# Date 2008-01-16 Time 02:02:13 PST -0800 (1200477733.25 s)
#phil __OFF__

Command line arguments: "../661.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18965
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 661

-------------------------------------------------------------------------------
  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: (70.25, 46.93, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9109 1.96123
Completeness in resolution range: 0.950369
Completeness with d_max=infinity: 0.947473

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9109
                             d_min =   1.9612

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: (70.25, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9109 1.96123
Completeness in resolution range: 0.950369
Completeness with d_max=infinity: 0.947473

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9113 -  4.1969 [2168/2197]  1954   214   9.9%
  bin  2:  4.1969 -  3.3435 [2069/2088]  1860   209  10.1%
  bin  3:  3.3435 -  2.9245 [2056/2076]  1850   206  10.0%
  bin  4:  2.9245 -  2.6588 [2045/2070]  1846   199   9.7%
  bin  5:  2.6588 -  2.4691 [2027/2046]  1819   208  10.3%
  bin  6:  2.4691 -  2.3241 [2009/2056]  1808   201  10.0%
  bin  7:  2.3241 -  2.2081 [1981/2013]  1782   199  10.0%
  bin  8:  2.2081 -  2.1123 [2007/2043]  1808   199   9.9%
  bin  9:  2.1123 -  2.0312 [1986/2015]  1786   200  10.1%
  bin 10:  2.0312 -  1.9612 [1241/2008]  1117   124  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_661/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.77 -     2.39: 29
        2.39 -     3.02: 2063
        3.02 -     3.65: 4683
        3.65 -     4.27: 9175
        4.27 -     4.90: 12631
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.765 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.787 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.959 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.987 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28576 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_661/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_661/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 70.25 46.93 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4466   r_free= 0.4486   ksol= 0.00   Bsol= 0.00   scale= 0.820    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.244703                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6811 0.99   1405  155 0.3737 0.3599      6.5439      6.5409|
|  2:  4.6811 -  3.7348 0.99   1358  148 0.3553 0.3507      6.6999      6.6839|
|  3:  3.7348 -  3.2683 0.99   1326  153 0.4006 0.3834      6.5997      6.6721|
|  4:  3.2683 -  2.9721 0.99   1324  148 0.4153 0.4416      6.4619      6.4377|
|  5:  2.9721 -  2.7605 0.99   1310  144 0.4564 0.4768      6.3343      6.3568|
|  6:  2.7605 -  2.5987 0.98   1299  144 0.4704 0.5025       6.235      6.2017|
|  7:  2.5987 -  2.4691 0.99   1307  144 0.4950 0.4546      6.2381      6.1685|
|  8:  2.4691 -  2.3621 0.98   1287  144 0.4975 0.5015      6.1436      6.1688|
|  9:  2.3621 -  2.2715 0.98   1293  146 0.4917 0.4745      6.1018      6.0554|
| 10:  2.2715 -  2.1933 0.98   1278  136 0.5110 0.5316      6.0918      6.1264|
| 11:  2.1933 -  2.1250 0.99   1278  144 0.5118 0.4867      6.0226       6.016|
| 12:  2.1250 -  2.0644 0.98   1274  141 0.4878 0.5424      5.9558      5.9972|
| 13:  2.0644 -  2.0102 0.97   1271  137 0.5161 0.4988      5.8725       5.828|
| 14:  2.0102 -  1.9612 0.48    620   75 0.5316 0.5583      5.8294      5.7444|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9113 -  4.6811  1405   155  0.71  32.95   0.81     0.74      64809.38|
|  2:  4.6811 -  3.7348  1358   148  0.74  31.65   0.90     0.81      87339.07|
|  3:  3.7348 -  3.2683  1326   153  0.65  39.65   0.86     0.78      94172.29|
|  4:  3.2683 -  2.9721  1324   148  0.58  45.33   0.84     0.68      85338.20|
|  5:  2.9721 -  2.7605  1310   144  0.48  53.16   0.77     0.58      74266.72|
|  6:  2.7605 -  2.5987  1299   144  0.46  55.41   0.76     0.53      63844.57|
|  7:  2.5987 -  2.4691  1307   144  0.46  55.02   0.75     0.52      56871.06|
|  8:  2.4691 -  2.3621  1287   144  0.45  56.15   0.74     0.53      51497.56|
|  9:  2.3621 -  2.2715  1293   146  0.45  55.94   0.77     0.53      46319.49|
| 10:  2.2715 -  2.1933  1278   136  0.43  57.87   0.77     0.51      43748.51|
| 11:  2.1933 -  2.1250  1278   144  0.40  59.86   0.78     0.49      41577.61|
| 12:  2.1250 -  2.0644  1274   141  0.36  63.22   0.78     0.45      41972.17|
| 13:  2.0644 -  2.0102  1271   137  0.31  66.56   0.76     0.40      37097.51|
| 14:  2.0102 -  1.9612   620    75  0.32  65.84   0.72     0.37      30165.05|
|alpha:            min =        0.37 max =            0.81 mean =         0.58|
|beta:             min =    30165.05 max =        94172.29 mean =     59933.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.98 mean =        51.98|
|phase err.(test): min =        0.00 max =           89.99 mean =        52.37|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.956585              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.907   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.890165              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.082   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      710 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1526 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2664 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3964 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5113 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6600 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7795 |
|-----------------------------------------------------------------------------|
|-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 |       53.361 |
| 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 |       1.845 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    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 = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4550   r_free= 0.4576   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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: 6.249636                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4381   r_free= 0.4388   ksol= 0.34   Bsol= 4.84   scale= 1.023    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.22,8.07,9.94,0.00,0.00,0.00); trace/3= 8.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.241224                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.572111              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.975   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.831502              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.962   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4381      final r-factor (work) = 0.3466          |
| start r-factor (free) = 0.4388      final r-factor (free) = 0.3720          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.1484 = 8.57 * 0.50 * 6.2499 + 1.00 * 53.3610                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.3835 = 8.57 * 0.50 * 6.1267 + 1.00 * 0.1243                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3466      final r-factor (work) = 0.2900          |
| start r-factor (free) = 0.3720      final r-factor (free) = 0.3380          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1086 = 0.83 * 1.00 * 6.1267 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9973 = 0.83 * 1.00 * 5.9943 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.74   11.56    None  None   None       |
|    all(noH): 2823   0      0.00    71.74   11.56    None  None   None       |
|    Sol.    : 438    0      0.00    68.02   27.27    None  None   None       |
|    Mac.    : 2385   0      0.00    71.74   8.67     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 -   7.174: 1325   |   5:    35.871 -  43.046:   83        |
|      1:     7.174 -  14.349:  717   |   6:    43.046 -  50.220:   43        |
|      2:    14.349 -  21.523:  329   |   7:    50.220 -  57.394:   15        |
|      3:    21.523 -  28.697:  177   |   8:    57.394 -  64.568:    5        |
