558
peak=   -3.626 closest distance to " CB  ALA A 161 " =    2.497
peak=   -3.613 closest distance to " OG  SER A  87 " =    1.347
peak=   -3.612 closest distance to " O   PRO A 163 " =    2.021
peak=   -3.606 closest distance to " N   GLN A  58 " =    1.724
peak=   -3.604 closest distance to " CG1 VAL A 112 " =    2.606
peak=   -3.600 closest distance to " O   SER A  22 " =    2.278
peak=   -3.599 closest distance to " O   HOH Z 389 " =    2.094
peak=   -3.591 closest distance to " O   HOH Z 394 " =    1.461
peak=   -3.587 closest distance to " OG  SER A  62 " =    4.513
peak=   -3.583 closest distance to " O   HOH Z 131 " =    4.038
peak=   -3.574 closest distance to " O   HOH Z 211 " =    1.408
peak=   -3.573 closest distance to " CD2 TYR A 293 " =    1.886
peak=   -3.572 closest distance to " O   HOH Z 231 " =    1.149
peak=   -3.551 closest distance to " CA  GLY A 241 " =    2.259
peak=   -3.547 closest distance to " O   HOH Z 389 " =    1.432
peak=   -3.544 closest distance to " O   HOH Z 407 " =    3.054
peak=   -3.540 closest distance to " OD2 ASP A 191 " =    1.292
peak=   -3.538 closest distance to " CE2 TYR A  30 " =    2.780
peak=   -3.537 closest distance to " ND2 ASN A 249 " =    2.482
peak=   -3.537 closest distance to " CE  LYS A  76 " =    2.750
peak=   -3.521 closest distance to " CZ  TYR A 169 " =    1.669
peak=   -3.515 closest distance to " CB  TYR A  15 " =    2.115
peak=   -3.513 closest distance to " CE  MET A 105 " =    2.412
peak=   -3.512 closest distance to " O   HOH Z 134 " =    3.708
peak=   -3.512 closest distance to " CB  PRO A 163 " =    2.372
peak=   -3.504 closest distance to " OG  SER A  97 " =    2.175
peak=   -3.500 closest distance to " CA  GLY A 133 " =    2.006
peak=   -3.499 closest distance to " CB  ASN A  39 " =    2.270
peak=   -3.496 closest distance to " O   HOH Z 350 " =    1.732
peak=   -3.489 closest distance to " ND2 ASN A 252 " =    1.778
peak=   -3.488 closest distance to " CG1 VAL A 112 " =    2.806
peak=   -3.487 closest distance to " ND2 ASN A  45 " =    1.151
peak=   -3.483 closest distance to " O   HOH Z 348 " =    1.779
peak=   -3.483 closest distance to " O   HOH Z  51 " =    0.978
peak=   -3.463 closest distance to " CD1 LEU A 228 " =    2.192
peak=   -3.463 closest distance to " O   HOH Z 423 " =    2.426
peak=   -3.459 closest distance to " O   ALA A 161 " =    1.695
peak=   -3.451 closest distance to " OD1 ASN A 301 " =    2.018
peak=   -3.449 closest distance to " OE2 GLU A 152 " =    1.154
peak=   -3.446 closest distance to " CE BMET A  47 " =    1.229
peak=   -3.446 closest distance to " CB  ASP A 132 " =    2.351
peak=   -3.439 closest distance to " O   HOH Z 166 " =    1.890
peak=   -3.436 closest distance to " O   ILE A  49 " =    1.726
peak=   -3.432 closest distance to " CG  TRP A 266 " =    1.960
peak=   -3.425 closest distance to " CB  ALA A 244 " =    2.094
peak=   -3.424 closest distance to " N   ALA A 226 " =    2.047
peak=   -3.423 closest distance to " O   HOH Z 166 " =    1.554
peak=   -3.422 closest distance to " O   HOH Z 377 " =    1.020
peak=   -3.415 closest distance to " CE1 PHE A  59 " =    2.007
peak=   -3.415 closest distance to " O   HOH Z 427 " =    1.621
peak=   -3.414 closest distance to " CB  CYS A 201 " =    2.554
peak=   -3.406 closest distance to " CD2 LEU A   5 " =    1.121
peak=   -3.404 closest distance to " N   HIS A 115 " =    2.176
peak=   -3.398 closest distance to " N   VAL A  72 " =    1.607
