# Date 2008-01-16 Time 02:55:18 PST -0800 (1200480918.27 s)
#phil __OFF__

Command line arguments: "../1024.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19754
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1024

-------------------------------------------------------------------------------
  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: (71.3037, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96125
Completeness in resolution range: 0.935438
Completeness with d_max=infinity: 0.932676

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0711
                             d_min =   1.9613

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: (71.3037, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96125
Completeness in resolution range: 0.935438
Completeness with d_max=infinity: 0.932676

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0715 -  4.1978 [2197/2227]  1980   217   9.9%
  bin  2:  4.1978 -  3.3439 [2111/2130]  1898   213  10.1%
  bin  3:  3.3439 -  2.9247 [2080/2100]  1871   209  10.0%
  bin  4:  2.9247 -  2.6589 [2078/2103]  1879   199   9.6%
  bin  5:  2.6589 -  2.4692 [2046/2065]  1833   213  10.4%
  bin  6:  2.4692 -  2.3242 [2039/2086]  1837   202   9.9%
  bin  7:  2.3242 -  2.2082 [2029/2061]  1826   203  10.0%
  bin  8:  2.2082 -  2.1123 [2021/2057]  1819   202  10.0%
  bin  9:  2.1123 -  2.0312 [2023/2052]  1820   203  10.0%
  bin 10:  2.0312 -  1.9613 [ 965/2060]   867    98  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1024/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 29
        2.38 -     3.01: 1994
        3.01 -     3.64: 4634
        3.64 -     4.27: 9128
        4.27 -     4.90: 12631
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.748 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.790 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 107 " - " O   HOH Z 340 "  1.991 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28411 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_1024/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1024/model_refine_001.geo

CPU time processing inputs: 9.15


============================ 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 = 71.30375 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 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4634   r_free= 0.4598   ksol= 0.00   Bsol= 0.00   scale= 0.805    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.263739                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6826 0.99   1424  159 0.3831 0.3786      6.5673       6.554|
|  2:  4.6826 -  3.7353 0.99   1376  148 0.3742 0.3769      6.7377      6.7832|
|  3:  3.7353 -  3.2687 0.99   1343  155 0.4245 0.3818      6.6303      6.6465|
|  4:  3.2687 -  2.9723 0.99   1349  148 0.4393 0.4516      6.4861      6.4718|
|  5:  2.9723 -  2.7607 0.99   1320  148 0.4875 0.5030      6.3507       6.369|
|  6:  2.7607 -  2.5988 0.98   1327  151 0.4896 0.5076      6.2611       6.232|
|  7:  2.5988 -  2.4692 0.99   1322  142 0.5140 0.4713      6.2475      6.1463|
|  8:  2.4692 -  2.3621 0.98   1305  145 0.5202 0.5127      6.1512      6.1918|
|  9:  2.3621 -  2.2715 0.98   1319  146 0.5054 0.4912      6.1124      6.0641|
| 10:  2.2715 -  2.1934 0.98   1288  147 0.5104 0.5394       6.081      6.0957|
| 11:  2.1934 -  2.1250 0.99   1325  143 0.5139 0.4880      6.0228      6.0305|
| 12:  2.1250 -  2.0644 0.98   1289  140 0.5148 0.5768      5.9462      6.0004|
| 13:  2.0644 -  2.0102 0.92   1210  145 0.5298 0.4808      5.8824      5.8209|
| 14:  2.0102 -  1.9613 0.33    433   42 0.5310 0.5819      5.8137      5.7977|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0715 -  4.6826  1424   159  0.71  33.26   0.80     0.74      67007.72|
|  2:  4.6826 -  3.7353  1376   148  0.72  33.35   0.89     0.79      95804.98|
|  3:  3.7353 -  3.2687  1343   155  0.62  42.50   0.84     0.74     105309.67|
|  4:  3.2687 -  2.9723  1349   148  0.52  49.98   0.82     0.64      98862.99|
|  5:  2.9723 -  2.7607  1320   148  0.42  57.90   0.74     0.52      82900.89|
|  6:  2.7607 -  2.5988  1327   151  0.41  59.27   0.74     0.50      71177.52|
|  7:  2.5988 -  2.4692  1322   142  0.42  58.06   0.74     0.47      59406.14|
|  8:  2.4692 -  2.3621  1305   145  0.42  58.23   0.72     0.51      53737.46|
|  9:  2.3621 -  2.2715  1319   146  0.42  58.57   0.76     0.49      47662.02|
| 10:  2.2715 -  2.1934  1288   147  0.39  60.67   0.75     0.47      47452.01|
| 11:  2.1934 -  2.1250  1325   143  0.33  65.23   0.78     0.41      45694.35|
| 12:  2.1250 -  2.0644  1289   140  0.27  70.22   0.75     0.34      45614.43|
| 13:  2.0644 -  2.0102  1210   145  0.25  71.30   0.74     0.32      39788.33|
| 14:  2.0102 -  1.9613   433    42  0.29  68.18   0.68     0.34      31864.08|
|alpha:            min =        0.32 max =            0.79 mean =         0.53|
|beta:             min =    31864.08 max =       105309.67 mean =     65788.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.98 mean =        55.23|
|phase err.(test): min =        0.00 max =           89.97 mean =        55.44|
|-----------------------------------------------------------------------------|

