# Date 2008-01-16 Time 02:45:24 PST -0800 (1200480324.56 s)
#phil __OFF__

Command line arguments: "../964.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30771
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 964

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 48.1033, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, 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: (70.9525, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 2.02048
Completeness in resolution range: 0.971821
Completeness with d_max=infinity: 0.968745

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1439
                             d_min =   2.0205

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 2.02048
Completeness in resolution range: 0.971821
Completeness with d_max=infinity: 0.968745

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1443 -  4.3224 [2114/2141]  1903   211  10.0%
  bin  2:  4.3224 -  3.4441 [2030/2046]  1826   204  10.0%
  bin  3:  3.4441 -  3.0126 [2012/2031]  1809   203  10.1%
  bin  4:  3.0126 -  2.7390 [1983/2013]  1791   192   9.7%
  bin  5:  2.7390 -  2.5436 [1968/1987]  1767   201  10.2%
  bin  6:  2.5436 -  2.3943 [1962/1998]  1768   194   9.9%
  bin  7:  2.3943 -  2.2748 [1960/1993]  1765   195   9.9%
  bin  8:  2.2748 -  2.1761 [1941/1975]  1744   197  10.1%
  bin  9:  2.1761 -  2.0925 [1939/1967]  1744   195  10.1%
  bin 10:  2.0925 -  2.0205 [1680/2006]  1513   167   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_964/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.58 -     2.24: 6
        2.24 -     2.91: 1384
        2.91 -     3.57: 4369
        3.57 -     4.24: 8986
        4.24 -     4.90: 12954
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.581 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.739 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.940 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.124 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27694 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_964/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_964/model_refine_001.geo

CPU time processing inputs: 9.64


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 48.10325 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5041   r_free= 0.4876   ksol= 0.00   Bsol= 0.00   scale= 0.761    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.301498                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.8205 0.99   1374  153 0.4133 0.4112      6.6288      6.6126|
|  2:  4.8205 -  3.8469 0.99   1321  146 0.4375 0.4746       6.862       6.937|
|  3:  3.8469 -  3.3667 0.99   1299  146 0.4779 0.4211      6.7452       6.668|
|  4:  3.3667 -  3.0616 0.99   1285  138 0.4969 0.4519      6.5754       6.498|
|  5:  3.0616 -  2.8437 0.99   1274  143 0.5404 0.4919      6.4066      6.3946|
|  6:  2.8437 -  2.6770 0.99   1277  146 0.5320 0.5137      6.3143      6.2461|
|  7:  2.6770 -  2.5436 0.99   1266  139 0.5185 0.4680      6.2512      6.1605|
|  8:  2.5436 -  2.4334 0.98   1270  142 0.5320 0.4974      6.2044      6.1919|
|  9:  2.4334 -  2.3400 0.98   1259  139 0.5378 0.6053      6.1212       6.164|
| 10:  2.3400 -  2.2596 0.98   1246  136 0.5589 0.5369       6.133      6.1416|
| 11:  2.2596 -  2.1891 1.00   1264  147 0.5411 0.5400      6.0532      6.1067|
| 12:  2.1891 -  2.1267 0.97   1257  128 0.5500 0.5004      5.9886       6.015|
| 13:  2.1267 -  2.0709 0.98   1240  138 0.5443 0.5324      5.9055       5.882|
| 14:  2.0709 -  2.0205 0.79    998  118 0.5478 0.5152      5.8543      5.7573|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.8205  1374   153  0.64  39.47   0.78     0.67      89608.90|
|  2:  4.8205 -  3.8469  1321   146  0.66  38.93   0.85     0.70     123129.61|
|  3:  3.8469 -  3.3667  1299   146  0.56  46.72   0.78     0.66     127929.38|
|  4:  3.3667 -  3.0616  1285   138  0.47  53.83   0.77     0.55     108998.53|
|  5:  3.0616 -  2.8437  1274   143  0.42  58.52   0.71     0.49      84295.50|
|  6:  2.8437 -  2.6770  1277   146  0.41  58.75   0.69     0.46      68869.50|
|  7:  2.6770 -  2.5436  1266   139  0.39  60.35   0.72     0.44      62885.47|
|  8:  2.5436 -  2.4334  1270   142  0.32  66.04   0.73     0.36      62380.57|
|  9:  2.4334 -  2.3400  1259   139  0.24  72.42   0.68     0.27      62284.50|
| 10:  2.3400 -  2.2596  1246   136  0.20  75.40   0.69     0.22      59039.69|
| 11:  2.2596 -  2.1891  1264   147  0.22  73.76   0.73     0.27      53225.81|
| 12:  2.1891 -  2.1267  1257   128  0.25  71.55   0.72     0.30      47473.60|
| 13:  2.1267 -  2.0709  1240   138  0.25  71.30   0.70     0.30      40253.49|
| 14:  2.0709 -  2.0205   998   118  0.21  74.64   0.70     0.23      33780.17|
|alpha:            min =        0.22 max =            0.70 mean =         0.43|
|beta:             min =    33780.17 max =       127929.38 mean =     74234.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           89.99 mean =        61.06|
|phase err.(test): min =        0.00 max =           89.95 mean =        61.31|