|      4:    28.697 -  35.871:  124   |   9:    64.568 -  71.742:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2900 r_free = 0.3380             target_work(ml) = 5.959         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2897 r_free = 0.3382             target_work(ml) = 5.959         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2897   r_free= 0.3382   ksol= 0.34   Bsol= 4.84   scale= 1.104    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.22,8.07,9.94,0.00,0.00,0.00); trace/3= 8.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.958829                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2842   r_free= 0.3327   ksol= 0.33   Bsol= 27.13   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,4.07,6.52,0.00,0.00,0.00); trace/3= 4.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.955654                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.122460              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.265   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.383145              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.999  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2842      final r-factor (work) = 0.1961          |
| start r-factor (free) = 0.3327      final r-factor (free) = 0.2497          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.4788 = 6.12 * 0.50 * 5.9958 + 1.00 * 0.1243                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8228 = 6.12 * 0.50 * 5.7979 + 1.00 * 0.0740                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1961      final r-factor (work) = 0.1740          |
| start r-factor (free) = 0.2497      final r-factor (free) = 0.2251          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2345 = 0.38 * 1.00 * 5.7979 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1455 = 0.38 * 1.00 * 5.5728 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.66   11.84    None  None   None       |
|    all(noH): 2823   0      0.00    71.66   11.84    None  None   None       |
|    Sol.    : 438    0      1.53    68.68   32.08    None  None   None       |
|    Mac.    : 2385   0      0.00    71.66   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 -   7.166: 1442   |   5:    35.830 -  42.996:  116        |
|      1:     7.166 -  14.332:  707   |   6:    42.996 -  50.162:   75        |
|      2:    14.332 -  21.498:  195   |   7:    50.162 -  57.328:   28        |
|      3:    21.498 -  28.664:  123   |   8:    57.328 -  64.494:    9        |
|      4:    28.664 -  35.830:  124   |   9:    64.494 -  71.660:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1740 r_free = 0.2251             target_work(ml) = 5.519         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1736 r_free = 0.2250             target_work(ml) = 5.518         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1736   r_free= 0.2250   ksol= 0.33   Bsol= 27.13   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,4.07,6.52,0.00,0.00,0.00); trace/3= 4.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.518302                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1720   r_free= 0.2223   ksol= 0.32   Bsol= 35.22   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.50,2.83,3.90,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.512225                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.947883              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.410  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.745385              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.135  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1720      final r-factor (work) = 0.1396          |
| start r-factor (free) = 0.2223      final r-factor (free) = 0.1821          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5117 = 1.95 * 0.50 * 5.5832 + 1.00 * 0.0740                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3376 = 1.95 * 0.50 * 5.4252 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1396      final r-factor (work) = 0.1312          |
| start r-factor (free) = 0.1821      final r-factor (free) = 0.1750          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0538 = 0.75 * 1.00 * 5.4252 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9583 = 0.75 * 1.00 * 5.2920 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.59   12.52    None  None   None       |
|    all(noH): 2823   0      0.00    81.59   12.52    None  None   None       |
|    Sol.    : 438    0      1.95    72.92   36.04    None  None   None       |
|    Mac.    : 2385   0      0.00    81.59   8.20     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 -   8.159: 1620   |   5:    40.793 -  48.951:   96        |
|      1:     8.159 -  16.317:  601   |   6:    48.951 -  57.110:   74        |
|      2:    16.317 -  24.476:  163   |   7:    57.110 -  65.268:   31        |
|      3:    24.476 -  32.634:  105   |   8:    65.268 -  73.427:   12        |
|      4:    32.634 -  40.793:  117   |   9:    73.427 -  81.585:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1312 r_free = 0.1750             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1311 r_free = 0.1750             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1750   ksol= 0.32   Bsol= 35.22   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.50,2.83,3.90,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.273179                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1312   r_free= 0.1749   ksol= 0.32   Bsol= 37.76   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.67,3.27,0.00,0.00,0.00); trace/3= 2.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.273622                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.106649              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.923  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.525739              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.356  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1312      final r-factor (work) = 0.1173          |
| start r-factor (free) = 0.1749      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6282 = 2.11 * 0.50 * 5.2922 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5660 = 2.11 * 0.50 * 5.2271 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1173      final r-factor (work) = 0.1149          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7620 = 0.53 * 1.00 * 5.2271 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7314 = 0.53 * 1.00 * 5.1732 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.46   12.37    None  None   None       |
|    all(noH): 2823   0      0.00    86.46   12.37    None  None   None       |
|    Sol.    : 438    0      1.51    73.74   35.51    None  None   None       |
|    Mac.    : 2385   0      0.00    86.46   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 -   8.646: 1708   |   5:    43.232 -  51.879:   90        |
|      1:     8.646 -  17.293:  556   |   6:    51.879 -  60.525:   58        |
|      2:    17.293 -  25.939:  151   |   7:    60.525 -  69.171:   18        |
|      3:    25.939 -  34.586:  119   |   8:    69.171 -  77.818:    7        |
|      4:    34.586 -  43.232:  112   |   9:    77.818 -  86.464:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1149 r_free = 0.1599             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1149 r_free = 0.1599             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1599   ksol= 0.32   Bsol= 37.76   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.67,3.27,0.00,0.00,0.00); trace/3= 2.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168117                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1599   ksol= 0.32   Bsol= 37.76   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.67,3.27,0.00,0.00,0.00); trace/3= 2.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168129                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.398233              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.516  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.209829              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.117  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1149      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2630 = 2.40 * 0.50 * 5.1730 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2406 = 2.40 * 0.50 * 5.1518 + 1.00 * 0.0629                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0927 = 0.21 * 1.00 * 5.1518 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0905 = 0.21 * 1.00 * 5.1504 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.88   11.82    None  None   None       |