============================== 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 = 12.779225             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.482   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.074495              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.569   (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:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      700 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1520 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2649 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3940 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5068 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6573 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7749 |
|-----------------------------------------------------------------------------|
|-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 |       53.619 |
| 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 |       1.799 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    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 = 11.857)------------------------------------------|
|    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 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4702   r_free= 0.4676   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.267004                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4552   r_free= 0.4506   ksol= 0.33   Bsol= 7.45   scale= 1.008    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.59,7.67,9.30,0.00,0.00,0.00); trace/3= 8.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.261078                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.350825             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.546   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.005474              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.762   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4552      final r-factor (work) = 0.3689          |
| start r-factor (free) = 0.4506      final r-factor (free) = 0.4000          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.0393 = 10.35 * 0.50 * 6.2643 + 1.00 * 53.6189                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.0253 = 10.35 * 0.50 * 6.1621 + 1.00 * 0.1341                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3689      final r-factor (work) = 0.3215          |
| start r-factor (free) = 0.4000      final r-factor (free) = 0.3780          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2101 = 1.01 * 1.00 * 6.1621 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1078 = 1.01 * 1.00 * 6.0594 + 1.00 * 0.0152                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.84   11.91    None  None   None       |
|    all(noH): 2823   0      0.00    66.84   11.91    None  None   None       |
|    Sol.    : 438    0      0.00    65.29   25.89    None  None   None       |
|    Mac.    : 2385   0      0.00    66.84   9.34     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.684: 1144   |   5:    33.419 -  40.103:   86        |
|      1:     6.684 -  13.368:  735   |   6:    40.103 -  46.787:   50        |
|      2:    13.368 -  20.051:  426   |   7:    46.787 -  53.470:   15        |
|      3:    20.051 -  26.735:  206   |   8:    53.470 -  60.154:    7        |
|      4:    26.735 -  33.419:  150   |   9:    60.154 -  66.838:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3215 r_free = 0.3780             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3209 r_free = 0.3782             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3209   r_free= 0.3782   ksol= 0.33   Bsol= 7.45   scale= 1.099    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.59,7.67,9.30,0.00,0.00,0.00); trace/3= 8.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.034525                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3170   r_free= 0.3745   ksol= 0.32   Bsol= 34.71   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.67,3.80,6.02,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.034179                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.151207              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.545   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.519394              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.641  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3170      final r-factor (work) = 0.2338          |
| start r-factor (free) = 0.3745      final r-factor (free) = 0.2951          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7370 = 5.15 * 0.50 * 6.0579 + 1.00 * 0.1341                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2996 = 5.15 * 0.50 * 5.9127 + 1.00 * 0.0709                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2338      final r-factor (work) = 0.2138          |
| start r-factor (free) = 0.2951      final r-factor (free) = 0.2728          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1931 = 0.52 * 1.00 * 5.9127 + 1.00 * 0.1221                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9965 = 0.52 * 1.00 * 5.7481 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.91   12.15    None  None   None       |
|    all(noH): 2823   0      0.00    68.91   12.15    None  None   None       |
|    Sol.    : 438    0      1.07    68.42   31.08    None  None   None       |
|    Mac.    : 2385   0      0.00    68.91   8.68     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.891: 1279   |   5:    34.453 -  41.343:  119        |
|      1:     6.891 -  13.781:  764   |   6:    41.343 -  48.234:   74        |
|      2:    13.781 -  20.672:  271   |   7:    48.234 -  55.125:   29        |
|      3:    20.672 -  27.562:  135   |   8:    55.125 -  62.015:    7        |
|      4:    27.562 -  34.453:  142   |   9:    62.015 -  68.906:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2138 r_free = 0.2728             target_work(ml) = 5.711         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2135 r_free = 0.2727             target_work(ml) = 5.710         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2135   r_free= 0.2727   ksol= 0.32   Bsol= 34.71   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.67,3.80,6.02,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.710206                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2125   r_free= 0.2700   ksol= 0.33   Bsol= 43.65   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,2.58,3.89,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.709021                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.970837              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.723  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.572169              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.867  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2125      final r-factor (work) = 0.1552          |
| start r-factor (free) = 0.2700      final r-factor (free) = 0.2047          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4945 = 3.97 * 0.50 * 5.7538 + 1.00 * 0.0709                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1603 = 3.97 * 0.50 * 5.5876 + 1.00 * 0.0665                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1552      final r-factor (work) = 0.1390          |
| start r-factor (free) = 0.2047      final r-factor (free) = 0.1897          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.9709 = 3.57 * 1.00 * 5.5876 + 1.00 * 0.0109                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.2268 = 3.57 * 1.00 * 5.3781 + 1.00 * 0.0153                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.33   13.47    None  None   None       |
|    all(noH): 2823   0      0.00    89.33   13.47    None  None   None       |
|    Sol.    : 438    0      2.16    87.42   39.28    None  None   None       |
|    Mac.    : 2385   0      0.00    89.33   8.73     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.933: 1642   |   5:    44.663 -  53.596:   93        |
|      1:     8.933 -  17.865:  575   |   6:    53.596 -  62.529:   62        |
|      2:    17.865 -  26.798:  178   |   7:    62.529 -  71.461:   35        |
|      3:    26.798 -  35.731:  102   |   8:    71.461 -  80.394:   15        |
|      4:    35.731 -  44.663:  115   |   9:    80.394 -  89.326:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1390 r_free = 0.1897             target_work(ml) = 5.338         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1388 r_free = 0.1894             target_work(ml) = 5.337         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1388   r_free= 0.1894   ksol= 0.33   Bsol= 43.65   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,2.58,3.89,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.336575                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1387   r_free= 0.1894   ksol= 0.33   Bsol= 43.65   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.59,2.31,3.00,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.336665                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.850066              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.321  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.311859              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.216  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1387      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1894      final r-factor (free) = 0.1708          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4240 = 3.85 * 0.50 * 5.3804 + 1.00 * 0.0665                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2437 = 3.85 * 0.50 * 5.2826 + 1.00 * 0.0746                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1708      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6626 = 0.31 * 1.00 * 5.2826 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6373 = 0.31 * 1.00 * 5.2146 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.89   12.73    None  None   None       |