|-----------------------------------------------------------------------------|

============================== 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 = 17.717102             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.669   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.773221              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.094   (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:       23 |
| 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:      672 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1470 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2562 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3820 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4972 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6440 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7587 |
|-----------------------------------------------------------------------------|
|-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 |       54.651 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.770 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    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 = 12.410)------------------------------------------|
|    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: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5087   r_free= 0.4913   ksol= 0.00   Bsol= 0.00   scale= 0.734    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.302746                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4980   r_free= 0.4799   ksol= 0.30   Bsol= 24.53   scale= 0.946   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.96,11.57,7.99,0.00,0.00,0.00); trace/3= 8.51                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.297166                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.370369             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.498   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.504292              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.416   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4980      final r-factor (work) = 0.4311          |
| start r-factor (free) = 0.4799      final r-factor (free) = 0.4392          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 106.2287 = 16.37 * 0.50 * 6.3014 + 1.00 * 54.6508                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.2184 = 16.37 * 0.50 * 6.2395 + 1.00 * 0.1466                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4311      final r-factor (work) = 0.3890          |
| start r-factor (free) = 0.4392      final r-factor (free) = 0.4310          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4009 = 1.50 * 1.00 * 6.2395 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3217 = 1.50 * 1.00 * 6.1810 + 1.00 * 0.0237                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    128.03  15.70    None  None   None       |
|    all(noH): 2823   0      0.00    128.03  15.70    None  None   None       |
|    Sol.    : 438    0      0.00    128.03  27.72    None  None   None       |
|    Mac.    : 2385   0      0.00    86.65   13.50    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 -  12.803: 1495   |   5:    64.013 -  76.816:   15        |
|      1:    12.803 -  25.605:  790   |   6:    76.816 -  89.619:   12        |
|      2:    25.605 -  38.408:  331   |   7:    89.619 - 102.422:    1        |
|      3:    38.408 -  51.211:  118   |   8:   102.422 - 115.224:    2        |
|      4:    51.211 -  64.013:   57   |   9:   115.224 - 128.027:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3890 r_free = 0.4310             target_work(ml) = 6.168         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3880 r_free = 0.4296             target_work(ml) = 6.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3880   r_free= 0.4296   ksol= 0.30   Bsol= 24.53   scale= 1.074   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.96,11.57,7.99,0.00,0.00,0.00); trace/3= 8.51                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.166622                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3863   r_free= 0.4247   ksol= 0.31   Bsol= 52.16   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.94,7.45,4.83,0.00,0.00,0.00); trace/3= 5.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.167473                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.958722              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.756  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.569501              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.554  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3863      final r-factor (work) = 0.3279          |
| start r-factor (free) = 0.4247      final r-factor (free) = 0.3965          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.8910 = 9.96 * 0.50 * 6.1744 + 1.00 * 0.1463                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4257 = 9.96 * 0.50 * 6.0905 + 1.00 * 0.0990                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3279      final r-factor (work) = 0.3199          |