|    all(noH): 2823   0      0.00    84.88   11.82    None  None   None       |
|    Sol.    : 438    0      1.66    69.87   33.02    None  None   None       |
|    Mac.    : 2385   0      0.00    84.88   7.93     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 -   8.488: 1702   |   5:    42.440 -  50.928:   79        |
|      1:     8.488 -  16.976:  586   |   6:    50.928 -  59.416:   44        |
|      2:    16.976 -  25.464:  141   |   7:    59.416 -  67.904:   12        |
|      3:    25.464 -  33.952:  142   |   8:    67.904 -  76.392:    5        |
|      4:    33.952 -  42.440:  108   |   9:    76.392 -  84.881:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1572             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1572             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1572   ksol= 0.32   Bsol= 37.76   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.67,3.27,0.00,0.00,0.00); trace/3= 2.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.146339                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6811 0.99   1405  155 0.0989 0.1293      5.3846      5.5358|
|  2:  4.6811 -  3.7348 0.99   1358  148 0.0866 0.1134      5.4359      5.6362|
|  3:  3.7348 -  3.2683 0.99   1326  153 0.1044 0.1536      5.4579      5.8466|
|  4:  3.2683 -  2.9721 0.99   1324  148 0.1214 0.1557      5.4504      5.5963|
|  5:  2.9721 -  2.7605 0.99   1310  144 0.1282 0.1620      5.3118      5.4768|
|  6:  2.7605 -  2.5987 0.98   1299  144 0.1214 0.1891      5.2029      5.4679|
|  7:  2.5987 -  2.4691 0.99   1307  144 0.1244 0.1661      5.1686      5.4231|
|  8:  2.4691 -  2.3621 0.98   1287  144 0.1163 0.1682      5.0711      5.2783|
|  9:  2.3621 -  2.2715 0.98   1293  146 0.1177 0.1823       5.036      5.2983|
| 10:  2.2715 -  2.1933 0.98   1278  136 0.1137 0.1739      4.9707      5.2412|
| 11:  2.1933 -  2.1250 0.99   1278  144 0.1149 0.1763      4.9367      5.2849|
| 12:  2.1250 -  2.0644 0.98   1274  141 0.1087 0.1642      4.8582      5.0737|
| 13:  2.0644 -  2.0102 0.97   1271  137 0.1170 0.1845       4.786       5.091|
| 14:  2.0102 -  1.9612 0.48    620   75 0.1047 0.1578       4.653      4.8264|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9113 -  4.6811  1405   155  0.94   8.95   0.99     0.96       7220.14|
|  2:  4.6811 -  3.7348  1358   148  0.95   7.89   1.02     1.01       8848.20|
|  3:  3.7348 -  3.2683  1326   153  0.93  11.38   1.03     1.03      10218.28|
|  4:  3.2683 -  2.9721  1324   148  0.92  13.66   1.01     0.99      10231.44|
|  5:  2.9721 -  2.7605  1310   144  0.90  15.86   0.99     0.96       7963.56|
|  6:  2.7605 -  2.5987  1299   144  0.90  15.97   0.99     0.97       7023.44|
|  7:  2.5987 -  2.4691  1307   144  0.91  15.24   0.99     0.96       6148.31|
|  8:  2.4691 -  2.3621  1287   144  0.90  15.78   1.00     0.97       5536.89|
|  9:  2.3621 -  2.2715  1293   146  0.91  15.57   1.01     0.99       5067.59|
| 10:  2.2715 -  2.1933  1278   136  0.90  15.69   1.01     0.98       4516.40|
| 11:  2.1933 -  2.1250  1278   144  0.90  16.13   1.01     0.97       4276.98|
| 12:  2.1250 -  2.0644  1274   141  0.92  14.83   1.01     1.00       3837.75|
| 13:  2.0644 -  2.0102  1271   137  0.90  16.32   1.02     1.02       3278.30|
| 14:  2.0102 -  1.9612   620    75  0.91  14.71   1.00     0.98       2483.78|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2483.78 max =        10231.44 mean =      6373.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.75 mean =        14.05|
|phase err.(test): min =        0.00 max =           88.90 mean =        13.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1572   ksol= 0.32   Bsol= 40.30   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.40,-0.10,0.50,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.146409                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1572   ksol= 0.32   Bsol= 40.30   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.40,-0.10,0.50,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.146409                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6811 0.99   1405  155 0.0989 0.1291      5.3853      5.5358|
|  2:  4.6811 -  3.7348 0.99   1358  148 0.0865 0.1133      5.4352      5.6353|
|  3:  3.7348 -  3.2683 0.99   1326  153 0.1044 0.1536      5.4575      5.8466|
|  4:  3.2683 -  2.9721 0.99   1324  148 0.1214 0.1557      5.4504      5.5964|
|  5:  2.9721 -  2.7605 0.99   1310  144 0.1282 0.1621      5.3119      5.4771|
|  6:  2.7605 -  2.5987 0.98   1299  144 0.1214 0.1891      5.2031       5.468|
|  7:  2.5987 -  2.4691 0.99   1307  144 0.1244 0.1661      5.1688      5.4232|
|  8:  2.4691 -  2.3621 0.98   1287  144 0.1163 0.1683      5.0712      5.2786|
|  9:  2.3621 -  2.2715 0.98   1293  146 0.1177 0.1822       5.036      5.2982|
| 10:  2.2715 -  2.1933 0.98   1278  136 0.1137 0.1739      4.9708      5.2414|
| 11:  2.1933 -  2.1250 0.99   1278  144 0.1149 0.1763      4.9368       5.285|
| 12:  2.1250 -  2.0644 0.98   1274  141 0.1087 0.1642      4.8583      5.0738|
| 13:  2.0644 -  2.0102 0.97   1271  137 0.1170 0.1845      4.7861      5.0911|
| 14:  2.0102 -  1.9612 0.48    620   75 0.1047 0.1578      4.6531      4.8266|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9113 -  4.6811  1405   155  0.94   8.95   0.99     0.96       7228.15|
|  2:  4.6811 -  3.7348  1358   148  0.95   7.89   1.02     1.01       8843.48|
|  3:  3.7348 -  3.2683  1326   153  0.93  11.37   1.03     1.03      10207.53|
|  4:  3.2683 -  2.9721  1324   148  0.92  13.66   1.01     0.99      10232.04|
|  5:  2.9721 -  2.7605  1310   144  0.90  15.87   0.99     0.96       7966.20|
|  6:  2.7605 -  2.5987  1299   144  0.90  15.97   0.99     0.97       7026.40|
|  7:  2.5987 -  2.4691  1307   144  0.91  15.24   0.99     0.96       6151.15|
|  8:  2.4691 -  2.3621  1287   144  0.90  15.78   1.00     0.97       5538.72|
|  9:  2.3621 -  2.2715  1293   146  0.91  15.57   1.01     0.99       5068.78|
| 10:  2.2715 -  2.1933  1278   136  0.90  15.69   1.01     0.98       4516.97|
| 11:  2.1933 -  2.1250  1278   144  0.90  16.13   1.01     0.97       4277.86|
| 12:  2.1250 -  2.0644  1274   141  0.92  14.83   1.01     1.00       3838.42|
| 13:  2.0644 -  2.0102  1271   137  0.90  16.33   1.02     1.02       3279.26|
| 14:  2.0102 -  1.9612   620    75  0.91  14.72   1.00     0.98       2484.71|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2484.71 max =        10232.04 mean =      6373.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.76 mean =        14.06|
|phase err.(test): min =        0.00 max =           88.90 mean =        13.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.77    87.65   14.59    None  None   None       |
|    all(noH): 2823   0      2.77    87.65   14.59    None  None   None       |
|    Sol.    : 438    0      4.43    72.64   35.79    None  None   None       |
|    Mac.    : 2385   0      2.77    87.65   10.70    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:     2.772 -  11.260: 1702   |   5:    45.212 -  53.700:   79        |
|      1:    11.260 -  19.748:  586   |   6:    53.700 -  62.188:   44        |
|      2:    19.748 -  28.236:  141   |   7:    62.188 -  70.676:   12        |
|      3:    28.236 -  36.724:  142   |   8:    70.676 -  79.164:    5        |
|      4:    36.724 -  45.212:  108   |   9:    79.164 -  87.652:    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)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.377 - 5.750
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 322
   mapped sites are within: 0.736 - 5.750

peak=   10.825 closest distance to " CB  VAL A 230 " =    1.468
peak=    8.251 closest distance to " CG2 VAL A 296 " =    1.215
peak=    6.325 closest distance to " CG  LEU A   5 " =    1.305
peak=    5.434 closest distance to " NH2 ARG A  56 " =    2.145
peak=    5.395 closest distance to " CD2 LEU A   5 " =    1.187
peak=    5.375 closest distance to " NE2 GLN A  11 " =    1.150
peak=    5.208 closest distance to " O   HOH Z 278 " =    1.144
peak=    5.156 closest distance to " CG  PRO A  54 " =    1.230
peak=    5.141 closest distance to " CG  LEU A 228 " =    1.218
peak=    5.117 closest distance to " CB  SER A  63 " =    1.275
peak=    5.032 closest distance to " O   HOH Z 126 " =    1.886
peak=    5.019 closest distance to " CB  GLN A 223 " =    1.454
peak=    4.932 closest distance to " CB  GLN A 183 " =    1.291