peak=   -3.392 closest distance to " CD  LYS A 289 " =    2.442
peak=   -3.392 closest distance to " O   HOH Z 102 " =    1.582
peak=   -3.387 closest distance to " CD1 LEU A 101 " =    2.283
peak=   -3.374 closest distance to " O   HOH Z 313 " =    1.660
peak=   -3.371 closest distance to " ND2 ASN A  45 " =    2.077
peak=   -3.367 closest distance to " O   HOH Z  90 " =    2.716
peak=   -3.358 closest distance to " O   HOH Z 103 " =    1.751
peak=   -3.358 closest distance to " C   LEU A 222 " =    0.843
peak=   -3.356 closest distance to " CD  PRO A 213 " =    2.063
peak=   -3.356 closest distance to " O   SER A 210 " =    1.901
peak=   -3.349 closest distance to " CA  GLY A  98 " =    1.829
peak=   -3.344 closest distance to " ND2 ASN A 187 " =    1.506
peak=   -3.343 closest distance to " CD2 HIS A 207 " =    2.403
peak=   -3.343 closest distance to " CE3 TRP A 150 " =    1.976
peak=   -3.341 closest distance to " O   PRO A 198 " =    1.317
peak=   -3.336 closest distance to " CG1 VAL A 197 " =    2.273
peak=   -3.333 closest distance to " CG1 VAL A 230 " =    1.864
peak=   -3.332 closest distance to " O   HOH Z 292 " =    1.537
peak=   -3.330 closest distance to " C   ASN A 285 " =    2.199
peak=   -3.327 closest distance to " CA  ASN A 127 " =    1.204
peak=   -3.320 closest distance to " CA  GLY A  35 " =    2.039
peak=   -3.318 closest distance to " NE2 GLN A 278 " =    1.917
peak=   -3.317 closest distance to " O   HOH Z 111 " =    2.132
peak=   -3.313 closest distance to " OE1 GLN A  88 " =    1.152
peak=   -3.307 closest distance to " O   HOH Z 165 " =    2.184
peak=   -3.305 closest distance to " O   HOH Z 371 " =    2.350
peak=   -3.304 closest distance to " CB  ALA A 248 " =    2.382
peak=   -3.301 closest distance to " CG2 VAL A 202 " =    2.716
peak=   -3.295 closest distance to " CD1 LEU A 101 " =    2.801
peak=   -3.284 closest distance to " OG ASER A 134 " =    1.171
peak=   -3.279 closest distance to " N   ALA A 248 " =    1.528
peak=   -3.278 closest distance to " O   GLY A  80 " =    2.469
peak=   -3.276 closest distance to " O   VAL A 189 " =    2.562
peak=   -3.267 closest distance to " O   SER A 271 " =    2.101
peak=   -3.267 closest distance to " O   HOH Z 345 " =    2.127
peak=   -3.265 closest distance to " O   HOH Z 309 " =    2.443
peak=   -3.265 closest distance to " O   HOH Z 134 " =    3.428
peak=   -3.258 closest distance to " O   HOH Z 283 " =    2.437
peak=   -3.256 closest distance to " O   HOH Z 298 " =    1.163
peak=   -3.255 closest distance to " CB  ALA A 114 " =    2.371
peak=   -3.249 closest distance to " O   PRO A 243 " =    2.535
peak=   -3.244 closest distance to " OD1 ASN A 148 " =    1.397
peak=   -3.243 closest distance to " CB  ALA A 291 " =    2.359
peak=   -3.242 closest distance to " CG2 THR A 178 " =    2.240
peak=   -3.239 closest distance to " O   HOH Z 384 " =    2.109
peak=   -3.238 closest distance to " C   GLY A 229 " =    1.243
peak=   -3.236 closest distance to " O   HOH Z 385 " =    2.093
peak=   -3.228 closest distance to " ND2 ASN A  39 " =    1.407
peak=   -3.227 closest distance to " O   ASN A 301 " =    1.628
peak=   -3.220 closest distance to " O   HOH Z 352 " =    1.414
peak=   -3.211 closest distance to " O   GLU A 152 " =    1.432
peak=   -3.209 closest distance to " CG  ASP A 231 " =    0.768
peak=   -3.207 closest distance to " CB  ALA A   7 " =    2.092
peak=   -3.206 closest distance to " O   HOH Z 417 " =    2.564
peak=   -3.205 closest distance to " CA  ASP A 298 " =    1.073