|    all(noH): 2823   0      0.00    91.89   12.73    None  None   None       |
|    Sol.    : 438    0      1.87    79.18   36.01    None  None   None       |
|    Mac.    : 2385   0      0.00    91.89   8.45     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.189: 1707   |   5:    45.945 -  55.134:   73        |
|      1:     9.189 -  18.378:  585   |   6:    55.134 -  64.323:   47        |
|      2:    18.378 -  27.567:  145   |   7:    64.323 -  73.511:   13        |
|      3:    27.567 -  36.756:  135   |   8:    73.511 -  82.700:    9        |
|      4:    36.756 -  45.945:  107   |   9:    82.700 -  91.889:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1184 r_free = 0.1647             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1182 r_free = 0.1643             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1643   ksol= 0.33   Bsol= 43.65   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.59,2.31,3.00,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.194421                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1642   ksol= 0.33   Bsol= 43.65   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.38,2.22,2.74,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.194270                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.664254              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.622  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.190847              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.096  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1182      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0204 = 2.66 * 0.50 * 5.2141 + 1.00 * 0.0746                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9706 = 2.66 * 0.50 * 5.1815 + 1.00 * 0.0682                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9999 = 0.19 * 1.00 * 5.1815 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0041 = 0.19 * 1.00 * 5.1699 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.63   12.63    None  None   None       |
|    all(noH): 2823   0      0.00    91.63   12.63    None  None   None       |
|    Sol.    : 438    0      1.88    78.77   35.45    None  None   None       |
|    Mac.    : 2385   0      0.00    91.63   8.44     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.163: 1723   |   5:    45.816 -  54.979:   73        |
|      1:     9.163 -  18.326:  580   |   6:    54.979 -  64.142:   43        |
|      2:    18.326 -  27.490:  144   |   7:    64.142 -  73.306:   11        |
|      3:    27.490 -  36.653:  131   |   8:    73.306 -  82.469:    9        |
|      4:    36.653 -  45.816:  107   |   9:    82.469 -  91.632:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1141 r_free = 0.1588             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1140 r_free = 0.1587             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1587   ksol= 0.33   Bsol= 43.65   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.38,2.22,2.74,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.165958                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6826 0.99   1424  159 0.0994 0.1319      5.3906      5.5563|
|  2:  4.6826 -  3.7353 0.99   1376  148 0.0877 0.1128      5.4471      5.6549|
|  3:  3.7353 -  3.2687 0.99   1343  155 0.1068 0.1633      5.4745      5.8867|
|  4:  3.2687 -  2.9723 0.99   1349  148 0.1249 0.1506      5.4677      5.5828|
|  5:  2.9723 -  2.7607 0.99   1320  148 0.1318 0.1701      5.3273      5.5175|
|  6:  2.7607 -  2.5988 0.98   1327  151 0.1269 0.1859      5.2293      5.4756|
|  7:  2.5988 -  2.4692 0.99   1322  142 0.1273 0.1703      5.1883      5.4108|
|  8:  2.4692 -  2.3621 0.98   1305  145 0.1156 0.1690      5.0494      5.3009|
|  9:  2.3621 -  2.2715 0.98   1319  146 0.1196 0.1869      5.0361      5.3276|
| 10:  2.2715 -  2.1934 0.98   1288  147 0.1173 0.1694      4.9815      5.2109|
| 11:  2.1934 -  2.1250 0.99   1325  143 0.1183 0.1820      4.9606      5.2905|
| 12:  2.1250 -  2.0644 0.98   1289  140 0.1166 0.1658      4.8894      5.0839|
| 13:  2.0644 -  2.0102 0.92   1210  145 0.1199 0.1808      4.8024      5.0541|
| 14:  2.0102 -  1.9613 0.33    433   42 0.1070 0.1634      4.6454      4.8687|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0715 -  4.6826  1424   159  0.94   8.83   0.98     0.96       7224.39|
|  2:  4.6826 -  3.7353  1376   148  0.95   8.17   1.01     1.00       9143.83|
|  3:  3.7353 -  3.2687  1343   155  0.93  11.67   1.03     1.02      10547.09|
|  4:  3.2687 -  2.9723  1349   148  0.92  14.13   1.01     0.98      10533.49|
|  5:  2.9723 -  2.7607  1320   148  0.90  16.16   0.99     0.97       8339.47|
|  6:  2.7607 -  2.5988  1327   151  0.89  16.68   0.99     0.96       7342.93|
|  7:  2.5988 -  2.4692  1322   142  0.91  15.48   0.99     0.97       6425.43|
|  8:  2.4692 -  2.3621  1305   145  0.90  15.69   0.99     0.95       5215.04|
|  9:  2.3621 -  2.2715  1319   146  0.90  16.02   1.01     0.99       5055.50|
| 10:  2.2715 -  2.1934  1288   147  0.91  15.56   1.00     0.97       4549.87|
| 11:  2.1934 -  2.1250  1325   143  0.89  16.81   1.00     0.96       4563.00|
| 12:  2.1250 -  2.0644  1289   140  0.90  16.29   1.01     1.01       4103.60|
| 13:  2.0644 -  2.0102  1210   145  0.91  15.78   1.00     0.99       3332.59|
| 14:  2.0102 -  1.9613   433    42  0.90  15.95   1.00     0.97       2513.54|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2513.54 max =        10547.09 mean =      6595.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.37|
|phase err.(test): min =        0.00 max =           89.19 mean =        13.76|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1592   ksol= 0.32   Bsol= 46.90   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.08,-0.19,0.28,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167175                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1592   ksol= 0.32   Bsol= 46.90   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.08,-0.19,0.28,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167175                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6826 0.99   1424  159 0.0983 0.1335      5.3858      5.5683|
|  2:  4.6826 -  3.7353 0.99   1376  148 0.0888 0.1145      5.4595      5.6685|
|  3:  3.7353 -  3.2687 0.99   1343  155 0.1076 0.1637      5.4808      5.8853|
|  4:  3.2687 -  2.9723 0.99   1349  148 0.1254 0.1505      5.4706       5.584|
|  5:  2.9723 -  2.7607 0.99   1320  148 0.1323 0.1696      5.3285      5.5138|
|  6:  2.7607 -  2.5988 0.98   1327  151 0.1269 0.1855      5.2285      5.4776|
|  7:  2.5988 -  2.4692 0.99   1322  142 0.1274 0.1702      5.1886      5.4105|
|  8:  2.4692 -  2.3621 0.98   1305  145 0.1156 0.1696      5.0498      5.3038|
|  9:  2.3621 -  2.2715 0.98   1319  146 0.1193 0.1874       5.035      5.3284|
| 10:  2.2715 -  2.1934 0.98   1288  147 0.1169 0.1695      4.9804      5.2116|
| 11:  2.1934 -  2.1250 0.99   1325  143 0.1180 0.1821      4.9601      5.2913|
| 12:  2.1250 -  2.0644 0.98   1289  140 0.1165 0.1659      4.8898      5.0849|
| 13:  2.0644 -  2.0102 0.92   1210  145 0.1198 0.1813      4.8026      5.0543|
| 14:  2.0102 -  1.9613 0.33    433   42 0.1071 0.1639      4.6461      4.8708|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0715 -  4.6826  1424   159  0.94   9.10   0.98     0.96       7414.54|
|  2:  4.6826 -  3.7353  1376   148  0.95   8.34   1.01     1.00       9390.44|
|  3:  3.7353 -  3.2687  1343   155  0.93  11.79   1.03     1.02      10767.00|
|  4:  3.2687 -  2.9723  1349   148  0.92  14.13   1.00     0.98      10517.66|
|  5:  2.9723 -  2.7607  1320   148  0.90  16.13   0.99     0.96       8319.34|
|  6:  2.7607 -  2.5988  1327   151  0.89  16.71   0.98     0.96       7345.39|
|  7:  2.5988 -  2.4692  1322   142  0.91  15.50   0.99     0.97       6444.50|
|  8:  2.4692 -  2.3621  1305   145  0.90  15.72   0.98     0.95       5238.15|
|  9:  2.3621 -  2.2715  1319   146  0.90  16.04   1.01     0.98       5062.64|
| 10:  2.2715 -  2.1934  1288   147  0.90  15.57   1.00     0.97       4554.87|
| 11:  2.1934 -  2.1250  1325   143  0.89  16.81   1.00     0.96       4564.02|
| 12:  2.1250 -  2.0644  1289   140  0.90  16.30   1.01     1.00       4111.64|
| 13:  2.0644 -  2.0102  1210   145  0.91  15.81   1.00     0.99       3339.92|
| 14:  2.0102 -  1.9613   433    42  0.90  15.96   0.99     0.97       2520.70|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2520.70 max =        10767.00 mean =      6649.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.43|
|phase err.(test): min =        0.00 max =           88.95 mean =        13.82|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.34    93.97   14.96    None  None   None       |
|    all(noH): 2823   0      2.34    93.97   14.96    None  None   None       |
|    Sol.    : 438    0      4.22    81.11   37.78    None  None   None       |
|    Mac.    : 2385   0      2.34    93.97   10.77    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:     2.337 -  11.500: 1723   |   5:    48.153 -  57.316:   73        |
|      1:    11.500 -  20.664:  580   |   6:    57.316 -  66.479:   43        |
|      2:    20.664 -  29.827:  144   |   7:    66.479 -  75.643:   11        |
|      3:    29.827 -  38.990:  131   |   8:    75.643 -  84.806:    9        |
|      4:    38.990 -  48.153:  107   |   9:    84.806 -  93.969:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.402 - 5.639
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 321 from: 327
   mapped sites are within: 0.731 - 5.639