| start r-factor (free) = 0.3965      final r-factor (free) = 0.3815          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4917 = 0.57 * 1.00 * 6.0905 + 1.00 * 0.0232                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4604 = 0.57 * 1.00 * 6.0567 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    127.03  14.11    None  None   None       |
|    all(noH): 2823   0      0.00    127.03  14.11    None  None   None       |
|    Sol.    : 438    0      0.00    127.03  27.89    None  None   None       |
|    Mac.    : 2385   0      0.00    71.04   11.58    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 -  12.703: 1665   |   5:    63.514 -  76.217:   15        |
|      1:    12.703 -  25.406:  728   |   6:    76.217 -  88.920:    5        |
|      2:    25.406 -  38.109:  286   |   7:    88.920 - 101.623:    2        |
|      3:    38.109 -  50.812:   85   |   8:   101.623 - 114.326:    1        |
|      4:    50.812 -  63.514:   35   |   9:   114.326 - 127.029:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3199 r_free = 0.3815             target_work(ml) = 6.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3198 r_free = 0.3819             target_work(ml) = 6.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3198   r_free= 0.3819   ksol= 0.31   Bsol= 52.16   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.94,7.45,4.83,0.00,0.00,0.00); trace/3= 5.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.045957                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3202   r_free= 0.3808   ksol= 0.31   Bsol= 52.16   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,5.83,3.72,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.047173                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.582959              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.613  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.419990              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.181  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3202      final r-factor (work) = 0.2751          |
| start r-factor (free) = 0.3808      final r-factor (free) = 0.3227          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0058 = 5.58 * 0.50 * 6.0566 + 1.00 * 0.0990                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7804 = 5.58 * 0.50 * 5.9829 + 1.00 * 0.0793                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2751      final r-factor (work) = 0.2615          |
| start r-factor (free) = 0.3227      final r-factor (free) = 0.3080          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5239 = 0.42 * 1.00 * 5.9829 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4842 = 0.42 * 1.00 * 5.8899 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    118.25  13.87    None  None   None       |
|    all(noH): 2823   0      0.00    118.25  13.87    None  None   None       |
|    Sol.    : 438    0      0.62    118.25  30.96    None  None   None       |
|    Mac.    : 2385   0      0.00    67.97   10.73    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 -  11.825: 1641   |   5:    59.125 -  70.950:   18        |
|      1:    11.825 -  23.650:  689   |   6:    70.950 -  82.775:    5        |
|      2:    23.650 -  35.475:  283   |   7:    82.775 -  94.600:    3        |
|      3:    35.475 -  47.300:  124   |   8:    94.600 - 106.425:    0        |
|      4:    47.300 -  59.125:   59   |   9:   106.425 - 118.250:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2615 r_free = 0.3080             target_work(ml) = 5.878         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2613 r_free = 0.3079             target_work(ml) = 5.877         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2613   r_free= 0.3079   ksol= 0.31   Bsol= 52.16   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,5.83,3.72,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.876992                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2610   r_free= 0.3084   ksol= 0.32   Bsol= 62.17   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,4.44,2.85,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.877720                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.030982              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.012  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.659434              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.851  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2610      final r-factor (work) = 0.1897          |
| start r-factor (free) = 0.3084      final r-factor (free) = 0.2360          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7266 = 8.03 * 0.50 * 5.8890 + 1.00 * 0.0793                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1806 = 8.03 * 0.50 * 5.7441 + 1.00 * 0.1154                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1897      final r-factor (work) = 0.1673          |