peak=    4.927 closest distance to " O   HOH Z 193 " =    1.727
peak=    4.910 closest distance to " CB  PRO A  54 " =    0.935
peak=    4.865 closest distance to " O   HOH Z 142 " =    1.724
peak=    4.739 closest distance to " CB  VAL A 296 " =    1.099
peak=    4.717 closest distance to " O   HOH Z 232 " =    2.280
peak=    4.698 closest distance to " CB  GLU A 152 " =    1.176
peak=    4.665 closest distance to " O   HOH Z 124 " =    1.451
peak=    4.664 closest distance to " CB  ARG A 275 " =    0.877
peak=    4.585 closest distance to " OD1 ASN A  69 " =    2.586
peak=    4.532 closest distance to " C   PRO A 198 " =    1.538
peak=    4.476 closest distance to " CG  PRO A 213 " =    1.209
peak=    4.470 closest distance to " CB  SER A   3 " =    1.366
peak=    4.466 closest distance to " CB  TYR A 169 " =    0.863
peak=    4.451 closest distance to " CD2 LEU A 228 " =    1.218
peak=    4.410 closest distance to " O   HOH Z 272 " =    1.862
peak=    4.402 closest distance to " CB  ASN A 148 " =    1.427
peak=    4.361 closest distance to " O   HOH Z 316 " =    2.893
peak=    4.353 closest distance to " O   SER A  87 " =    2.221
peak=    4.352 closest distance to " O   HOH Z 263 " =    1.563
peak=    4.346 closest distance to " CB  VAL A 230 " =    1.196
peak=    4.345 closest distance to " O   HOH Z 298 " =    1.833
peak=    4.306 closest distance to " O   HOH Z 234 " =    3.688
peak=    4.294 closest distance to " O   HOH Z 427 " =    2.913
peak=    4.259 closest distance to " O   HOH Z 128 " =    1.989
peak=    4.257 closest distance to " CA  ALA A  21 " =    1.116
peak=    4.256 closest distance to " O   HOH Z  97 " =    1.948
peak=    4.242 closest distance to " O   HOH Z 236 " =    1.803
peak=    4.239 closest distance to " CG1BVAL A  72 " =    1.546
peak=    4.235 closest distance to " O   HOH Z  48 " =    1.595
peak=    4.233 closest distance to " CB  GLU A 128 " =    1.068
peak=    4.200 closest distance to " O   HOH Z 368 " =    2.060
peak=    4.184 closest distance to " ND2 ASN A 187 " =    1.597
peak=    4.181 closest distance to " O   HOH Z 411 " =    3.723
peak=    4.138 closest distance to " O   HOH Z 303 " =    2.012
peak=    4.128 closest distance to " O   HOH Z 280 " =    2.976
peak=    4.128 closest distance to " CB  TRP A 179 " =    1.320
peak=    4.085 closest distance to " CD1AILE A 234 " =    0.990
peak=    4.067 closest distance to " O   HOH Z 132 " =    0.956
peak=    4.062 closest distance to " O   HOH Z 203 " =    1.654
peak=    4.036 closest distance to " O   HOH Z  78 " =    1.783
peak=    4.013 closest distance to " CA  THR A 221 " =    0.900
peak=    4.013 closest distance to " O   HOH Z  59 " =    2.127
peak=    4.006 closest distance to " O   HOH Z 108 " =    1.219
peak=    3.980 closest distance to " O   HOH Z  93 " =    2.479
peak=    3.978 closest distance to " O   HOH Z 369 " =    1.900
peak=    3.972 closest distance to " OD2 ASP A 286 " =    2.763
peak=    3.968 closest distance to " CG  PRO A 243 " =    1.210
peak=    3.958 closest distance to " CG  PRO A 198 " =    1.286
peak=    3.951 closest distance to " O   HOH Z   9 " =    2.217
peak=    3.944 closest distance to " O   HOH Z  54 " =    1.577
peak=    3.928 closest distance to " O   HOH Z 371 " =    3.197
peak=    3.911 closest distance to " O   HOH Z 126 " =    2.081
peak=    3.910 closest distance to " O   HOH Z 344 " =    2.691
peak=    3.907 closest distance to " CA  VAL A  41 " =    0.840
peak=    3.899 closest distance to " CB  GLU A 277 " =    3.508
peak=    3.894 closest distance to " O   TRP A 274 " =    1.892
peak=    3.880 closest distance to " O   HOH Z 346 " =    1.549
peak=    3.872 closest distance to " O   HOH Z 423 " =    1.887
peak=    3.868 closest distance to " O   HOH Z 273 " =    2.656
peak=    3.867 closest distance to " CB  VAL A 265 " =    1.255
peak=    3.858 closest distance to " O   HOH Z  61 " =    1.601
peak=    3.839 closest distance to " O   HOH Z 389 " =    1.851
peak=    3.838 closest distance to " O   HOH Z 426 " =    1.484
peak=    3.811 closest distance to " CB  GLN A  88 " =    1.221
peak=    3.791 closest distance to " O   HOH Z 197 " =    3.069
peak=    3.770 closest distance to " NH1BARG A 190 " =    2.011
peak=    3.762 closest distance to " CB  ARG A 139 " =    0.938
peak=    3.758 closest distance to " CB  ARG A  79 " =    1.383
peak=    3.755 closest distance to " O   HOH Z 403 " =    1.661
peak=    3.748 closest distance to " O   HOH Z 193 " =    1.990
peak=    3.737 closest distance to " OG BSER A 164 " =    2.163
peak=    3.734 closest distance to " CA  ASN A 215 " =    1.139
peak=    3.688 closest distance to " CB  VAL A 202 " =    1.572
peak=    3.685 closest distance to " CA  ALA A 248 " =    1.371
peak=    3.678 closest distance to " O   HOH Z 134 " =    1.406
peak=    3.677 closest distance to " O   HOH Z 133 " =    1.597
peak=    3.674 closest distance to " CA  ALA A  51 " =    0.971
peak=    3.667 closest distance to " O   HOH Z 345 " =    3.272
peak=    3.661 closest distance to " NH2 ARG A 156 " =    1.107
peak=    3.657 closest distance to " CB  ASN A  39 " =    0.844
peak=    3.652 closest distance to " O   HOH Z 112 " =    1.612
peak=    3.651 closest distance to " O   HOH Z 145 " =    2.022
peak=    3.650 closest distance to " O   HOH Z  88 " =    3.014
peak=    3.646 closest distance to " O   HOH Z  21 " =    1.767
peak=    3.645 closest distance to " CA  TYR A  30 " =    0.973
peak=    3.638 closest distance to " OE1 GLU A   2 " =    2.161
peak=    3.630 closest distance to " O   HOH Z 158 " =    3.025
peak=    3.627 closest distance to " O   HOH Z 419 " =    1.726
peak=    3.621 closest distance to " O   MET A 105 " =    1.789
peak=    3.620 closest distance to " CB  LEU A 143 " =    1.174
peak=    3.615 closest distance to " O   HOH Z 250 " =    1.290
peak=    3.596 closest distance to " CG  ARG A  66 " =    2.658
peak=    3.594 closest distance to " O   HOH Z 214 " =    2.071
peak=    3.589 closest distance to " CB  SER A 216 " =    0.736
peak=    3.588 closest distance to " CE1 TYR A 186 " =    1.269
peak=    3.578 closest distance to " C   ALA A 299 " =    0.972
peak=    3.576 closest distance to " O   HOH Z 128 " =    2.091
peak=    3.572 closest distance to " O   HOH Z 329 " =    3.700
peak=    3.571 closest distance to " O   HOH Z 216 " =    2.430
peak=    3.571 closest distance to " O   HOH Z 130 " =    2.353
peak=    3.569 closest distance to " CB  TRP A 266 " =    0.967
peak=    3.568 closest distance to " CB  TYR A 169 " =    0.761
peak=    3.565 closest distance to " O   HOH Z 189 " =    2.614
peak=    3.564 closest distance to " N   ASN A  39 " =    1.172
peak=    3.559 closest distance to " O   HOH Z 260 " =    1.344
peak=    3.558 closest distance to " CD BLYS A 290 " =    1.166
peak=    3.556 closest distance to " O   HOH Z 425 " =    1.997
peak=    3.552 closest distance to " CD  ARG A 269 " =    1.008
peak=    3.544 closest distance to " CD1 LEU A 300 " =    1.182
peak=    3.537 closest distance to " O   HOH Z  61 " =    1.582
peak=    3.534 closest distance to " CG2 ILE A 120 " =    1.285
peak=    3.527 closest distance to " O   HOH Z 247 " =    1.294
peak=    3.522 closest distance to " O   HOH Z 402 " =    1.437
peak=    3.521 closest distance to " O   HOH Z 334 " =    1.412
peak=    3.521 closest distance to " CA  PHE A 283 " =    1.202
peak=    3.520 closest distance to " O   HOH Z 135 " =    1.724
peak=    3.517 closest distance to " O   HOH Z  85 " =    1.437
peak=    3.515 closest distance to " O   HOH Z 248 " =    1.788
peak=    3.510 closest distance to " O   HOH Z 209 " =    2.267
peak=    3.507 closest distance to " CG  LEU A 167 " =    1.179
peak=    3.506 closest distance to " NE2 GLN A  58 " =    4.205
peak=    3.500 closest distance to " CA  ASP A 140 " =    1.174
peak=    3.500 closest distance to " O   HOH Z  44 " =    1.800
peak=    3.497 closest distance to " O   HOH Z  43 " =    2.137
peak=    3.497 closest distance to " O   HOH Z 280 " =    1.685
peak=    3.496 closest distance to " CE2 TRP A 179 " =    1.686
peak=    3.492 closest distance to " O   HOH Z  68 " =    1.979
peak=    3.489 closest distance to " O   HOH Z 295 " =    1.527
peak=    3.487 closest distance to " CA  THR A 264 " =    0.782
peak=    3.486 closest distance to " O   HOH Z 265 " =    2.386
peak=    3.485 closest distance to " O   HOH Z 276 " =    1.279
peak=    3.480 closest distance to " O   HOH Z 261 " =    2.238
peak=    3.479 closest distance to " O   HOH Z 344 " =    1.315