peak=   10.495 closest distance to " CG2 VAL A 230 " =    1.465
peak=    7.319 closest distance to " CG2 VAL A 296 " =    1.129
peak=    6.920 closest distance to " NH2 ARG A  56 " =    2.285
peak=    5.897 closest distance to " O   HOH Z 278 " =    1.107
peak=    5.825 closest distance to " CG  LEU A   5 " =    1.222
peak=    5.676 closest distance to " CD2 LEU A   5 " =    1.234
peak=    5.539 closest distance to " O   HOH Z  37 " =    1.270
peak=    5.197 closest distance to " CB  GLN A 223 " =    1.415
peak=    5.147 closest distance to " CG  LEU A 228 " =    1.265
peak=    5.085 closest distance to " NE2 GLN A  11 " =    1.146
peak=    5.014 closest distance to " CB  SER A  63 " =    1.322
peak=    4.760 closest distance to " CG  PRO A 213 " =    1.230
peak=    4.749 closest distance to " O   HOH Z 132 " =    0.985
peak=    4.706 closest distance to " CB  GLN A 183 " =    1.231
peak=    4.693 closest distance to " O   HOH Z 126 " =    1.838
peak=    4.596 closest distance to " O   HOH Z 427 " =    2.958
peak=    4.594 closest distance to " O   HOH Z 247 " =    1.334
peak=    4.584 closest distance to " O   HOH Z 368 " =    2.088
peak=    4.572 closest distance to " CB  VAL A 230 " =    1.246
peak=    4.570 closest distance to " C   PRO A 198 " =    1.541
peak=    4.563 closest distance to " CB  VAL A 296 " =    1.131
peak=    4.517 closest distance to " CB  SER A   3 " =    1.438
peak=    4.502 closest distance to " OD1 ASN A  69 " =    2.645
peak=    4.501 closest distance to " O   HOH Z 232 " =    2.308
peak=    4.481 closest distance to " CB  GLU A 152 " =    1.163
peak=    4.477 closest distance to " CD1AILE A 234 " =    0.990
peak=    4.466 closest distance to " CD2 LEU A 228 " =    1.236
peak=    4.464 closest distance to " O   HOH Z 108 " =    1.476
peak=    4.400 closest distance to " O   HOH Z 263 " =    1.618
peak=    4.376 closest distance to " CB  TYR A 169 " =    0.840
peak=    4.373 closest distance to " O   HOH Z 193 " =    1.862
peak=    4.356 closest distance to " O   HOH Z 371 " =    3.272
peak=    4.328 closest distance to " O   HOH Z  48 " =    1.626
peak=    4.303 closest distance to " CG  PRO A 198 " =    1.393
peak=    4.300 closest distance to " O   HOH Z 411 " =    3.750
peak=    4.258 closest distance to " O   HOH Z 236 " =    1.856
peak=    4.238 closest distance to " CB  ASN A 148 " =    1.441
peak=    4.221 closest distance to " O   HOH Z 316 " =    2.946
peak=    4.216 closest distance to " O   HOH Z 303 " =    2.069
peak=    4.207 closest distance to " CB  GLU A 128 " =    1.062
peak=    4.184 closest distance to " O   HOH Z 209 " =    2.396
peak=    4.172 closest distance to " O   HOH Z  97 " =    1.970
peak=    4.166 closest distance to " O   HOH Z 202 " =    1.149
peak=    4.166 closest distance to " CG  PRO A 243 " =    1.185
peak=    4.157 closest distance to " O   HOH Z 272 " =    1.891
peak=    4.145 closest distance to " O   HOH Z 369 " =    1.913
peak=    4.136 closest distance to " O   HOH Z 126 " =    1.510
peak=    4.121 closest distance to " O   HOH Z 298 " =    1.802
peak=    4.116 closest distance to " CB  VAL A 265 " =    1.252
peak=    4.115 closest distance to " CG  ARG A  66 " =    2.626
peak=    4.108 closest distance to " O   HOH Z 260 " =    1.151
peak=    4.089 closest distance to " O   HOH Z 280 " =    2.973
peak=    4.081 closest distance to " O   HOH Z 124 " =    1.384
peak=    4.033 closest distance to " O   HOH Z 183 " =    1.372
peak=    4.032 closest distance to " CA  ALA A  21 " =    1.157
peak=    4.027 closest distance to " O   HOH Z  80 " =    1.666
peak=    4.016 closest distance to " CB  ARG A 275 " =    0.833
peak=    4.015 closest distance to " O   HOH Z 144 " =    1.540
peak=    4.010 closest distance to " O   HOH Z 193 " =    1.977
peak=    4.007 closest distance to " O   HOH Z 126 " =    1.614
peak=    4.004 closest distance to " O   SER A  87 " =    2.291
peak=    3.983 closest distance to " CD1 LEU A 300 " =    1.163
peak=    3.971 closest distance to " CB  VAL A 202 " =    1.525
peak=    3.967 closest distance to " O   HOH Z  78 " =    1.786
peak=    3.964 closest distance to " O   HOH Z  88 " =    3.264
peak=    3.955 closest distance to " NH2BARG A 102 " =    0.883
peak=    3.949 closest distance to " CB  TRP A 266 " =    0.951
peak=    3.939 closest distance to " OD2 ASP A 286 " =    2.840
peak=    3.929 closest distance to " O   HOH Z  15 " =    2.045
peak=    3.923 closest distance to " CA  ALA A  51 " =    1.040
peak=    3.915 closest distance to " CB  ARG A  79 " =    1.450
peak=    3.913 closest distance to " O   HOH Z  21 " =    1.725
peak=    3.911 closest distance to " CA  THR A 221 " =    0.897
peak=    3.903 closest distance to " O   HOH Z 423 " =    1.809
peak=    3.897 closest distance to " O   HOH Z 346 " =    1.568
peak=    3.885 closest distance to " O   HOH Z 425 " =    1.384
peak=    3.884 closest distance to " CG  ARG A 138 " =    1.032
peak=    3.871 closest distance to " CA  TYR A  30 " =    0.936
peak=    3.861 closest distance to " O   HOH Z 112 " =    1.247
peak=    3.852 closest distance to " CB  GLU A 277 " =    3.569
peak=    3.847 closest distance to " CA  LEU A 282 " =    1.004
peak=    3.835 closest distance to " O   HOH Z  20 " =    1.848
peak=    3.830 closest distance to " NH1 ARG A  56 " =    0.895
peak=    3.822 closest distance to " CB  LEU A 228 " =    1.317
peak=    3.816 closest distance to " CG1BVAL A  72 " =    1.567
peak=    3.815 closest distance to " O   HOH Z 133 " =    1.698
peak=    3.807 closest distance to " O   HOH Z 295 " =    1.571
peak=    3.804 closest distance to " CG  PRO A 280 " =    0.750
peak=    3.801 closest distance to " O   HOH Z 403 " =    1.688
peak=    3.797 closest distance to " O   HOH Z 426 " =    1.506
peak=    3.794 closest distance to " O   HOH Z 193 " =    1.650
peak=    3.787 closest distance to " CG2 THR A 221 " =    1.027
peak=    3.785 closest distance to " O   HOH Z 234 " =    3.703
peak=    3.785 closest distance to " O   HOH Z 128 " =    1.989
peak=    3.781 closest distance to " O   HOH Z  63 " =    2.084
peak=    3.774 closest distance to " NH2 ARG A 156 " =    1.204
peak=    3.771 closest distance to " CD BLYS A 290 " =    1.071
peak=    3.762 closest distance to " O   HOH Z 344 " =    2.889
peak=    3.762 closest distance to " CG  GLN A  88 " =    1.084
peak=    3.760 closest distance to " CB  LEU A 143 " =    1.154
peak=    3.758 closest distance to " O   HOH Z 345 " =    3.399
peak=    3.750 closest distance to " O   HOH Z  61 " =    1.569
peak=    3.748 closest distance to " O   HOH Z 132 " =    2.323
peak=    3.745 closest distance to " CD2 LEU A 255 " =    1.492
peak=    3.744 closest distance to " O   HOH Z 132 " =    2.659
peak=    3.733 closest distance to " CB  SER A 216 " =    0.772
peak=    3.732 closest distance to " O   HOH Z  54 " =    1.544