| start r-factor (free) = 0.2360      final r-factor (free) = 0.2162          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7983 = 0.66 * 1.00 * 5.7441 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6565 = 0.66 * 1.00 * 5.5229 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.12  14.38    None  None   None       |
|    all(noH): 2823   0      0.00    105.12  14.38    None  None   None       |
|    Sol.    : 438    0      0.00    105.12  38.98    None  None   None       |
|    Mac.    : 2385   0      0.00    79.12   9.86     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 -  10.512: 1657   |   5:    52.560 -  63.072:   79        |
|      1:    10.512 -  21.024:  612   |   6:    63.072 -  73.584:   36        |
|      2:    21.024 -  31.536:  189   |   7:    73.584 -  84.096:   17        |
|      3:    31.536 -  42.048:  130   |   8:    84.096 -  94.608:    2        |
|      4:    42.048 -  52.560:   99   |   9:    94.608 - 105.120:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1673 r_free = 0.2162             target_work(ml) = 5.487         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1670 r_free = 0.2163             target_work(ml) = 5.486         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1670   r_free= 0.2163   ksol= 0.32   Bsol= 62.17   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,4.44,2.85,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.486300                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1667   r_free= 0.2161   ksol= 0.32   Bsol= 62.17   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.42,2.90,2.80,0.00,0.00,0.00); trace/3= 2.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.484894                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.603063              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.235  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.158393              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.839  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1667      final r-factor (work) = 0.1426          |
| start r-factor (free) = 0.2161      final r-factor (free) = 0.1897          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0650 = 3.60 * 0.50 * 5.5228 + 1.00 * 0.1154                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8421 = 3.60 * 0.50 * 5.4188 + 1.00 * 0.0800                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1426      final r-factor (work) = 0.1400          |
| start r-factor (free) = 0.1897      final r-factor (free) = 0.1846          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8740 = 0.16 * 1.00 * 5.4188 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8658 = 0.16 * 1.00 * 5.3437 + 1.00 * 0.0194                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.90   13.51    None  None   None       |
|    all(noH): 2823   0      0.00    97.90   13.51    None  None   None       |
|    Sol.    : 438    0      1.74    97.90   36.59    None  None   None       |
|    Mac.    : 2385   0      0.00    76.62   9.27     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 -   9.790: 1666   |   5:    48.949 -  58.738:   69        |
|      1:     9.790 -  19.580:  631   |   6:    58.738 -  68.528:   37        |
|      2:    19.580 -  29.369:  169   |   7:    68.528 -  78.318:   15        |
|      3:    29.369 -  39.159:  117   |   8:    78.318 -  88.108:    2        |
|      4:    39.159 -  48.949:  115   |   9:    88.108 -  97.897:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1400 r_free = 0.1846             target_work(ml) = 5.326         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1397 r_free = 0.1846             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1397   r_free= 0.1846   ksol= 0.32   Bsol= 62.17   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.42,2.90,2.80,0.00,0.00,0.00); trace/3= 2.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.324966                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.8205 0.99   1374  153 0.1079 0.1404      5.4758      5.6138|
|  2:  4.8205 -  3.8469 0.99   1321  146 0.0987 0.1277      5.5651      5.7594|
|  3:  3.8469 -  3.3667 0.99   1299  146 0.1262 0.1764      5.6385      5.9986|
|  4:  3.3667 -  3.0616 0.99   1285  138 0.1501 0.1834      5.6273      5.7447|
|  5:  3.0616 -  2.8437 0.99   1274  143 0.1699 0.1936      5.5375      5.6449|
|  6:  2.8437 -  2.6770 0.99   1277  146 0.1572 0.2238      5.4132      5.6526|
|  7:  2.6770 -  2.5436 0.99   1266  139 0.1574 0.2051      5.3609      5.5506|
|  8:  2.5436 -  2.4334 0.98   1270  142 0.1534 0.2009      5.2835      5.5078|
|  9:  2.4334 -  2.3400 0.98   1259  139 0.1574 0.2060      5.2297        5.42|
| 10:  2.3400 -  2.2596 0.98   1246  136 0.1527 0.2201      5.1991      5.4591|
| 11:  2.2596 -  2.1891 1.00   1264  147 0.1534 0.2048      5.1543      5.4015|