peak=    3.479 closest distance to " CG1 ILE A  33 " =    1.376
peak=    3.469 closest distance to " CA  ASN A 176 " =    1.057
peak=    3.468 closest distance to " OD1 ASN A 148 " =    1.699
peak=    3.466 closest distance to " CD1 ILE A 106 " =    1.213
peak=    3.464 closest distance to " O   HOH Z 422 " =    2.688
peak=    3.463 closest distance to " NZ  LYS A 117 " =    3.186
peak=    3.460 closest distance to " O   HOH Z 164 " =    2.067
peak=    3.460 closest distance to " OG  SER A  22 " =    2.754
peak=    3.458 closest distance to " O   HOH Z 407 " =    2.510
peak=    3.455 closest distance to " O   ALA A 158 " =    1.333
peak=    3.454 closest distance to " CB  ALA A 295 " =    1.255
peak=    3.451 closest distance to " O   HOH Z 303 " =    1.701
peak=    3.450 closest distance to " CA  ALA A 291 " =    0.984
peak=    3.448 closest distance to " O   HOH Z 374 " =    2.441
peak=    3.447 closest distance to " O   HOH Z  10 " =    1.790
peak=    3.446 closest distance to " N   ARG A 156 " =    1.296
peak=    3.445 closest distance to " O   HOH Z 151 " =    1.722
peak=    3.442 closest distance to " O   HOH Z 108 " =    2.128
peak=    3.441 closest distance to " O   HOH Z 406 " =    1.612
peak=    3.438 closest distance to " O   HOH Z 425 " =    1.346
peak=    3.430 closest distance to " O   HOH Z 207 " =    1.716
peak=    3.425 closest distance to " CA  VAL A 126 " =    0.935
peak=    3.425 closest distance to " O   HOH Z  80 " =    1.582
peak=    3.425 closest distance to " CB  LEU A 228 " =    1.350
peak=    3.424 closest distance to " O   HOH Z 192 " =    1.747
peak=    3.419 closest distance to " O   HOH Z 172 " =    3.756
peak=    3.418 closest distance to " O   HOH Z 411 " =    1.769
peak=    3.417 closest distance to " O   HOH Z 227 " =    1.664
peak=    3.416 closest distance to " O   HOH Z 355 " =    1.814
peak=    3.415 closest distance to " O   HOH Z 189 " =    2.795
peak=    3.409 closest distance to " CG  MET A 185 " =    1.101
peak=    3.406 closest distance to " O   HOH Z 227 " =    2.128
peak=    3.403 closest distance to " CB BVAL A  41 " =    1.079
peak=    3.402 closest distance to " O   HOH Z 279 " =    2.113
peak=    3.398 closest distance to " O   HOH Z  40 " =    1.850
peak=    3.398 closest distance to " O   HOH Z 175 " =    2.114
peak=    3.395 closest distance to " CA  ASP A 191 " =    0.795
peak=    3.393 closest distance to " N   SER A 135 " =    1.341
peak=    3.392 closest distance to " O   HOH Z 222 " =    2.419
peak=    3.392 closest distance to " O   HOH Z 173 " =    2.169
peak=    3.392 closest distance to " NE2 GLN A  58 " =    5.750
peak=    3.390 closest distance to " CG2 ILE A  20 " =    1.543
peak=    3.386 closest distance to " CG2 THR A 221 " =    1.124
peak=    3.384 closest distance to " O   HOH Z   3 " =    1.630
peak=    3.377 closest distance to " O   HOH Z 284 " =    1.662
peak=    3.376 closest distance to " CB  ALA A   9 " =    1.589
peak=    3.375 closest distance to " CB  GLN A 278 " =    0.848
peak=    3.373 closest distance to " O   HOH Z 366 " =    2.965
peak=    3.364 closest distance to " CB  ALA A   1 " =    1.226
peak=    3.364 closest distance to " O   HOH Z 367 " =    3.486
peak=    3.360 closest distance to " O   HOH Z 128 " =    1.821
peak=    3.360 closest distance to " CA  LEU A 282 " =    1.121
peak=    3.360 closest distance to " O   HOH Z 171 " =    2.400
peak=    3.359 closest distance to " O   HOH Z  50 " =    1.539
peak=    3.356 closest distance to " O   ALA A   1 " =    1.744
peak=    3.354 closest distance to " CA  ALA A 158 " =    1.165
peak=    3.354 closest distance to " CA  LYS A 117 " =    1.231
peak=    3.351 closest distance to " O   HOH Z 251 " =    1.623
peak=    3.347 closest distance to " OG1 THR A 294 " =    2.345
peak=    3.346 closest distance to " NZ  LYS A  76 " =    1.219
peak=    3.345 closest distance to " OE1 GLN A  11 " =    1.743
peak=    3.344 closest distance to " O   HOH Z 357 " =    1.833
peak=    3.342 closest distance to " CZ2 TRP A 274 " =    1.609
peak=    3.340 closest distance to " CB  PRO A 198 " =    0.917
peak=    3.338 closest distance to " CB  ASP A 140 " =    0.760
peak=    3.336 closest distance to " O   HOH Z 116 " =    1.730
peak=    3.332 closest distance to " CB  SER A  26 " =    1.638
peak=    3.330 closest distance to " O   HOH Z 148 " =    3.208
peak=    3.330 closest distance to " O   HOH Z 180 " =    2.116
peak=    3.322 closest distance to " CA  GLN A 194 " =    1.244
peak=    3.320 closest distance to " O   HOH Z  48 " =    1.542
peak=    3.320 closest distance to " CG BARG A 102 " =    1.815
peak=    3.319 closest distance to " O   HOH Z 215 " =    1.663
peak=    3.319 closest distance to " O   HOH Z 337 " =    3.693
peak=    3.315 closest distance to " CB  ALA A 248 " =    0.975
peak=    3.313 closest distance to " O   HOH Z  49 " =    2.413
peak=    3.312 closest distance to " O   HOH Z 388 " =    1.878
peak=    3.311 closest distance to " N   PHE A 130 " =    1.397
peak=    3.311 closest distance to " CB  SER A 141 " =    0.978
peak=    3.307 closest distance to " CB  ARG A 190 " =    1.769
peak=    3.307 closest distance to " CG  MET A 185 " =    1.235
peak=    3.305 closest distance to " O   HOH Z  71 " =    1.876
peak=    3.300 closest distance to " CD2 LEU A 255 " =    1.369
peak=    3.295 closest distance to " O   HOH Z 394 " =    1.721
peak=    3.293 closest distance to " O   THR A  31 " =    1.495
peak=    3.292 closest distance to " O   HOH Z 245 " =    1.427
peak=    3.290 closest distance to " N   ARG A 190 " =    1.014
peak=    3.289 closest distance to " O   HOH Z 163 " =    1.935
peak=    3.289 closest distance to " O   HOH Z 313 " =    1.766
peak=    3.285 closest distance to " CA  LYS A 290 " =    1.319
peak=    3.285 closest distance to " CA  SER A  87 " =    0.880
peak=    3.285 closest distance to " CB  ALA A 291 " =    1.384
peak=    3.285 closest distance to " O   ALA A   1 " =    1.521
peak=    3.284 closest distance to " O   HOH Z 236 " =    1.583
peak=    3.282 closest distance to " O   SER A  26 " =    1.595
peak=    3.281 closest distance to " O   HOH Z 368 " =    3.613
peak=    3.279 closest distance to " CD1 ILE A  33 " =    1.633
peak=    3.278 closest distance to " O   HOH Z  63 " =    2.312
peak=    3.278 closest distance to " O   PHE A  38 " =    1.883
peak=    3.267 closest distance to " OG  SER A  97 " =    2.628
peak=    3.265 closest distance to " NH2 ARG A 219 " =    1.806
peak=    3.261 closest distance to " O   HOH Z 128 " =    1.943
peak=    3.260 closest distance to " O   HOH Z   1 " =    1.930
peak=    3.260 closest distance to " O   HOH Z 147 " =    1.632
peak=    3.260 closest distance to " O   HOH Z 193 " =    1.619
peak=    3.260 closest distance to " CD2 HIS A  81 " =    1.180
peak=    3.259 closest distance to " O   HOH Z 286 " =    2.320
peak=    3.259 closest distance to " O   HOH Z 126 " =    1.629
peak=    3.258 closest distance to " O   HOH Z 291 " =    1.545
peak=    3.258 closest distance to " O   HOH Z 209 " =    2.373
peak=    3.255 closest distance to " O   HOH Z 435 " =    2.028
peak=    3.250 closest distance to " O   HOH Z 438 " =    2.000
peak=    3.250 closest distance to " O   HOH Z  59 " =    2.054
peak=    3.245 closest distance to " CB  SER A  62 " =    1.322
peak=    3.244 closest distance to " CB  ASN A 142 " =    1.042
peak=    3.239 closest distance to " O   HOH Z 352 " =    1.285
peak=    3.233 closest distance to " CG2 VAL A 257 " =    0.905
peak=    3.233 closest distance to " OD1BASN A 224 " =    2.156
peak=    3.231 closest distance to " CD  LYS A 166 " =    1.353
peak=    3.227 closest distance to " O   HOH Z  68 " =    1.561
peak=    3.226 closest distance to " CB  ILE A  20 " =    1.401
peak=    3.226 closest distance to " NH1AARG A 145 " =    0.996
peak=    3.223 closest distance to " CA  ALA A 295 " =    1.053
peak=    3.222 closest distance to " CB  TRP A 150 " =    1.545
peak=    3.220 closest distance to " O   HOH Z 281 " =    4.486
peak=    3.219 closest distance to " O   HOH Z 151 " =    1.793
peak=    3.216 closest distance to " CD2 TRP A 179 " =    1.370
peak=    3.211 closest distance to " OD1 ASP A 286 " =    1.639
peak=    3.209 closest distance to " CB  VAL A 268 " =    0.820
peak=    3.206 closest distance to " O   HOH Z 185 " =    2.253
peak=    3.203 closest distance to " CB  THR A  31 " =    1.677
peak=    3.193 closest distance to " O   HOH Z 141 " =    1.553