peak=    3.732 closest distance to " O   HOH Z 134 " =    1.478
peak=    3.729 closest distance to " O   HOH Z  55 " =    2.260
peak=    3.724 closest distance to " O   HOH Z 189 " =    2.605
peak=    3.718 closest distance to " CB  ALA A 291 " =    1.394
peak=    3.716 closest distance to " O   HOH Z 389 " =    1.925
peak=    3.714 closest distance to " O   HOH Z 135 " =    1.911
peak=    3.691 closest distance to " O   HOH Z  43 " =    1.988
peak=    3.688 closest distance to " O   HOH Z  92 " =    0.860
peak=    3.687 closest distance to " O   HOH Z 116 " =    1.686
peak=    3.676 closest distance to " O   HOH Z  68 " =    1.637
peak=    3.669 closest distance to " CD  ARG A 159 " =    0.779
peak=    3.669 closest distance to " CG  LEU A 167 " =    1.151
peak=    3.667 closest distance to " O   HOH Z  93 " =    2.574
peak=    3.663 closest distance to " NZ  LYS A 117 " =    3.285
peak=    3.658 closest distance to " O   TRP A 274 " =    1.857
peak=    3.657 closest distance to " O   HOH Z  68 " =    2.057
peak=    3.656 closest distance to " ND2 ASN A 187 " =    1.581
peak=    3.655 closest distance to " O   HOH Z 271 " =    1.978
peak=    3.640 closest distance to " CD  LYS A 119 " =    1.700
peak=    3.630 closest distance to " O   HOH Z 273 " =    2.523
peak=    3.626 closest distance to " O   ALA A 158 " =    1.352
peak=    3.625 closest distance to " O   HOH Z 184 " =    1.596
peak=    3.624 closest distance to " N   ARG A 156 " =    1.317
peak=    3.621 closest distance to " CA  VAL A  41 " =    0.902
peak=    3.617 closest distance to " CB  ASN A 148 " =    1.879
peak=    3.607 closest distance to " CG2 VAL A 174 " =    1.412
peak=    3.597 closest distance to " NE2 GLN A  58 " =    5.639
peak=    3.596 closest distance to " CB  ALA A 248 " =    1.020
peak=    3.594 closest distance to " O   HOH Z 327 " =    2.413
peak=    3.593 closest distance to " CA  ALA A 295 " =    1.018
peak=    3.592 closest distance to " O   HOH Z  30 " =    1.219
peak=    3.587 closest distance to " O   MET A 105 " =    1.769
peak=    3.587 closest distance to " CA  MET A  40 " =    1.083
peak=    3.578 closest distance to " ND1 HIS A  86 " =    1.647
peak=    3.575 closest distance to " O   HOH Z 203 " =    1.695
peak=    3.574 closest distance to " O   HOH Z 171 " =    3.778
peak=    3.570 closest distance to " CG1 ILE A  33 " =    1.337
peak=    3.568 closest distance to " O   HOH Z  66 " =    2.319
peak=    3.565 closest distance to " CB  ASN A  39 " =    0.787
peak=    3.561 closest distance to " CB  ASN A 187 " =    1.021
peak=    3.557 closest distance to " CB  ARG A 139 " =    0.910
peak=    3.554 closest distance to " CA  SER A  87 " =    0.849
peak=    3.553 closest distance to " CZ  PHE A 192 " =    1.016
peak=    3.549 closest distance to " O   HOH Z 180 " =    2.086
peak=    3.548 closest distance to " OD1 ASN A 217 " =    1.704
peak=    3.545 closest distance to " OG  SER A  22 " =    2.814
peak=    3.543 closest distance to " O   HOH Z 281 " =    4.370
peak=    3.539 closest distance to " CD  ARG A 269 " =    0.912
peak=    3.538 closest distance to " CB  TRP A 179 " =    1.389
peak=    3.536 closest distance to " CA  THR A 264 " =    0.804
peak=    3.532 closest distance to " CA  ASN A 215 " =    1.181
peak=    3.514 closest distance to " O   HOH Z   9 " =    2.051
peak=    3.510 closest distance to " O   HOH Z 227 " =    1.698
peak=    3.504 closest distance to " O   HOH Z  61 " =    1.617
peak=    3.499 closest distance to " OE1 GLU A   2 " =    2.174
peak=    3.495 closest distance to " CB  GLN A  88 " =    1.237
peak=    3.495 closest distance to " CA  VAL A 126 " =    0.872
peak=    3.494 closest distance to " CA  ASP A 191 " =    0.731
peak=    3.492 closest distance to " O   HOH Z  59 " =    2.108
peak=    3.487 closest distance to " O   HOH Z 108 " =    2.253
peak=    3.478 closest distance to " CG2 VAL A 257 " =    0.946
peak=    3.477 closest distance to " CG BARG A 102 " =    1.866
peak=    3.475 closest distance to " CG1 ILE A  49 " =    1.466
peak=    3.474 closest distance to " CA  ALA A 154 " =    1.062
peak=    3.466 closest distance to " OG BSER A 164 " =    2.185
peak=    3.466 closest distance to " NH2 ARG A 219 " =    1.800
peak=    3.465 closest distance to " CD1 ILE A  33 " =    1.599
peak=    3.464 closest distance to " O   HOH Z 410 " =    1.551
peak=    3.463 closest distance to " CZ  PHE A 218 " =    1.032
peak=    3.462 closest distance to " O   HOH Z  49 " =    2.483
peak=    3.460 closest distance to " O   HOH Z 163 " =    1.510
peak=    3.459 closest distance to " O   HOH Z 329 " =    3.799
peak=    3.453 closest distance to " N   ASN A  39 " =    1.217
peak=    3.450 closest distance to " O   GLN A  58 " =    1.618
peak=    3.444 closest distance to " O   HOH Z 197 " =    2.936
peak=    3.442 closest distance to " O   HOH Z  44 " =    1.789
peak=    3.441 closest distance to " CG1 VAL A 153 " =    0.992
peak=    3.433 closest distance to " CA  ALA A 158 " =    1.108
peak=    3.430 closest distance to " O   HOH Z 151 " =    1.709
peak=    3.430 closest distance to " CA  GLY A 267 " =    1.052
peak=    3.430 closest distance to " C   ALA A 299 " =    0.981
peak=    3.430 closest distance to " CA  ALA A 248 " =    1.268
peak=    3.425 closest distance to " NZ  LYS A 166 " =    3.149
peak=    3.425 closest distance to " CB  ILE A 234 " =    0.851
peak=    3.424 closest distance to " CD1 LEU A 101 " =    1.182
peak=    3.423 closest distance to " OE1 GLN A  11 " =    1.798
peak=    3.420 closest distance to " CD  LYS A 166 " =    1.351
peak=    3.417 closest distance to " O   HOH Z 118 " =    1.670
peak=    3.416 closest distance to " O   HOH Z  58 " =    1.458
peak=    3.399 closest distance to " O   HOH Z 374 " =    2.505
peak=    3.398 closest distance to " O   HOH Z 313 " =    1.855
peak=    3.393 closest distance to " O   HOH Z 172 " =    3.880
peak=    3.391 closest distance to " O   HOH Z 420 " =    1.912
peak=    3.388 closest distance to " NH2BARG A 145 " =    1.978
peak=    3.386 closest distance to " O   ALA A   1 " =    1.551
peak=    3.386 closest distance to " O   HOH Z 407 " =    2.356
peak=    3.379 closest distance to " O   HOH Z 261 " =    1.797
peak=    3.376 closest distance to " O   HOH Z 128 " =    2.244
peak=    3.372 closest distance to " O   HOH Z 227 " =    2.006
peak=    3.364 closest distance to " O   HOH Z 158 " =    2.924
peak=    3.362 closest distance to " O   HOH Z 437 " =    2.259
peak=    3.360 closest distance to " O   HOH Z 215 " =    1.566
peak=    3.357 closest distance to " CB  LEU A 255 " =    0.893
peak=    3.353 closest distance to " O   HOH Z 276 " =    1.238
peak=    3.353 closest distance to " O   HOH Z 374 " =    1.021
peak=    3.349 closest distance to " CG  MET A 188 " =    1.407
peak=    3.344 closest distance to " O   HOH Z 409 " =    3.158