peak=   -3.205 closest distance to " CG  PHE A 283 " =    2.592
peak=   -3.204 closest distance to " O   HOH Z 357 " =    2.127
peak=   -3.201 closest distance to " O   HOH Z  60 " =    2.145
peak=   -3.201 closest distance to " CZ  PHE A  59 " =    1.426
peak=   -3.197 closest distance to " O   HOH Z 149 " =    2.190
peak=   -3.196 closest distance to " CG2 THR A  42 " =    1.751
peak=   -3.194 closest distance to " O   HOH Z 208 " =    2.019
peak=   -3.193 closest distance to " OH  TYR A 172 " =    1.820
peak=   -3.190 closest distance to " CG  GLU A 152 " =    1.762
peak=   -3.190 closest distance to " CE2 TRP A  70 " =    2.159
peak=   -3.187 closest distance to " OG  SER A  63 " =    1.250
peak=   -3.187 closest distance to " CB  SER A 210 " =    1.158
peak=   -3.185 closest distance to " CA  GLY A  57 " =    2.153
peak=   -3.184 closest distance to " CD1 TYR A 247 " =    2.787
peak=   -3.183 closest distance to " O   HOH Z 111 " =    4.339
peak=   -3.183 closest distance to " O   ALA A   1 " =    1.621
peak=   -3.182 closest distance to " NH2AARG A 275 " =    5.182
peak=   -3.178 closest distance to " O   GLN A 240 " =    1.880
peak=   -3.177 closest distance to " O   HOH Z 353 " =    2.000
peak=   -3.171 closest distance to " O   HOH Z 313 " =    1.125
peak=   -3.171 closest distance to " OXT GLY A 302 " =    3.003
peak=   -3.165 closest distance to " CE  LYS A 166 " =    1.239
peak=   -3.162 closest distance to " CG2 VAL A 296 " =    1.343
peak=   -3.158 closest distance to " O   HOH Z 189 " =    2.059
peak=   -3.156 closest distance to " CG  GLN A 278 " =    2.070
peak=   -3.155 closest distance to " OD1 ASP A 191 " =    1.740
peak=   -3.155 closest distance to " C   LYS A  76 " =    1.538
peak=   -3.145 closest distance to " O   HOH Z 346 " =    1.744
peak=   -3.143 closest distance to " OD2 ASP A  27 " =    1.719
peak=   -3.141 closest distance to " NH1 ARG A  66 " =    3.696
peak=   -3.136 closest distance to " CB  ALA A 291 " =    2.145
peak=   -3.133 closest distance to " O   ALA A 292 " =    1.998
peak=   -3.128 closest distance to " CZ  ARG A 259 " =    0.964
peak=   -3.122 closest distance to " O   HOH Z   1 " =    1.500
peak=   -3.122 closest distance to " CG1 VAL A 250 " =    2.761
peak=   -3.119 closest distance to " O   HOH Z   2 " =    1.828
peak=   -3.118 closest distance to " C   ARG A 269 " =    1.408
peak=   -3.117 closest distance to " ND2 ASN A  45 " =    1.403
peak=   -3.113 closest distance to " ND2 ASN A  60 " =    1.551
peak=   -3.113 closest distance to " CB  ALA A  64 " =    2.723
peak=   -3.106 closest distance to " CD1 ILE A 199 " =    2.479
peak=   -3.096 closest distance to " NE2 GLN A 194 " =    1.718
peak=   -3.086 closest distance to " O   ALA A  51 " =    1.342
peak=   -3.080 closest distance to " N   MET A 188 " =    1.821
peak=   -3.080 closest distance to " O   ASP A  27 " =    1.971
peak=   -3.054 closest distance to " CG  PRO A 163 " =    2.624
peak=   -3.044 closest distance to " O   HOH Z  97 " =    1.523
peak=   -3.043 closest distance to " CG2 THR A  52 " =    2.882
peak=   -3.034 closest distance to " OG  SER A 206 " =    1.690
peak=   -3.024 closest distance to " NH2 ARG A 219 " =    1.641

================= 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    :  0.4567 0.4500   6.259159e+00   6.239173e+00
   1_bss:  0.4488 0.4347   6.253701e+00   6.224261e+00
   1_xyz:  0.3574 0.3762   6.107301e+00   6.132843e+00