peak=    3.192 closest distance to " CB  SER A 212 " =    1.179
peak=    3.188 closest distance to " NH2BARG A 145 " =    2.163
peak=    3.188 closest distance to " O   HOH Z 427 " =    3.066
peak=    3.187 closest distance to " OD1 ASP A 231 " =    1.838
peak=    3.187 closest distance to " ND1 HIS A  81 " =    1.520
peak=    3.177 closest distance to " O   GLY A  91 " =    1.638
peak=    3.172 closest distance to " O   HOH Z 163 " =    1.839
peak=    3.169 closest distance to " O   GLN A  58 " =    1.563
peak=    3.168 closest distance to " O   HOH Z 327 " =    1.868
peak=    3.166 closest distance to " NZ  LYS A 119 " =    1.437
peak=    3.164 closest distance to " CG  ARG A 138 " =    1.058
peak=    3.164 closest distance to " O   HOH Z  80 " =    2.282
peak=    3.162 closest distance to " CB  GLU A  46 " =    1.097
peak=    3.161 closest distance to " O   HOH Z 383 " =    2.067
peak=    3.160 closest distance to " O   HOH Z  63 " =    2.021
peak=    3.159 closest distance to " O   HOH Z 213 " =    2.147
peak=    3.159 closest distance to " O   HOH Z 353 " =    2.708
peak=    3.157 closest distance to " CA  GLY A 267 " =    0.860
peak=    3.151 closest distance to " ND1 HIS A  86 " =    1.595
peak=    3.150 closest distance to " CA  ALA A 233 " =    1.345
peak=    3.144 closest distance to " O   SER A 164 " =    1.327
peak=    3.141 closest distance to " CG  GLN A  77 " =    1.992
peak=    3.140 closest distance to " O   HOH Z 409 " =    3.408
peak=    3.137 closest distance to " CB  LEU A 255 " =    0.821
peak=    3.129 closest distance to " CB  ALA A 114 " =    1.261
peak=    3.127 closest distance to " CD2 TYR A 186 " =    0.999
peak=    3.124 closest distance to " O   HOH Z 420 " =    1.848
peak=    3.115 closest distance to " CA  ARG A  36 " =    1.054
peak=    3.103 closest distance to " CB  ASN A 110 " =    1.178
peak=    3.098 closest distance to " O   GLN A 278 " =    1.304
peak=    3.094 closest distance to " CA  ILE A 106 " =    0.794
peak=    3.093 closest distance to " O   HOH Z 102 " =    1.192
peak=    3.088 closest distance to " CG  MET A 188 " =    1.256
peak=    3.086 closest distance to " O   HOH Z  40 " =    2.420
peak=    3.081 closest distance to " CA  ALA A 154 " =    1.078
peak=    3.074 closest distance to " NH2BARG A 190 " =    2.101
peak=    3.068 closest distance to " CD  LYS A 119 " =    1.399
peak=    3.053 closest distance to " O   HOH Z 423 " =    3.029
peak=    3.014 closest distance to " O   HOH Z  68 " =    2.596
peak=    3.004 closest distance to " O   HOH Z 427 " =    3.675
peak=    3.003 closest distance to " O   HOH Z 280 " =    2.374

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 189         
Filter by distance & map next to the model:
   mapped sites are within: 0.631 - 5.287
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 186 from: 189
   mapped sites are within: 0.727 - 5.287

peak=   -5.880 closest distance to " CG2 VAL A 230 " =    0.735
peak=   -4.607 closest distance to " O   HOH Z 290 " =    0.974
peak=   -4.396 closest distance to " CB  ALA A 161 " =    2.570
peak=   -4.347 closest distance to " O   HOH Z 266 " =    4.490
peak=   -4.300 closest distance to " CD  ARG A 156 " =    1.987
peak=   -4.195 closest distance to " SG  CYS A 254 " =    3.169
peak=   -4.177 closest distance to " O   VAL A  67 " =    2.590
peak=   -4.129 closest distance to " N   GLN A  58 " =    1.727
peak=   -4.079 closest distance to " CE2 TYR A  30 " =    2.856
peak=   -4.073 closest distance to " OXT GLY A 302 " =    2.748
peak=   -4.038 closest distance to " CG2 VAL A 296 " =    1.374
peak=   -3.979 closest distance to " CD1 LEU A 101 " =    2.571
peak=   -3.960 closest distance to " C   ALA A 158 " =    1.267
peak=   -3.940 closest distance to " O   HOH Z 231 " =    1.580
peak=   -3.934 closest distance to " CG  ASP A 231 " =    0.786
peak=   -3.930 closest distance to " CG  GLN A 223 " =    1.936
peak=   -3.863 closest distance to " C   HIS A 108 " =    1.216
peak=   -3.849 closest distance to " CB  TYR A  15 " =    2.228
peak=   -3.849 closest distance to " O   PRO A 163 " =    2.032
peak=   -3.820 closest distance to " CB  PRO A 243 " =    2.556
peak=   -3.782 closest distance to " CD2 LEU A 300 " =    2.889
peak=   -3.771 closest distance to " OG BSER A 134 " =    1.712
peak=   -3.770 closest distance to " CG  ASP A  50 " =    2.482
peak=   -3.760 closest distance to " O   HOH Z  11 " =    1.935
peak=   -3.758 closest distance to " CD  ARG A 139 " =    1.650
peak=   -3.755 closest distance to " CB  ALA A 248 " =    1.966
peak=   -3.753 closest distance to " O   VAL A  67 " =    2.639
peak=   -3.749 closest distance to " CD  GLN A  88 " =    2.321
peak=   -3.725 closest distance to " N   ALA A 226 " =    2.061
peak=   -3.706 closest distance to " O   HOH Z  63 " =    0.925
peak=   -3.694 closest distance to " O   HOH Z  43 " =    1.772
peak=   -3.685 closest distance to " O   HOH Z  13 " =    1.395
peak=   -3.680 closest distance to " N   ALA A  43 " =    2.358
peak=   -3.676 closest distance to " CZ  TYR A 169 " =    1.725
peak=   -3.664 closest distance to " CG  LEU A 101 " =    2.509
peak=   -3.653 closest distance to " O   HOH Z 435 " =    2.722
peak=   -3.653 closest distance to " NE2 GLN A  88 " =    0.935
peak=   -3.647 closest distance to " CE  MET A 105 " =    2.002
peak=   -3.638 closest distance to " OG BSER A 134 " =    1.199
peak=   -3.637 closest distance to " CG  LEU A 228 " =    0.978
peak=   -3.630 closest distance to " OG ASER A 134 " =    1.660
peak=   -3.629 closest distance to " O   MET A  40 " =    2.635
peak=   -3.627 closest distance to " CG  LYS A 193 " =    2.264
peak=   -3.626 closest distance to " CA  GLY A  98 " =    1.967
peak=   -3.617 closest distance to " O   HOH Z 166 " =    1.510
peak=   -3.616 closest distance to " C   ASP A 231 " =    2.538
peak=   -3.607 closest distance to " NH2 ARG A  79 " =    1.885
peak=   -3.606 closest distance to " O   HOH Z 166 " =    1.850
peak=   -3.604 closest distance to " O   ALA A 161 " =    1.596
peak=   -3.601 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.598 closest distance to " CB  PRO A 163 " =    2.627
peak=   -3.588 closest distance to " O   HOH Z 389 " =    1.770
peak=   -3.587 closest distance to " CD1 LEU A 228 " =    2.235
peak=   -3.583 closest distance to " OG  SER A  97 " =    2.216
peak=   -3.582 closest distance to " CG  PHE A 283 " =    2.735
peak=   -3.580 closest distance to " O   HOH Z 351 " =    1.456
peak=   -3.579 closest distance to " CZ3 TRP A 179 " =    1.336
peak=   -3.565 closest distance to " O   HOH Z 222 " =    1.428
peak=   -3.562 closest distance to " CD2 LEU A 237 " =    2.761
peak=   -3.529 closest distance to " O   HOH Z 126 " =    1.908
peak=   -3.528 closest distance to " NZ  LYS A 119 " =    3.387
peak=   -3.525 closest distance to " CG  MET A 105 " =    0.918
peak=   -3.523 closest distance to " O   GLY A 196 " =    1.103
peak=   -3.516 closest distance to " O   HOH Z 103 " =    1.828
peak=   -3.516 closest distance to " O   HOH Z 388 " =    2.060
peak=   -3.507 closest distance to " O   HOH Z  52 " =    1.546
peak=   -3.505 closest distance to " ND2 ASN A  45 " =    0.979
peak=   -3.504 closest distance to " C   GLN A 205 " =    1.987
peak=   -3.503 closest distance to " O   HOH Z 407 " =    3.211
peak=   -3.501 closest distance to " O   HOH Z  71 " =    1.036
peak=   -3.495 closest distance to " O   HOH Z 436 " =    1.531
peak=   -3.483 closest distance to " CB  ASN A  39 " =    1.963
peak=   -3.480 closest distance to " O   HOH Z 211 " =    1.561
peak=   -3.472 closest distance to " ND2 ASN A 187 " =    1.695
peak=   -3.471 closest distance to " N   THR A 157 " =    1.474
peak=   -3.463 closest distance to " O   HOH Z 118 " =    2.799
peak=   -3.462 closest distance to " CB  PRO A 280 " =    2.070
peak=   -3.456 closest distance to " N   ALA A 248 " =    1.629
peak=   -3.454 closest distance to " O   PRO A 198 " =    1.243
peak=   -3.451 closest distance to " O   HOH Z 292 " =    4.360
peak=   -3.450 closest distance to " CB  ALA A 291 " =    2.393
peak=   -3.449 closest distance to " CA  ASP A 298 " =    1.067
peak=   -3.445 closest distance to " CD  LYS A 289 " =    2.542
peak=   -3.442 closest distance to " O   HOH Z 165 " =    2.023
peak=   -3.438 closest distance to " OXT GLY A 302 " =    3.510
peak=   -3.431 closest distance to " O   HOH Z 423 " =    2.202
peak=   -3.429 closest distance to " SD BMET A  47 " =    2.676
peak=   -3.427 closest distance to " O   HOH Z 185 " =    2.285