peak=    3.341 closest distance to " N   PHE A 130 " =    1.306
peak=    3.339 closest distance to " CB  MET A  47 " =    1.075
peak=    3.338 closest distance to " O   HOH Z 383 " =    2.114
peak=    3.335 closest distance to " O   HOH Z 419 " =    1.744
peak=    3.334 closest distance to " CA  TYR A 186 " =    1.387
peak=    3.332 closest distance to " OD1 ASP A 231 " =    1.827
peak=    3.330 closest distance to " O   HOH Z 284 " =    1.461
peak=    3.327 closest distance to " CA  ASN A  74 " =    1.124
peak=    3.327 closest distance to " CB  THR A  31 " =    1.615
peak=    3.321 closest distance to " O   HOH Z  10 " =    1.847
peak=    3.320 closest distance to " CG2AVAL A 121 " =    2.250
peak=    3.319 closest distance to " CA  LYS A 117 " =    1.263
peak=    3.314 closest distance to " O   HOH Z  22 " =    2.076
peak=    3.306 closest distance to " O   HOH Z 145 " =    1.790
peak=    3.306 closest distance to " CE  LYS A  76 " =    0.882
peak=    3.305 closest distance to " NH1AARG A 145 " =    1.044
peak=    3.302 closest distance to " CB  MET A  40 " =    0.920
peak=    3.302 closest distance to " O   HOH Z 156 " =    2.754
peak=    3.301 closest distance to " CB  PRO A 198 " =    0.853
peak=    3.293 closest distance to " O   HOH Z 417 " =    1.966
peak=    3.286 closest distance to " NZ  LYS A  76 " =    1.236
peak=    3.285 closest distance to " CB  GLU A  46 " =    1.054
peak=    3.283 closest distance to " O   HOH Z 151 " =    1.810
peak=    3.280 closest distance to " CA  GLY A 211 " =    1.170
peak=    3.276 closest distance to " O   HOH Z 303 " =    1.779
peak=    3.276 closest distance to " CD1 TRP A 266 " =    1.215
peak=    3.273 closest distance to " CD2 HIS A  81 " =    1.138
peak=    3.273 closest distance to " O   HOH Z   4 " =    1.850
peak=    3.271 closest distance to " CB  ALA A 161 " =    0.908
peak=    3.268 closest distance to " CA  ILE A 106 " =    0.824
peak=    3.259 closest distance to " O   HOH Z 355 " =    1.761
peak=    3.255 closest distance to " CD1 LEU A   5 " =    1.377
peak=    3.252 closest distance to " O   HOH Z 245 " =    1.374
peak=    3.251 closest distance to " O   HOH Z 153 " =    1.795
peak=    3.250 closest distance to " CA  ASN A 176 " =    1.204
peak=    3.249 closest distance to " O   HOH Z 359 " =    1.873
peak=    3.246 closest distance to " O   HOH Z 406 " =    1.625
peak=    3.242 closest distance to " NH1 ARG A  14 " =    0.976
peak=    3.241 closest distance to " N   TYR A  15 " =    0.917
peak=    3.239 closest distance to " NE2 GLN A  58 " =    4.071
peak=    3.239 closest distance to " O   HOH Z 175 " =    3.510
peak=    3.238 closest distance to " O   HOH Z 291 " =    1.604
peak=    3.237 closest distance to " O   HOH Z 403 " =    1.407
peak=    3.231 closest distance to " CB  ILE A 199 " =    0.811
peak=    3.229 closest distance to " O   HOH Z 332 " =    1.555
peak=    3.226 closest distance to " O   HOH Z 334 " =    1.486
peak=    3.224 closest distance to " CB  ALA A 295 " =    1.336
peak=    3.224 closest distance to " O   HOH Z  68 " =    2.642
peak=    3.222 closest distance to " NH2 ARG A  79 " =    1.315
peak=    3.220 closest distance to " O   HOH Z 422 " =    2.683
peak=    3.219 closest distance to " CB  THR A 157 " =    1.059
peak=    3.216 closest distance to " C   LYS A 290 " =    1.325
peak=    3.209 closest distance to " CB  ASN A 142 " =    0.975
peak=    3.206 closest distance to " N   ARG A 190 " =    1.005
peak=    3.205 closest distance to " CG2 THR A 294 " =    1.718
peak=    3.200 closest distance to " O   HOH Z 244 " =    1.585
peak=    3.194 closest distance to " OE1 GLU A 152 " =    0.916
peak=    3.193 closest distance to " O   THR A  31 " =    1.483
peak=    3.189 closest distance to " CG BARG A 275 " =    1.481
peak=    3.177 closest distance to " CA  GLN A 194 " =    1.185
peak=    3.177 closest distance to " NH2BARG A 190 " =    1.756
peak=    3.173 closest distance to " CG2 ILE A 120 " =    1.351
peak=    3.172 closest distance to " CA  ASP A 140 " =    1.192
peak=    3.172 closest distance to " CA  ARG A  36 " =    1.123
peak=    3.170 closest distance to " O   HOH Z 248 " =    1.901
peak=    3.166 closest distance to " CB  SER A 212 " =    1.168
peak=    3.166 closest distance to " CB  LYS A 117 " =    1.172
peak=    3.165 closest distance to " CA  ARG A  56 " =    2.113
peak=    3.165 closest distance to " CB  ARG A 190 " =    1.805
peak=    3.164 closest distance to " OD1BASN A 224 " =    2.192
peak=    3.162 closest distance to " O   HOH Z 423 " =    3.036
peak=    3.160 closest distance to " O   HOH Z  64 " =    2.402
peak=    3.159 closest distance to " C   TYR A 214 " =    1.530
peak=    3.157 closest distance to " CD2 LEU A 167 " =    0.744
peak=    3.157 closest distance to " CB  TYR A  30 " =    1.466
peak=    3.156 closest distance to " CB  SER A 273 " =    0.846
peak=    3.142 closest distance to " O   HOH Z 175 " =    2.149
peak=    3.139 closest distance to " N   SER A 135 " =    1.343
peak=    3.139 closest distance to " O   HOH Z 236 " =    1.616
peak=    3.138 closest distance to " CA  GLN A 223 " =    0.802
peak=    3.131 closest distance to " ND1 HIS A  81 " =    1.603
peak=    3.123 closest distance to " NH2AARG A 190 " =    1.152
peak=    3.122 closest distance to " CA  ALA A 244 " =    1.184
peak=    3.121 closest distance to " CG2 THR A 294 " =    3.898
peak=    3.119 closest distance to " OG  SER A 206 " =    1.230
peak=    3.118 closest distance to " CD  ARG A  14 " =    1.208
peak=    3.115 closest distance to " NE AARG A 275 " =    1.391
peak=    3.112 closest distance to " O   HOH Z 299 " =    2.417
peak=    3.107 closest distance to " CA  LEU A 101 " =    1.545
peak=    3.100 closest distance to " CG  GLU A 277 " =    2.326
peak=    3.098 closest distance to " O   HOH Z 388 " =    2.013
peak=    3.095 closest distance to " CA  LYS A  48 " =    1.336
peak=    3.088 closest distance to " O   HOH Z 367 " =    3.519
peak=    3.088 closest distance to " O   HOH Z 305 " =    3.523
peak=    3.074 closest distance to " O   HOH Z  53 " =    2.549
peak=    3.073 closest distance to " O   HOH Z 166 " =    3.365
peak=    3.073 closest distance to " O   GLN A 278 " =    1.526
peak=    3.063 closest distance to " CB  ALA A 100 " =    1.294
peak=    3.049 closest distance to " CB  LEU A 237 " =    0.974
peak=    3.048 closest distance to " O   HOH Z 217 " =    1.259
peak=    3.047 closest distance to " O   HOH Z 353 " =    2.741
peak=    3.035 closest distance to " NH2AARG A 190 " =    1.504
peak=    3.034 closest distance to " O   HOH Z  68 " =    1.801
peak=    3.031 closest distance to " CB  ILE A  20 " =    1.361
peak=    3.026 closest distance to " O   HOH Z 357 " =    1.846
peak=    3.018 closest distance to " O   HOH Z 140 " =    2.480
peak=    2.993 closest distance to " O   HOH Z  40 " =    1.504