   1_adp:  0.3031 0.3501   5.992790e+00   6.088538e+00
   1_occ:  0.3027 0.3495   5.991857e+00   6.089317e+00
   2_bss:  0.2982 0.3432   5.991576e+00   6.085198e+00
   2_xyz:  0.2059 0.2557   5.655761e+00   5.818728e+00
   2_adp:  0.1772 0.2299   5.526784e+00   5.721243e+00
   2_occ:  0.1770 0.2294   5.525693e+00   5.720237e+00
   3_bss:  0.1746 0.2271   5.520537e+00   5.714634e+00
   3_xyz:  0.1423 0.1894   5.342914e+00   5.557209e+00
   3_adp:  0.1344 0.1830   5.300807e+00   5.523460e+00
   3_occ:  0.1343 0.1830   5.299901e+00   5.522427e+00
   4_bss:  0.1344 0.1831   5.299144e+00   5.520755e+00
   4_xyz:  0.1203 0.1678   5.206359e+00   5.442446e+00
   4_adp:  0.1188 0.1634   5.189737e+00   5.418052e+00
   4_occ:  0.1187 0.1632   5.189058e+00   5.417012e+00
   5_bss:  0.1187 0.1631   5.188954e+00   5.416868e+00
   5_xyz:  0.1132 0.1577   5.152178e+00   5.390474e+00
   5_adp:  0.1121 0.1579   5.149285e+00   5.392785e+00
   5_occ:  0.1120 0.1579   5.148924e+00   5.392285e+00
   5_bss:  0.1120 0.1579   5.148904e+00   5.392257e+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:  0.378  20.001   6.834   9.968   8.286   0.000   0.000   0.000
   1_xyz:  0.378  20.001   6.834   9.968   8.286   0.000   0.000   0.000
   1_adp:  0.378  20.001   6.834   9.968   8.286   0.000   0.000   0.000
   1_occ:  0.378  20.001   6.834   9.968   8.286   0.000   0.000   0.000
   2_bss:  0.346  36.033   3.681   5.672   5.061   0.000   0.000   0.000
   2_xyz:  0.346  36.033   3.681   5.672   5.061   0.000   0.000   0.000
   2_adp:  0.346  36.033   3.681   5.672   5.061   0.000   0.000   0.000
   2_occ:  0.346  36.033   3.681   5.672   5.061   0.000   0.000   0.000
   3_bss:  0.317  41.866   2.198   2.965   3.949   0.000   0.000   0.000
   3_xyz:  0.317  41.866   2.198   2.965   3.949   0.000   0.000   0.000
   3_adp:  0.317  41.866   2.198   2.965   3.949   0.000   0.000   0.000
   3_occ:  0.317  41.866   2.198   2.965   3.949   0.000   0.000   0.000
   4_bss:  0.325  46.064   2.113   2.426   3.807   0.000   0.000   0.000
   4_xyz:  0.325  46.064   2.113   2.426   3.807   0.000   0.000   0.000
   4_adp:  0.325  46.064   2.113   2.426   3.807   0.000   0.000   0.000
   4_occ:  0.325  46.064   2.113   2.426   3.807   0.000   0.000   0.000
   5_bss:  0.325  44.704   2.146   2.322   3.826   0.000   0.000   0.000
   5_xyz:  0.325  44.704   2.146   2.322   3.826   0.000   0.000   0.000
   5_adp:  0.325  44.704   2.146   2.322   3.826   0.000   0.000   0.000
   5_occ:  0.325  44.704   2.146   2.322   3.826   0.000   0.000   0.000
   5_bss:  0.325  47.531  -0.598  -0.482   1.080   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.921 0.4843  0.5580    60876.391
   1_bss:  52.428 0.4886  0.7187    57576.665
   1_xyz:  42.126 0.6158  0.8847    40230.078
   1_adp:  37.312 0.6744  0.9941    34153.925
   1_occ:  37.383 0.6735  0.9913    34160.628
   2_bss:  36.958 0.6784  0.8787    33553.341
   2_xyz:  25.291 0.8078  1.0055    16428.732
   2_adp:  21.949 0.8429  1.0255    13183.780
   2_occ:  21.905 0.8433  1.0257    13134.933
   3_bss:  21.694 0.8451  0.9629    12900.842
   3_xyz:  17.747 0.8827  0.9846     9049.868
   3_adp:  16.898 0.8907  0.9845     8495.591
   3_occ:  16.876 0.8909  0.9843     8478.629
   4_bss:  16.854 0.8911  0.9753     8457.124
   4_xyz:  15.213 0.9049  0.9826     7132.061
   4_adp:  14.627 0.9100  0.9827     6824.911
   4_occ:  14.606 0.9101  0.9827     6805.825
   5_bss:  14.604 0.9102  0.9821     6804.641
   5_xyz:  14.034 0.9148  0.9837     6413.787