peak=   -3.424 closest distance to " NH2 ARG A  66 " =    1.900
peak=   -3.424 closest distance to " CZ  PHE A  59 " =    1.524
peak=   -3.422 closest distance to " NH2AARG A 275 " =    5.083
peak=   -3.420 closest distance to " O   HOH Z 389 " =    4.591
peak=   -3.415 closest distance to " N   SER A 276 " =    1.244
peak=   -3.405 closest distance to " N   THR A 235 " =    1.256
peak=   -3.404 closest distance to " O   HOH Z 311 " =    3.569
peak=   -3.392 closest distance to " C   MET A 188 " =    1.529
peak=   -3.391 closest distance to " CG1 VAL A 112 " =    2.688
peak=   -3.388 closest distance to " N   HIS A 115 " =    2.020
peak=   -3.383 closest distance to " O   HOH Z 394 " =    1.561
peak=   -3.378 closest distance to " OG  SER A  62 " =    1.442
peak=   -3.373 closest distance to " CG  TRP A 266 " =    1.674
peak=   -3.363 closest distance to " O   ALA A  51 " =    1.450
peak=   -3.362 closest distance to " O   HOH Z 353 " =    2.206
peak=   -3.358 closest distance to " O   HOH Z  97 " =    1.610
peak=   -3.358 closest distance to " O   HOH Z  15 " =    1.574
peak=   -3.349 closest distance to " CG  PHE A  59 " =    2.181
peak=   -3.343 closest distance to " CE BMET A  47 " =    1.811
peak=   -3.334 closest distance to " O   HOH Z 132 " =    0.799
peak=   -3.327 closest distance to " CD1 PHE A  59 " =    1.801
peak=   -3.316 closest distance to " O   HOH Z  92 " =    1.683
peak=   -3.313 closest distance to " C   ASN A 285 " =    2.390
peak=   -3.311 closest distance to " O   HOH Z 292 " =    2.846
peak=   -3.306 closest distance to " O   HOH Z 283 " =    1.586
peak=   -3.303 closest distance to " O   HOH Z 344 " =    2.594
peak=   -3.303 closest distance to " O   HOH Z 148 " =    1.745
peak=   -3.293 closest distance to " O   HOH Z 210 " =    1.072
peak=   -3.292 closest distance to " O   HOH Z  47 " =    1.452
peak=   -3.282 closest distance to " O   PRO A 198 " =    1.257
peak=   -3.277 closest distance to " CB  PHE A 192 " =    1.811
peak=   -3.277 closest distance to " O   HOH Z 191 " =    5.287
peak=   -3.276 closest distance to " CG1 VAL A 296 " =    1.393
peak=   -3.275 closest distance to " O   HOH Z 231 " =    1.136
peak=   -3.274 closest distance to " CG  GLU A  53 " =    1.559
peak=   -3.270 closest distance to " CG  GLU A   2 " =    1.999
peak=   -3.268 closest distance to " O   HOH Z  11 " =    1.817
peak=   -3.267 closest distance to " O   HOH Z 295 " =    1.340
peak=   -3.265 closest distance to " O   VAL A 197 " =    1.264
peak=   -3.264 closest distance to " CD2 LEU A 237 " =    2.793
peak=   -3.259 closest distance to " O   HOH Z 339 " =    1.806
peak=   -3.255 closest distance to " O   HOH Z 196 " =    2.124
peak=   -3.255 closest distance to " OG  SER A  26 " =    1.102
peak=   -3.252 closest distance to " CE2 PHE A 218 " =    2.602
peak=   -3.251 closest distance to " O   HOH Z 417 " =    2.745
peak=   -3.250 closest distance to " CA  GLY A 241 " =    2.994
peak=   -3.248 closest distance to " O   VAL A 174 " =    2.005
peak=   -3.245 closest distance to " CG1 VAL A 112 " =    2.652
peak=   -3.239 closest distance to " CG  GLU A 277 " =    1.122
peak=   -3.237 closest distance to " O   ALA A   8 " =    1.939
peak=   -3.234 closest distance to " O   SER A 210 " =    1.877
peak=   -3.225 closest distance to " O   HOH Z  38 " =    1.859
peak=   -3.224 closest distance to " CG2 VAL A 112 " =    2.586
peak=   -3.222 closest distance to " CE3 TRP A 150 " =    2.039
peak=   -3.221 closest distance to " OE1 GLN A  73 " =    2.335
peak=   -3.216 closest distance to " OG  SER A 206 " =    1.587
peak=   -3.211 closest distance to " O   HOH Z 281 " =    2.772
peak=   -3.210 closest distance to " O   HOH Z 174 " =    2.294
peak=   -3.210 closest distance to " CG1 VAL A 197 " =    2.211
peak=   -3.209 closest distance to " O   HOH Z 377 " =    0.727
peak=   -3.209 closest distance to " OD1 ASP A 191 " =    1.523
peak=   -3.208 closest distance to " O   ILE A 120 " =    1.253
peak=   -3.203 closest distance to " CD2 TYR A 293 " =    2.205
peak=   -3.202 closest distance to " CE  MET A  93 " =    1.083
peak=   -3.197 closest distance to " OG1 THR A 178 " =    1.236
peak=   -3.195 closest distance to " N   MET A 105 " =    2.633
peak=   -3.192 closest distance to " O   HOH Z 175 " =    4.319
peak=   -3.188 closest distance to " ND2 ASN A  60 " =    1.394
peak=   -3.182 closest distance to " O   GLY A 211 " =    1.342
peak=   -3.176 closest distance to " CE  LYS A  76 " =    2.882
peak=   -3.175 closest distance to " CA  GLY A 133 " =    1.953
peak=   -3.174 closest distance to " O   HOH Z  44 " =    2.045
peak=   -3.173 closest distance to " O   HOH Z 369 " =    2.174
peak=   -3.168 closest distance to " OD1 ASN A 249 " =    1.220
peak=   -3.167 closest distance to " O   HOH Z  19 " =    2.239
peak=   -3.162 closest distance to " O   HOH Z 148 " =    3.046
peak=   -3.158 closest distance to " CG2 ILE A 263 " =    2.237
peak=   -3.153 closest distance to " CD1 ILE A 199 " =    2.437
peak=   -3.151 closest distance to " N   ASP A 171 " =    2.486
peak=   -3.150 closest distance to " O   HOH Z 431 " =    1.696
peak=   -3.144 closest distance to " CG  GLU A 152 " =    2.502
peak=   -3.144 closest distance to " CE3 TRP A 274 " =    2.437
peak=   -3.136 closest distance to " OG  SER A   3 " =    1.639
peak=   -3.133 closest distance to " CB  ASP A 132 " =    2.198
peak=   -3.132 closest distance to " OG BSER A 210 " =    2.084
peak=   -3.121 closest distance to " O   ASP A 231 " =    2.387
peak=   -3.118 closest distance to " O   HOH Z 297 " =    2.680
peak=   -3.103 closest distance to " O   SER A  22 " =    2.208
peak=   -3.101 closest distance to " CD1 TYR A 247 " =    2.402
peak=   -3.095 closest distance to " OE1 GLN A  88 " =    1.115
peak=   -3.087 closest distance to " O   HOH Z 234 " =    4.238
peak=   -3.085 closest distance to " CB  ASN A  69 " =    1.174
peak=   -3.073 closest distance to " O   HOH Z 250 " =    1.426
peak=   -3.069 closest distance to " O   HOH Z 313 " =    1.821
peak=   -3.061 closest distance to " O   PRO A 243 " =    2.561
peak=   -3.058 closest distance to " O   HOH Z 385 " =    2.311
peak=   -3.058 closest distance to " CG  PRO A 163 " =    2.705
peak=   -3.021 closest distance to " O   HOH Z 228 " =    1.536

================= 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    :  0.4466 0.4486   6.244703e+00   6.237944e+00
   1_bss:  0.4381 0.4388   6.241224e+00   6.225291e+00
   1_xyz:  0.3466 0.3720   6.085899e+00   6.128948e+00
   1_adp:  0.2900 0.3380   5.959377e+00   6.066190e+00
   1_occ:  0.2897 0.3382   5.958829e+00   6.066616e+00
   2_bss:  0.2842 0.3327   5.955654e+00   6.060890e+00
   2_xyz:  0.1961 0.2497   5.627948e+00   5.809459e+00
   2_adp:  0.1740 0.2251   5.518889e+00   5.718064e+00
   2_occ:  0.1736 0.2250   5.518302e+00   5.717990e+00
   3_bss:  0.1720 0.2223   5.512225e+00   5.711012e+00
   3_xyz:  0.1396 0.1821   5.319813e+00   5.529614e+00
   3_adp:  0.1312 0.1750   5.273903e+00   5.492801e+00
   3_occ:  0.1311 0.1750   5.273179e+00   5.492259e+00
   4_bss:  0.1312 0.1749   5.273622e+00   5.492742e+00
   4_xyz:  0.1173 0.1613   5.181417e+00   5.411281e+00
   4_adp:  0.1149 0.1599   5.168216e+00   5.402094e+00
   4_occ:  0.1149 0.1599   5.168117e+00   5.402204e+00
   5_bss:  0.1149 0.1599   5.168129e+00   5.402210e+00
   5_xyz:  0.1104 0.1586   5.145490e+00   5.393509e+00
   5_adp:  0.1115 0.1572   5.146636e+00   5.387729e+00
   5_occ:  0.1114 0.1572   5.146339e+00   5.387560e+00
   5_bss:  0.1114 0.1572   5.146409e+00   5.387595e+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:  0.344   4.839   7.222   8.075   9.940   0.000   0.000   0.000
   1_xyz:  0.344   4.839   7.222   8.075   9.940   0.000   0.000   0.000
   1_adp:  0.344   4.839   7.222   8.075   9.940   0.000   0.000   0.000
   1_occ:  0.344   4.839   7.222   8.075   9.940   0.000   0.000   0.000
   2_bss:  0.331  27.131   3.599   4.074   6.524   0.000   0.000   0.000
   2_xyz:  0.331  27.131   3.599   4.074   6.524   0.000   0.000   0.000
   2_adp:  0.331  27.131   3.599   4.074   6.524   0.000   0.000   0.000
   2_occ:  0.331  27.131   3.599   4.074   6.524   0.000   0.000   0.000
   3_bss:  0.316  35.221   2.501   2.828   3.897   0.000   0.000   0.000
   3_xyz:  0.316  35.221   2.501   2.828   3.897   0.000   0.000   0.000
   3_adp:  0.316  35.221   2.501   2.828   3.897   0.000   0.000   0.000
   3_occ:  0.316  35.221   2.501   2.828   3.897   0.000   0.000   0.000