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.598 - 5.493
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 188 from: 190
   mapped sites are within: 0.779 - 5.493

peak=   -5.784 closest distance to " CG2 VAL A 230 " =    0.859
peak=   -4.325 closest distance to " CG  LEU A 101 " =    2.587
peak=   -4.273 closest distance to " CD  ARG A 156 " =    1.993
peak=   -4.263 closest distance to " O   ILE A 109 " =    2.658
peak=   -4.174 closest distance to " O   HOH Z 290 " =    1.125
peak=   -4.061 closest distance to " SG  CYS A 254 " =    3.263
peak=   -4.043 closest distance to " O   HOH Z 231 " =    1.724
peak=   -4.036 closest distance to " O   HOH Z 266 " =    4.497
peak=   -3.997 closest distance to " O   HOH Z  92 " =    1.506
peak=   -3.916 closest distance to " CA  ASP A  27 " =    2.427
peak=   -3.903 closest distance to " CD1 LEU A 228 " =    2.354
peak=   -3.897 closest distance to " CG2 THR A   4 " =    1.973
peak=   -3.848 closest distance to " CG  GLN A 223 " =    2.050
peak=   -3.844 closest distance to " CD1 LEU A 101 " =    2.702
peak=   -3.830 closest distance to " O   PRO A 163 " =    1.983
peak=   -3.824 closest distance to " CE2 TYR A  30 " =    2.842
peak=   -3.814 closest distance to " O   HOH Z 166 " =    1.853
peak=   -3.811 closest distance to " O   HOH Z 377 " =    1.717
peak=   -3.804 closest distance to " CG1 VAL A 296 " =    1.426
peak=   -3.795 closest distance to " N   GLN A  58 " =    1.806
peak=   -3.790 closest distance to " O   HOH Z  13 " =    1.295
peak=   -3.786 closest distance to " O   HOH Z 274 " =    2.885
peak=   -3.779 closest distance to " CG  ASP A 231 " =    0.791
peak=   -3.776 closest distance to " OG ASER A 134 " =    1.455
peak=   -3.754 closest distance to " OG BSER A 134 " =    1.753
peak=   -3.745 closest distance to " CD  GLN A  88 " =    2.292
peak=   -3.738 closest distance to " CD2 LEU A 237 " =    2.754
peak=   -3.734 closest distance to " CD2 LEU A 300 " =    2.837
peak=   -3.734 closest distance to " C   ALA A 158 " =    1.318
peak=   -3.715 closest distance to " N   THR A 157 " =    1.516
peak=   -3.715 closest distance to " CG2 VAL A 296 " =    1.348
peak=   -3.710 closest distance to " O   HOH Z 275 " =    1.497
peak=   -3.694 closest distance to " C   ASN A 187 " =    1.765
peak=   -3.688 closest distance to " CG  LEU A 228 " =    0.925
peak=   -3.683 closest distance to " CG  ASP A  50 " =    2.313
peak=   -3.675 closest distance to " CB  PRO A 163 " =    2.633
peak=   -3.674 closest distance to " O   HOH Z 436 " =    1.504
peak=   -3.673 closest distance to " ND2 ASN A  60 " =    1.624
peak=   -3.673 closest distance to " N   ALA A  43 " =    2.375
peak=   -3.670 closest distance to " CD  GLN A  88 " =    0.779
peak=   -3.638 closest distance to " N   HIS A 115 " =    2.149
peak=   -3.635 closest distance to " NH2 ARG A  79 " =    1.859
peak=   -3.628 closest distance to " O   ALA A 161 " =    1.418
peak=   -3.628 closest distance to " C   ASN A 285 " =    2.480
peak=   -3.626 closest distance to " CB  ALA A  43 " =    2.436
peak=   -3.626 closest distance to " OG  SER A  87 " =    1.456
peak=   -3.625 closest distance to " CG  TRP A 266 " =    1.631
peak=   -3.625 closest distance to " O   HOH Z 388 " =    1.943
peak=   -3.612 closest distance to " O   HOH Z  43 " =    1.722
peak=   -3.603 closest distance to " N   ALA A 226 " =    2.092
peak=   -3.600 closest distance to " O   HOH Z  71 " =    1.061
peak=   -3.582 closest distance to " CG  MET A 105 " =    0.976
peak=   -3.581 closest distance to " CD  LYS A 289 " =    2.539
peak=   -3.579 closest distance to " NH2AARG A 275 " =    5.281
peak=   -3.574 closest distance to " O   GLY A 211 " =    1.467
peak=   -3.571 closest distance to " CH2 TRP A 179 " =    1.296
peak=   -3.563 closest distance to " O   HOH Z 407 " =    3.221
peak=   -3.545 closest distance to " O   HOH Z  52 " =    1.513
peak=   -3.536 closest distance to " O   GLY A 196 " =    1.162
peak=   -3.528 closest distance to " OG BSER A 134 " =    1.237
peak=   -3.516 closest distance to " O   HOH Z  98 " =    1.957
peak=   -3.514 closest distance to " O   VAL A  67 " =    2.601
peak=   -3.499 closest distance to " CG  PRO A 163 " =    2.504
peak=   -3.494 closest distance to " O   PRO A 198 " =    1.270
peak=   -3.492 closest distance to " O   HOH Z 266 " =    4.566
peak=   -3.487 closest distance to " O   HOH Z  63 " =    1.068
peak=   -3.485 closest distance to " CB  PRO A 243 " =    2.632
peak=   -3.484 closest distance to " ND2 ASN A  45 " =    0.996
peak=   -3.484 closest distance to " O   HOH Z  38 " =    1.706
peak=   -3.479 closest distance to " O   HOH Z 184 " =    1.604
peak=   -3.479 closest distance to " O   HOH Z 292 " =    4.504
peak=   -3.471 closest distance to " CG2 VAL A 112 " =    2.585
peak=   -3.470 closest distance to " O   HOH Z 166 " =    1.478
peak=   -3.470 closest distance to " OG  SER A  26 " =    1.100
peak=   -3.460 closest distance to " O   HOH Z 389 " =    1.869
peak=   -3.452 closest distance to " CB  ASN A  39 " =    2.039
peak=   -3.452 closest distance to " CB  ALA A 248 " =    1.977
peak=   -3.447 closest distance to " CD  ARG A 139 " =    1.629
peak=   -3.445 closest distance to " O   HOH Z 252 " =    4.093
peak=   -3.436 closest distance to " CE1 TYR A 169 " =    2.559
peak=   -3.434 closest distance to " CG  GLU A  53 " =    1.556
peak=   -3.431 closest distance to " O   HOH Z 151 " =    1.480
peak=   -3.430 closest distance to " OD1 ASN A 148 " =    1.595
peak=   -3.427 closest distance to " N   SER A 276 " =    1.343
peak=   -3.425 closest distance to " CB  TYR A  15 " =    2.182
peak=   -3.409 closest distance to " NH2 ARG A  66 " =    2.012
peak=   -3.408 closest distance to " O   HOH Z 353 " =    2.209
peak=   -3.403 closest distance to " O   HOH Z 234 " =    4.207
peak=   -3.400 closest distance to " O   HOH Z 351 " =    1.370
peak=   -3.397 closest distance to " CA  VAL A 232 " =    2.409
peak=   -3.397 closest distance to " O   HOH Z 241 " =    1.281
peak=   -3.397 closest distance to " O   HOH Z 394 " =    1.530
peak=   -3.396 closest distance to " CZ  TYR A 172 " =    1.644
peak=   -3.393 closest distance to " CD2 LEU A 237 " =    2.802
peak=   -3.388 closest distance to " CB  PHE A 283 " =    2.793
peak=   -3.381 closest distance to " CE2 PHE A 218 " =    2.544
peak=   -3.378 closest distance to " C   HIS A 108 " =    1.180
peak=   -3.375 closest distance to " O   HOH Z 211 " =    1.579
peak=   -3.375 closest distance to " CD2 TYR A 293 " =    2.138
peak=   -3.364 closest distance to " O   HOH Z  98 " =    2.216
peak=   -3.356 closest distance to " O   SER A 271 " =    2.242
peak=   -3.351 closest distance to " O   HOH Z 185 " =    2.328
peak=   -3.349 closest distance to " ND2 ASN A  60 " =    1.550
peak=   -3.340 closest distance to " O   HOH Z 426 " =    1.645
peak=   -3.331 closest distance to " O   HOH Z 283 " =    1.667
peak=   -3.329 closest distance to " CB  CYS A 254 " =    2.261
peak=   -3.325 closest distance to " CD2 LEU A 167 " =    1.806
peak=   -3.325 closest distance to " O   ALA A   7 " =    1.700
peak=   -3.323 closest distance to " OE1 GLN A  88 " =    1.106
peak=   -3.318 closest distance to " O   HOH Z  11 " =    1.797
peak=   -3.317 closest distance to " O   HOH Z 435 " =    2.744
peak=   -3.315 closest distance to " O   HOH Z 231 " =    1.187
peak=   -3.315 closest distance to " CZ  TYR A 169 " =    1.776
peak=   -3.309 closest distance to " O   HOH Z 148 " =    1.778
peak=   -3.308 closest distance to " O   VAL A  67 " =    2.756
peak=   -3.305 closest distance to " CG  GLU A   2 " =    1.805
peak=   -3.303 closest distance to " O   HOH Z 396 " =    1.672
peak=   -3.303 closest distance to " CB  GLN A  55 " =    1.459
peak=   -3.302 closest distance to " CE3 TRP A 150 " =    2.046
peak=   -3.300 closest distance to " CG  ASN A  45 " =    1.712
peak=   -3.285 closest distance to " CD1 ILE A 263 " =    2.446
peak=   -3.284 closest distance to " O   HOH Z 385 " =    2.074
peak=   -3.283 closest distance to " CD1 PHE A  59 " =    1.905
peak=   -3.265 closest distance to " O   HOH Z 134 " =    2.491
peak=   -3.261 closest distance to " O   GLY A 203 " =    2.478
peak=   -3.261 closest distance to " O   HOH Z 350 " =    1.913
peak=   -3.259 closest distance to " O   HOH Z 103 " =    1.850
peak=   -3.258 closest distance to " CA  ASP A 298 " =    1.088
peak=   -3.258 closest distance to " OG  SER A  97 " =    2.203
peak=   -3.257 closest distance to " O   HOH Z  10 " =    1.573
peak=   -3.257 closest distance to " O   HOH Z 128 " =    4.112
peak=   -3.256 closest distance to " O   HOH Z 132 " =    1.055
peak=   -3.249 closest distance to " N   PHE A  59 " =    2.145
peak=   -3.247 closest distance to " CB  ALA A 291 " =    2.257
peak=   -3.245 closest distance to " CZ3 TRP A 274 " =    1.083
peak=   -3.244 closest distance to " O   GLY A  80 " =    2.502
peak=   -3.242 closest distance to " CE BMET A  47 " =    1.700
peak=   -3.234 closest distance to " CE  LYS A  76 " =    2.733
peak=   -3.233 closest distance to " CG  GLU A 277 " =    1.161
peak=   -3.227 closest distance to " C   LEU A 143 " =    1.297
peak=   -3.224 closest distance to " ND2 ASN A 249 " =    2.123
peak=   -3.215 closest distance to " OG  SER A  62 " =    1.511
peak=   -3.213 closest distance to " O   VAL A 197 " =    1.355
peak=   -3.213 closest distance to " C   MET A 188 " =    1.485
peak=   -3.212 closest distance to " NH1 ARG A  56 " =    2.504
peak=   -3.209 closest distance to " CG  LYS A 193 " =    2.393
peak=   -3.205 closest distance to " O   HOH Z 177 " =    1.529
peak=   -3.203 closest distance to " O   HOH Z 292 " =    2.900
peak=   -3.202 closest distance to " O   PRO A 198 " =    1.234
peak=   -3.199 closest distance to " CG1 VAL A 197 " =    2.259
peak=   -3.196 closest distance to " OXT GLY A 302 " =    3.373
peak=   -3.195 closest distance to " CA  GLY A 133 " =    1.909
peak=   -3.191 closest distance to " CB  ASP A 132 " =    2.212
peak=   -3.190 closest distance to " O   HOH Z 191 " =    5.493
peak=   -3.187 closest distance to " CB  ALA A 227 " =    2.380
peak=   -3.185 closest distance to " O   HOH Z 389 " =    4.401
peak=   -3.183 closest distance to " O   ALA A 100 " =    2.466
peak=   -3.167 closest distance to " CD  GLU A 236 " =    1.029
peak=   -3.164 closest distance to " OG  SER A 206 " =    1.742
peak=   -3.159 closest distance to " CB  ASP A 132 " =    2.218
peak=   -3.154 closest distance to " O   HOH Z 219 " =    1.045
peak=   -3.154 closest distance to " CD1 ILE A 239 " =    2.073
peak=   -3.152 closest distance to " O   HOH Z 310 " =    1.950
peak=   -3.151 closest distance to " CA  SER A  62 " =    2.498
peak=   -3.150 closest distance to " OD1 ASN A 249 " =    1.163
peak=   -3.148 closest distance to " CE  MET A 105 " =    2.014
peak=   -3.146 closest distance to " CB  VAL A 296 " =    1.231
peak=   -3.143 closest distance to " N   GLN A  77 " =    1.671
peak=   -3.139 closest distance to " O   HOH Z  98 " =    1.522
peak=   -3.136 closest distance to " O   THR A  18 " =    1.617
peak=   -3.134 closest distance to " O   HOH Z 423 " =    2.142
peak=   -3.131 closest distance to " O   HOH Z  97 " =    2.278
peak=   -3.127 closest distance to " O   HOH Z 119 " =    2.532
peak=   -3.123 closest distance to " O   HOH Z 313 " =    1.893
peak=   -3.123 closest distance to " OH  TYR A 214 " =    1.282
peak=   -3.121 closest distance to " N   ALA A 248 " =    1.626
peak=   -3.117 closest distance to " O   VAL A 174 " =    2.046
peak=   -3.109 closest distance to " CZ  PHE A  59 " =    1.576
peak=   -3.108 closest distance to " CD1 ILE A 199 " =    2.495
peak=   -3.106 closest distance to " O   HOH Z 377 " =    1.414
peak=   -3.099 closest distance to " OD1 ASP A 191 " =    1.607
peak=   -3.096 closest distance to " O   HOH Z 228 " =    1.509
peak=   -3.089 closest distance to " CA  GLY A 133 " =    2.234
peak=   -3.085 closest distance to " OD1 ASN A 301 " =    1.974
peak=   -3.075 closest distance to " CA  ASN A 127 " =    1.144
peak=   -3.070 closest distance to " O   HOH Z 165 " =    2.038
peak=   -3.056 closest distance to " O   HOH Z  60 " =    2.085
peak=   -3.056 closest distance to " O   HOH Z 298 " =    1.264