   5_adp:  14.050 0.9148  0.9798     6414.411
   5_occ:  14.041 0.9149  0.9798     6405.981
   5_bss:  14.041 0.9149  0.9820     6406.184
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3424e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3424e+01
   1_xyz:   1.594  0.012  0.102 18.065  0.006  4.107   1.2654e-01
   1_adp:   1.594  0.012  0.102 18.065  0.006  4.107   1.2654e-01
   1_occ:   1.594  0.012  0.102 18.065  0.006  4.107   1.2654e-01
   2_bss:   1.594  0.012  0.102 18.065  0.006  4.107   1.2654e-01
   2_xyz:   1.194  0.010  0.092 16.191  0.006  4.108   8.7864e-02
   2_adp:   1.194  0.010  0.092 16.191  0.006  4.108   8.7864e-02
   2_occ:   1.194  0.010  0.092 16.191  0.006  4.108   8.7864e-02
   3_bss:   1.194  0.010  0.092 16.191  0.006  4.108   8.7864e-02
   3_xyz:   0.900  0.005  0.068 15.684  0.003  4.114   5.2800e-02
   3_adp:   0.900  0.005  0.068 15.684  0.003  4.114   5.2800e-02
   3_occ:   0.900  0.005  0.068 15.684  0.003  4.114   5.2800e-02
   4_bss:   0.900  0.005  0.068 15.684  0.003  4.114   5.2800e-02
   4_xyz:   0.962  0.006  0.075 15.775  0.003  4.117   5.7923e-02
   4_adp:   0.962  0.006  0.075 15.775  0.003  4.117   5.7923e-02
   4_occ:   0.962  0.006  0.075 15.775  0.003  4.117   5.7923e-02
   5_bss:   0.962  0.006  0.075 15.775  0.003  4.117   5.7923e-02
   5_xyz:   0.984  0.007  0.077 15.543  0.004  4.120   6.0270e-02
   5_adp:   0.984  0.007  0.077 15.543  0.004  4.120   6.0270e-02
   5_occ:   0.984  0.007  0.077 15.543  0.004  4.120   6.0270e-02
   5_bss:   0.984  0.007  0.077 15.543  0.004  4.120   6.0270e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9253e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9253e+00
   1_xyz:  12.507  0.157  0.404 87.269  0.032  2.193   9.0087e-02
   1_adp:  12.507  0.157  0.404 87.269  0.032  2.193   9.0087e-02
   1_occ:  12.507  0.157  0.404 87.269  0.032  2.193   9.0087e-02
   2_bss:  12.507  0.157  0.404 87.269  0.032  2.193   9.0087e-02
   2_xyz:   8.368  0.103  0.311 87.567  0.038  2.300   9.4711e-02
   2_adp:   8.368  0.103  0.311 87.567  0.038  2.300   9.4711e-02
   2_occ:   8.368  0.103  0.311 87.567  0.038  2.300   9.4711e-02
   3_bss:   8.368  0.103  0.311 87.567  0.038  2.300   9.4711e-02
   3_xyz:   6.511  0.040  0.294 82.690  0.026  2.328   3.6774e-02
   3_adp:   6.511  0.040  0.294 82.690  0.026  2.328   3.6774e-02
   3_occ:   6.511  0.040  0.294 82.690  0.026  2.328   3.6774e-02
   4_bss:   6.511  0.040  0.294 82.690  0.026  2.328   3.6774e-02
   4_xyz:   8.259  0.051  0.332 83.600  0.035  2.344   3.6201e-02
   4_adp:   8.259  0.051  0.332 83.600  0.035  2.344   3.6201e-02
   4_occ:   8.259  0.051  0.332 83.600  0.035  2.344   3.6201e-02
   5_bss:   8.259  0.051  0.332 83.600  0.035  2.344   3.6201e-02
   5_xyz:   6.479  0.045  0.358 83.998  0.038  2.302   4.2238e-02
   5_adp:   6.479  0.045  0.358 83.998  0.038  2.302   4.2238e-02
   5_occ:   6.479  0.045  0.358 83.998  0.038  2.302   4.2238e-02
   5_bss:   6.479  0.045  0.358 83.998  0.038  2.302   4.2238e-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:  77.03   0.00  12.31  68.54   0.00   9.73  77.03   0.00  26.37
   1_occ:  77.03   0.00  12.31  68.54   0.00   9.73  77.03   0.00  26.37
   2_bss:  77.03   0.00  12.31  68.54   0.00   9.73  77.03   0.00  26.37
   2_xyz:  77.03   0.00  12.31  68.54   0.00   9.73  77.03   0.00  26.37
   2_adp:  81.45   0.00  12.18  71.57   0.00   8.37  81.45   1.33  32.95
   2_occ:  81.45   0.00  12.18  71.57   0.00   8.37  81.45   1.33  32.95