   4_bss:  0.319  37.757   2.369   2.672   3.274   0.000   0.000   0.000
   4_xyz:  0.319  37.757   2.369   2.672   3.274   0.000   0.000   0.000
   4_adp:  0.319  37.757   2.369   2.672   3.274   0.000   0.000   0.000
   4_occ:  0.319  37.757   2.369   2.672   3.274   0.000   0.000   0.000
   5_bss:  0.320  37.757   2.369   2.672   3.274   0.000   0.000   0.000
   5_xyz:  0.320  37.757   2.369   2.672   3.274   0.000   0.000   0.000
   5_adp:  0.320  37.757   2.369   2.672   3.274   0.000   0.000   0.000
   5_occ:  0.320  37.757   2.369   2.672   3.274   0.000   0.000   0.000
   5_bss:  0.322  40.300  -0.402  -0.100   0.502   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.020 0.4959  0.5754    59935.907
   1_bss:  52.135 0.4915  0.7220    56665.789
   1_xyz:  41.591 0.6219  0.9015    39201.065
   1_adp:  36.545 0.6828  0.9965    32073.380
   1_occ:  36.586 0.6824  0.9959    32128.204
   2_bss:  36.142 0.6873  0.8814    31480.703
   2_xyz:  25.154 0.8091  1.0001    16161.470
   2_adp:  21.878 0.8435  1.0273    13035.672
   2_occ:  21.877 0.8435  1.0268    13018.677
   3_bss:  21.612 0.8458  0.9682    12733.318
   3_xyz:  17.052 0.8889  0.9886     8444.912
   3_adp:  16.210 0.8967  0.9902     7878.744
   3_occ:  16.194 0.8969  0.9899     7868.632
   4_bss:  16.208 0.8968  0.9790     7892.409
   4_xyz:  14.595 0.9101  0.9854     6684.483
   4_adp:  14.357 0.9122  0.9853     6570.402
   4_occ:  14.355 0.9122  0.9853     6574.512
   5_bss:  14.355 0.9122  0.9853     6574.698
   5_xyz:  14.143 0.9140  0.9852     6438.277
   5_adp:  14.012 0.9151  0.9845     6376.294
   5_occ:  14.006 0.9152  0.9844     6373.652
   5_bss:  14.007 0.9152  0.9844     6374.260
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3361e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3361e+01
   1_xyz:   1.572  0.012  0.103 18.000  0.006  4.109   1.2432e-01
   1_adp:   1.572  0.012  0.103 18.000  0.006  4.109   1.2432e-01
   1_occ:   1.572  0.012  0.103 18.000  0.006  4.109   1.2432e-01
   2_bss:   1.572  0.012  0.103 18.000  0.006  4.109   1.2432e-01
   2_xyz:   1.086  0.008  0.078 16.088  0.005  4.123   7.4000e-02
   2_adp:   1.086  0.008  0.078 16.088  0.005  4.123   7.4000e-02
   2_occ:   1.086  0.008  0.078 16.088  0.005  4.123   7.4000e-02
   3_bss:   1.086  0.008  0.078 16.088  0.005  4.123   7.4000e-02
   3_xyz:   0.928  0.005  0.070 15.566  0.003  4.110   5.3782e-02
   3_adp:   0.928  0.005  0.070 15.566  0.003  4.110   5.3782e-02
   3_occ:   0.928  0.005  0.070 15.566  0.003  4.110   5.3782e-02
   4_bss:   0.928  0.005  0.070 15.566  0.003  4.110   5.3782e-02
   4_xyz:   1.002  0.006  0.079 15.752  0.003  4.111   6.0131e-02
   4_adp:   1.002  0.006  0.079 15.752  0.003  4.111   6.0131e-02
   4_occ:   1.002  0.006  0.079 15.752  0.003  4.111   6.0131e-02
   5_bss:   1.002  0.006  0.079 15.752  0.003  4.111   6.0131e-02
   5_xyz:   1.023  0.007  0.081 15.563  0.004  4.113   6.2907e-02
   5_adp:   1.023  0.007  0.081 15.563  0.004  4.113   6.2907e-02
   5_occ:   1.023  0.007  0.081 15.563  0.004  4.113   6.2907e-02
   5_bss:   1.023  0.007  0.081 15.563  0.004  4.113   6.2907e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9175e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9175e+00
   1_xyz:  13.243  0.147  0.444 86.616  0.050  2.222   8.9364e-02
   1_adp:  13.243  0.147  0.444 86.616  0.050  2.222   8.9364e-02
   1_occ:  13.243  0.147  0.444 86.616  0.050  2.222   8.9364e-02
   2_bss:  13.243  0.147  0.444 86.616  0.050  2.222   8.9364e-02
   2_xyz:   6.874  0.111  0.264 89.454  0.044  2.260   7.2583e-02
   2_adp:   6.874  0.111  0.264 89.454  0.044  2.260   7.2583e-02
   2_occ:   6.874  0.111  0.264 89.454  0.044  2.260   7.2583e-02
   3_bss:   6.874  0.111  0.264 89.454  0.044  2.260   7.2583e-02
   3_xyz:   7.329  0.039  0.378 82.708  0.030  2.400   2.9947e-02
   3_adp:   7.329  0.039  0.378 82.708  0.030  2.400   2.9947e-02
   3_occ:   7.329  0.039  0.378 82.708  0.030  2.400   2.9947e-02
   4_bss:   7.329  0.039  0.378 82.708  0.030  2.400   2.9947e-02
   4_xyz:   7.449  0.045  0.502 83.280  0.034  2.331   3.6409e-02
   4_adp:   7.449  0.045  0.502 83.280  0.034  2.331   3.6409e-02
   4_occ:   7.449  0.045  0.502 83.280  0.034  2.331   3.6409e-02
   5_bss:   7.449  0.045  0.502 83.280  0.034  2.331   3.6409e-02
   5_xyz:   6.617  0.044  0.564 82.656  0.035  2.296   4.6006e-02
   5_adp:   6.617  0.044  0.564 82.656  0.035  2.296   4.6006e-02
   5_occ:   6.617  0.044  0.564 82.656  0.035  2.296   4.6006e-02
   5_bss:   6.617  0.044  0.564 82.656  0.035  2.296   4.6006e-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:  71.74   0.00  11.56  71.74   0.00   8.67  68.02   0.00  27.27
   1_occ:  71.74   0.00  11.56  71.74   0.00   8.67  68.02   0.00  27.27
   2_bss:  71.74   0.00  11.56  71.74   0.00   8.67  68.02   0.00  27.27
   2_xyz:  71.74   0.00  11.56  71.74   0.00   8.67  68.02   0.00  27.27
   2_adp:  71.66   0.00  11.84  71.66   0.00   8.12  68.68   1.53  32.08
   2_occ:  71.66   0.00  11.84  71.66   0.00   8.12  68.68   1.53  32.08
   3_bss:  71.66   0.00  11.84  71.66   0.00   8.12  68.68   1.53  32.08
   3_xyz:  71.66   0.00  11.84  71.66   0.00   8.12  68.68   1.53  32.08
   3_adp:  81.59   0.00  12.52  81.59   0.00   8.20  72.92   1.95  36.04
   3_occ:  81.59   0.00  12.52  81.59   0.00   8.20  72.92   1.95  36.04
   4_bss:  81.59   0.00  12.52  81.59   0.00   8.20  72.92   1.95  36.04
   4_xyz:  81.59   0.00  12.52  81.59   0.00   8.20  72.92   1.95  36.04
   4_adp:  86.46   0.00  12.37  86.46   0.00   8.12  73.74   1.51  35.51
   4_occ:  86.46   0.00  12.37  86.46   0.00   8.12  73.74   1.51  35.51
   5_bss:  86.46   0.00  12.37  86.46   0.00   8.12  73.74   1.51  35.51
   5_xyz:  86.46   0.00  12.37  86.46   0.00   8.12  73.74   1.51  35.51
   5_adp:  84.88   0.00  11.82  84.88   0.00   7.93  69.87   1.66  33.02
   5_occ:  84.88   0.00  11.82  84.88   0.00   7.93  69.87   1.66  33.02
   5_bss:  87.65   2.77  14.59  87.65   2.77  10.70  72.64   4.43  35.79
------------------------------------------------------------------------
 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:    1.194    0.019    0.404
   1_adp:    1.194    0.019    0.404
   1_occ:    1.194    0.019    0.404
   2_bss:    1.194    0.019    0.404
   2_xyz:    1.416    0.037    0.552
   2_adp:    1.416    0.037    0.552
   2_occ:    1.416    0.037    0.552
   3_bss:    1.416    0.037    0.552
   3_xyz:    1.428    0.036    0.577
   3_adp:    1.428    0.036    0.577
   3_occ:    1.428    0.036    0.577
   4_bss:    1.428    0.036    0.577
   4_xyz:    1.545    0.047    0.611
   4_adp:    1.545    0.047    0.611
   4_occ:    1.545    0.047    0.611
   5_bss:    1.545    0.047    0.611
   5_xyz:    1.602    0.040    0.616
   5_adp:    1.602    0.040    0.616
   5_occ:    1.602    0.040    0.616
   5_bss:    1.602    0.040    0.616
------------------------------------------------------------------------

CPU time actual refinement: 335.23


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_661/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_661/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_661/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_661/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_661/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.07 
  Macro-tasks:
    bulk solvent and scale       = 42.40  
    individual site refinement   = 135.05 
    weights calculation          = 31.87  
    collect and process          = 6.54   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 215.98 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 102.57 
    alpha_beta                      = 8.29   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 113.25 
    fmodel                         = 7.33   
    r_factors                      = 0.17   
    phase_errors                   = 10.79  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 245.70 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.710 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    659 calls, 102.23 s
gradients_fft:          605 calls,  99.89 s

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

# Date 2008-01-16 Time 02:08:02 PST -0800 (1200478082.59 s)
Start R-work = 0.4466, R-free = 0.4486 (no bulk solvent and anisotropic scale)
Final R-work = 0.1289, R-free = 0.1739 (no bulk solvent and anisotropic scale)

Start R-work = 0.4381, R-free = 0.4388
Final R-work = 0.1114, R-free = 0.1572