================= 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    :  0.4634 0.4598   6.263739e+00   6.258112e+00
   1_bss:  0.4552 0.4506   6.261078e+00   6.252039e+00
   1_xyz:  0.3689 0.4000   6.127816e+00   6.178583e+00
   1_adp:  0.3215 0.3780   6.035346e+00   6.141215e+00
   1_occ:  0.3209 0.3782   6.034525e+00   6.141136e+00
   2_bss:  0.3170 0.3745   6.034179e+00   6.137566e+00
   2_xyz:  0.2338 0.2951   5.785672e+00   5.956678e+00
   2_adp:  0.2138 0.2728   5.711260e+00   5.895902e+00
   2_occ:  0.2135 0.2727   5.710206e+00   5.895565e+00
   3_bss:  0.2125 0.2700   5.709021e+00   5.892252e+00
   3_xyz:  0.1552 0.2047   5.426263e+00   5.642788e+00
   3_adp:  0.1390 0.1897   5.337671e+00   5.570309e+00
   3_occ:  0.1388 0.1894   5.336575e+00   5.569063e+00
   4_bss:  0.1387 0.1894   5.336665e+00   5.567548e+00
   4_xyz:  0.1209 0.1708   5.220353e+00   5.465953e+00
   4_adp:  0.1184 0.1647   5.195571e+00   5.433869e+00
   4_occ:  0.1182 0.1643   5.194421e+00   5.432542e+00
   5_bss:  0.1182 0.1642   5.194270e+00   5.432391e+00
   5_xyz:  0.1138 0.1597   5.168246e+00   5.411088e+00
   5_adp:  0.1141 0.1588   5.166498e+00   5.405806e+00
   5_occ:  0.1140 0.1587   5.165958e+00   5.405254e+00
   5_bss:  0.1141 0.1592   5.167175e+00   5.407604e+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:  0.332   7.445   8.590   7.670   9.298   0.000   0.000   0.000
   1_xyz:  0.332   7.445   8.590   7.670   9.298   0.000   0.000   0.000
   1_adp:  0.332   7.445   8.590   7.670   9.298   0.000   0.000   0.000
   1_occ:  0.332   7.445   8.590   7.670   9.298   0.000   0.000   0.000
   2_bss:  0.322  34.707   4.675   3.799   6.022   0.000   0.000   0.000
   2_xyz:  0.322  34.707   4.675   3.799   6.022   0.000   0.000   0.000
   2_adp:  0.322  34.707   4.675   3.799   6.022   0.000   0.000   0.000
   2_occ:  0.322  34.707   4.675   3.799   6.022   0.000   0.000   0.000
   3_bss:  0.333  43.650   3.011   2.584   3.891   0.000   0.000   0.000
   3_xyz:  0.333  43.650   3.011   2.584   3.891   0.000   0.000   0.000
   3_adp:  0.333  43.650   3.011   2.584   3.891   0.000   0.000   0.000
   3_occ:  0.333  43.650   3.011   2.584   3.891   0.000   0.000   0.000
   4_bss:  0.333  43.650   2.589   2.307   3.003   0.000   0.000   0.000
   4_xyz:  0.333  43.650   2.589   2.307   3.003   0.000   0.000   0.000
   4_adp:  0.333  43.650   2.589   2.307   3.003   0.000   0.000   0.000
   4_occ:  0.333  43.650   2.589   2.307   3.003   0.000   0.000   0.000
   5_bss:  0.333  43.650   2.376   2.223   2.740   0.000   0.000   0.000
   5_xyz:  0.333  43.650   2.376   2.223   2.740   0.000   0.000   0.000
   5_adp:  0.333  43.650   2.376   2.223   2.740   0.000   0.000   0.000
   5_occ:  0.333  43.650   2.376   2.223   2.740   0.000   0.000   0.000
   5_bss:  0.323  46.896  -0.083  -0.193   0.276   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.253 0.4544  0.5330    65794.579
   1_bss:  55.969 0.4424  0.6548    63086.898
   1_xyz:  45.951 0.5683  0.8332    46384.713
   1_adp:  41.853 0.6191  0.9342    40536.337
   1_occ:  41.891 0.6186  0.9331    40590.479
   2_bss:  41.600 0.6220  0.8269    40173.764
   2_xyz:  30.993 0.7454  0.9607    23537.893
   2_adp:  27.761 0.7819  0.9929    19940.018
   2_occ:  27.729 0.7823  0.9932    19889.462
   3_bss:  27.526 0.7843  0.9369    19654.509
   3_xyz:  19.927 0.8620  0.9877    10906.756
   3_adp:  18.044 0.8801  0.9918     9368.398
   3_occ:  18.006 0.8804  0.9918     9334.994
   4_bss:  17.989 0.8806  0.9727     9335.633
   4_xyz:  15.776 0.8999  0.9839     7499.608
   4_adp:  15.006 0.9068  0.9864     7057.724
   4_occ:  14.977 0.9071  0.9864     7038.000
   5_bss:  14.973 0.9071  0.9797     7036.238
   5_xyz:  14.474 0.9113  0.9796     6661.587
   5_adp:  14.322 0.9127  0.9799     6601.802
   5_occ:  14.311 0.9128  0.9798     6596.094
   5_bss:  14.366 0.9123  0.9759     6650.310
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3619e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3619e+01
   1_xyz:   1.636  0.013  0.105 18.237  0.006  4.110   1.3410e-01
   1_adp:   1.636  0.013  0.105 18.237  0.006  4.110   1.3410e-01
   1_occ:   1.636  0.013  0.105 18.237  0.006  4.110   1.3410e-01
   2_bss:   1.636  0.013  0.105 18.237  0.006  4.110   1.3410e-01
   2_xyz:   1.046  0.007  0.073 16.311  0.005  4.113   7.0867e-02
   2_adp:   1.046  0.007  0.073 16.311  0.005  4.113   7.0867e-02
   2_occ:   1.046  0.007  0.073 16.311  0.005  4.113   7.0867e-02
   3_bss:   1.046  0.007  0.073 16.311  0.005  4.113   7.0867e-02
   3_xyz:   1.073  0.007  0.080 15.766  0.004  4.126   6.6484e-02
   3_adp:   1.073  0.007  0.080 15.766  0.004  4.126   6.6484e-02
   3_occ:   1.073  0.007  0.080 15.766  0.004  4.126   6.6484e-02
   4_bss:   1.073  0.007  0.080 15.766  0.004  4.126   6.6484e-02
   4_xyz:   1.124  0.008  0.087 16.107  0.004  4.110   7.4559e-02
   4_adp:   1.124  0.008  0.087 16.107  0.004  4.110   7.4559e-02
   4_occ:   1.124  0.008  0.087 16.107  0.004  4.110   7.4559e-02
   5_bss:   1.124  0.008  0.087 16.107  0.004  4.110   7.4559e-02
   5_xyz:   1.066  0.008  0.083 15.768  0.004  4.112   6.8190e-02
   5_adp:   1.066  0.008  0.083 15.768  0.004  4.112   6.8190e-02
   5_occ:   1.066  0.008  0.083 15.768  0.004  4.112   6.8190e-02
   5_bss:   1.066  0.008  0.083 15.768  0.004  4.112   6.8190e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9513e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9513e+00
   1_xyz:  14.104  0.161  0.454 84.635  0.042  2.190   9.5256e-02
   1_adp:  14.104  0.161  0.454 84.635  0.042  2.190   9.5256e-02
   1_occ:  14.104  0.161  0.454 84.635  0.042  2.190   9.5256e-02
   2_bss:  14.104  0.161  0.454 84.635  0.042  2.190   9.5256e-02
   2_xyz:   7.249  0.068  0.240 81.772  0.033  2.267   5.4109e-02
   2_adp:   7.249  0.068  0.240 81.772  0.033  2.267   5.4109e-02
   2_occ:   7.249  0.068  0.240 81.772  0.033  2.267   5.4109e-02
   3_bss:   7.249  0.068  0.240 81.772  0.033  2.267   5.4109e-02
   3_xyz:   8.077  0.056  0.414 87.609  0.040  2.375   4.9050e-02
   3_adp:   8.077  0.056  0.414 87.609  0.040  2.375   4.9050e-02
   3_occ:   8.077  0.056  0.414 87.609  0.040  2.375   4.9050e-02
   4_bss:   8.077  0.056  0.414 87.609  0.040  2.375   4.9050e-02
   4_xyz:   9.161  0.058  0.567 82.792  0.034  2.272   5.2974e-02
   4_adp:   9.161  0.058  0.567 82.792  0.034  2.272   5.2974e-02
   4_occ:   9.161  0.058  0.567 82.792  0.034  2.272   5.2974e-02
   5_bss:   9.161  0.058  0.567 82.792  0.034  2.272   5.2974e-02
   5_xyz:   7.544  0.043  0.580 82.997  0.031  2.335   5.6344e-02
   5_adp:   7.544  0.043  0.580 82.997  0.031  2.335   5.6344e-02
   5_occ:   7.544  0.043  0.580 82.997  0.031  2.335   5.6344e-02
   5_bss:   7.544  0.043  0.580 82.997  0.031  2.335   5.6344e-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:  66.84   0.00  11.91  66.84   0.00   9.34  65.29   0.00  25.89
   1_occ:  66.84   0.00  11.91  66.84   0.00   9.34  65.29   0.00  25.89
   2_bss:  66.84   0.00  11.91  66.84   0.00   9.34  65.29   0.00  25.89
   2_xyz:  66.84   0.00  11.91  66.84   0.00   9.34  65.29   0.00  25.89
   2_adp:  68.91   0.00  12.15  68.91   0.00   8.68  68.42   1.07  31.08
   2_occ:  68.91   0.00  12.15  68.91   0.00   8.68  68.42   1.07  31.08
   3_bss:  68.91   0.00  12.15  68.91   0.00   8.68  68.42   1.07  31.08
   3_xyz:  68.91   0.00  12.15  68.91   0.00   8.68  68.42   1.07  31.08
   3_adp:  89.33   0.00  13.47  89.33   0.00   8.73  87.42   2.16  39.28
   3_occ:  89.33   0.00  13.47  89.33   0.00   8.73  87.42   2.16  39.28
   4_bss:  89.33   0.00  13.47  89.33   0.00   8.73  87.42   2.16  39.28
   4_xyz:  89.33   0.00  13.47  89.33   0.00   8.73  87.42   2.16  39.28
   4_adp:  91.89   0.00  12.73  91.89   0.00   8.45  79.18   1.87  36.01
   4_occ:  91.89   0.00  12.73  91.89   0.00   8.45  79.18   1.87  36.01
   5_bss:  91.89   0.00  12.73  91.89   0.00   8.45  79.18   1.87  36.01
   5_xyz:  91.89   0.00  12.73  91.89   0.00   8.45  79.18   1.87  36.01
   5_adp:  91.63   0.00  12.63  91.63   0.00   8.44  78.77   1.88  35.45
   5_occ:  91.63   0.00  12.63  91.63   0.00   8.44  78.77   1.88  35.45
   5_bss:  93.97   2.34  14.96  93.97   2.34  10.77  81.11   4.22  37.78
------------------------------------------------------------------------
 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:    1.213    0.020    0.408
   1_adp:    1.213    0.020    0.408
   1_occ:    1.213    0.020    0.408
   2_bss:    1.213    0.020    0.408
   2_xyz:    1.620    0.032    0.548
   2_adp:    1.620    0.032    0.548
   2_occ:    1.620    0.032    0.548
   3_bss:    1.620    0.032    0.548
   3_xyz:    1.612    0.025    0.627
   3_adp:    1.612    0.025    0.627
   3_occ:    1.612    0.025    0.627
   4_bss:    1.612    0.025    0.627
   4_xyz:    1.663    0.051    0.658
   4_adp:    1.663    0.051    0.658
   4_occ:    1.663    0.051    0.658
   5_bss:    1.663    0.051    0.658
   5_xyz:    1.805    0.055    0.670
   5_adp:    1.805    0.055    0.670
   5_occ:    1.805    0.055    0.670
   5_bss:    1.805    0.055    0.670
------------------------------------------------------------------------

CPU time actual refinement: 348.56


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1024/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_1024/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1024/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1024/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1024/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.40 
  Macro-tasks:
    bulk solvent and scale       = 40.14  
    individual site refinement   = 149.55 
    weights calculation          = 32.13  
    collect and process          = 6.58   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 228.51 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 110.25 
    alpha_beta                      = 8.29   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 120.94 
    fmodel                         = 7.28   
    r_factors                      = 0.25   
    phase_errors                   = 10.50  
    foms                           = 0.35   
    TOTAL for micro-tasks          = 261.45 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.854 micro seconds
Total CPU time: 6.03 minutes
from_scatterers_fft:    655 calls, 109.81 s
gradients_fft:          600 calls, 107.25 s

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

# Date 2008-01-16 Time 03:01:20 PST -0800 (1200481280.40 s)
Start R-work = 0.4634, R-free = 0.4598 (no bulk solvent and anisotropic scale)
Final R-work = 0.1305, R-free = 0.1754 (no bulk solvent and anisotropic scale)

Start R-work = 0.4552, R-free = 0.4506
Final R-work = 0.1141, R-free = 0.1592