   3_bss:  81.45   0.00  12.18  71.57   0.00   8.37  81.45   1.33  32.95
   3_xyz:  81.45   0.00  12.18  71.57   0.00   8.37  81.45   1.33  32.95
   3_adp:  83.58   0.00  12.79  82.41   0.00   8.39  83.58   1.45  36.71
   3_occ:  83.58   0.00  12.79  82.41   0.00   8.39  83.58   1.45  36.71
   4_bss:  83.58   0.00  12.79  82.41   0.00   8.39  83.58   1.45  36.71
   4_xyz:  83.58   0.00  12.79  82.41   0.00   8.39  83.58   1.45  36.71
   4_adp:  83.75   0.00  12.34  83.75   0.00   8.12  79.95   1.92  35.27
   4_occ:  83.75   0.00  12.34  83.75   0.00   8.12  79.95   1.92  35.27
   5_bss:  83.75   0.00  12.34  83.75   0.00   8.12  79.95   1.92  35.27
   5_xyz:  83.75   0.00  12.34  83.75   0.00   8.12  79.95   1.92  35.27
   5_adp:  85.69   0.00  12.33  85.69   0.00   8.06  80.32   1.69  35.58
   5_occ:  85.69   0.00  12.33  85.69   0.00   8.06  80.32   1.69  35.58
   5_bss:  88.52   2.83  15.16  88.52   2.83  10.89  83.14   4.52  38.40
------------------------------------------------------------------------
 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:    1.235    0.019    0.403
   1_adp:    1.235    0.019    0.403
   1_occ:    1.235    0.019    0.403
   2_bss:    1.235    0.019    0.403
   2_xyz:    1.504    0.032    0.593
   2_adp:    1.504    0.032    0.593
   2_occ:    1.504    0.032    0.593
   3_bss:    1.504    0.032    0.593
   3_xyz:    1.572    0.014    0.609
   3_adp:    1.572    0.014    0.609
   3_occ:    1.572    0.014    0.609
   4_bss:    1.572    0.014    0.609
   4_xyz:    1.631    0.029    0.640
   4_adp:    1.631    0.029    0.640
   4_occ:    1.631    0.029    0.640
   5_bss:    1.631    0.029    0.640
   5_xyz:    1.653    0.057    0.651
   5_adp:    1.653    0.057    0.651
   5_occ:    1.653    0.057    0.651
   5_bss:    1.653    0.057    0.651
------------------------------------------------------------------------

CPU time actual refinement: 324.43


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_512/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_512/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_512/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_512/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_512/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.27 
  Macro-tasks:
    bulk solvent and scale       = 40.81  
    individual site refinement   = 131.44 
    weights calculation          = 31.16  
    collect and process          = 6.41   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 209.94 
  Micro-tasks:
    mask                            = 1.89   
    f_calc                          = 99.17  
    alpha_beta                      = 8.24   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 109.63 
    fmodel                         = 6.98   
    r_factors                      = 0.20   
    phase_errors                   = 10.42  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 237.94 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.587 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    649 calls, 98.91 s
gradients_fft:          594 calls, 96.47 s

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

# Date 2008-01-16 Time 01:45:39 PST -0800 (1200476739.06 s)
Start R-work = 0.4567, R-free = 0.4500 (no bulk solvent and anisotropic scale)
Final R-work = 0.1296, R-free = 0.1744 (no bulk solvent and anisotropic scale)

Start R-work = 0.4488, R-free = 0.4347
Final R-work = 0.1120, R-free = 0.1579