| 12:  2.1891 -  2.1267 0.97   1257  128 0.1452 0.1956      5.0651      5.3194|
| 13:  2.1267 -  2.0709 0.98   1240  138 0.1514 0.2031      4.9868      5.1845|
| 14:  2.0709 -  2.0205 0.79    998  118 0.1402 0.2058       4.866      5.1106|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.8205  1374   153  0.93  10.88   0.96     0.93       9224.61|
|  2:  4.8205 -  3.8469  1321   146  0.94   9.90   1.00     0.98      11649.14|
|  3:  3.8469 -  3.3667  1299   146  0.91  13.84   1.01     1.01      14127.62|
|  4:  3.3667 -  3.0616  1285   138  0.90  15.85   1.00     0.97      13316.93|
|  5:  3.0616 -  2.8437  1274   143  0.87  19.42   0.99     0.98      12067.46|
|  6:  2.8437 -  2.6770  1277   146  0.87  19.21   0.98     0.94       9791.83|
|  7:  2.6770 -  2.5436  1266   139  0.87  19.22   0.99     0.97       8996.09|
|  8:  2.5436 -  2.4334  1270   142  0.88  18.40   0.99     0.95       7497.68|
|  9:  2.4334 -  2.3400  1259   139  0.87  19.74   1.00     0.96       7248.61|
| 10:  2.3400 -  2.2596  1246   136  0.87  19.52   1.00     0.95       6537.88|
| 11:  2.2596 -  2.1891  1264   147  0.87  19.95   1.00     0.94       6210.28|
| 12:  2.1891 -  2.1267  1257   128  0.89  18.21   1.00     0.99       5350.24|
| 13:  2.1267 -  2.0709  1240   138  0.88  18.72   0.99     0.97       4520.69|
| 14:  2.0709 -  2.0205   998   118  0.88  18.25   0.97     0.93       3567.30|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     3567.30 max =        14127.62 mean =      8697.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.13|
|phase err.(test): min =        0.00 max =           87.86 mean =        16.29|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1400   r_free= 0.1848   ksol= 0.32   Bsol= 66.28   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.87,0.27,0.59,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.325716                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1400   r_free= 0.1848   ksol= 0.32   Bsol= 66.28   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.87,0.27,0.59,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.325716                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.8205 0.99   1374  153 0.1094 0.1385      5.4774      5.6032|
|  2:  4.8205 -  3.8469 0.99   1321  146 0.0993 0.1307      5.5693      5.7744|
|  3:  3.8469 -  3.3667 0.99   1299  146 0.1273 0.1770      5.6468      6.0003|
|  4:  3.3667 -  3.0616 0.99   1285  138 0.1501 0.1850      5.6285      5.7511|
|  5:  3.0616 -  2.8437 0.99   1274  143 0.1699 0.1931      5.5382      5.6435|
|  6:  2.8437 -  2.6770 0.99   1277  146 0.1570 0.2229      5.4125      5.6524|
|  7:  2.6770 -  2.5436 0.99   1266  139 0.1573 0.2054      5.3609      5.5512|
|  8:  2.5436 -  2.4334 0.98   1270  142 0.1532 0.2013      5.2828      5.5081|
|  9:  2.4334 -  2.3400 0.98   1259  139 0.1569 0.2065      5.2292      5.4212|
| 10:  2.3400 -  2.2596 0.98   1246  136 0.1524 0.2212      5.1985      5.4598|
| 11:  2.2596 -  2.1891 1.00   1264  147 0.1533 0.2043      5.1536      5.3995|
| 12:  2.1891 -  2.1267 0.97   1257  128 0.1449 0.1968      5.0645      5.3222|
| 13:  2.1267 -  2.0709 0.98   1240  138 0.1514 0.2031      4.9863      5.1834|
| 14:  2.0709 -  2.0205 0.79    998  118 0.1400 0.2048      4.8637      5.1073|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.8205  1374   153  0.93  10.64   0.96     0.93       8823.63|
|  2:  4.8205 -  3.8469  1321   146  0.94   9.84   1.00     0.98      11604.86|
|  3:  3.8469 -  3.3667  1299   146  0.91  14.00   1.01     1.00      14449.84|
|  4:  3.3667 -  3.0616  1285   138  0.90  15.90   0.99     0.96      13373.16|
|  5:  3.0616 -  2.8437  1274   143  0.87  19.44   0.98     0.97      12094.15|
|  6:  2.8437 -  2.6770  1277   146  0.87  19.19   0.97     0.93       9780.72|
|  7:  2.6770 -  2.5436  1266   139  0.87  19.23   0.98     0.96       9011.65|
|  8:  2.5436 -  2.4334  1270   142  0.88  18.41   0.98     0.93       7507.48|
|  9:  2.4334 -  2.3400  1259   139  0.87  19.75   0.99     0.95       7253.42|
| 10:  2.3400 -  2.2596  1246   136  0.87  19.52   0.99     0.94       6538.53|
| 11:  2.2596 -  2.1891  1264   147  0.87  19.95   0.98     0.93       6216.22|
| 12:  2.1891 -  2.1267  1257   128  0.89  18.22   0.98     0.97       5351.90|
| 13:  2.1267 -  2.0709  1240   138  0.88  18.70   0.97     0.96       4509.71|
| 14:  2.0709 -  2.0205   998   118  0.88  18.19   0.95     0.92       3541.82|
|alpha:            min =        0.92 max =            1.00 mean =         0.95|
|beta:             min =     3541.82 max =        14449.84 mean =      8692.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        17.12|
|phase err.(test): min =        0.00 max =           87.85 mean =        16.24|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.08    99.98   15.58    None  None   None       |
|    all(noH): 2823   0      2.08    99.98   15.58    None  None   None       |
|    Sol.    : 438    0      3.82    99.98   38.67    None  None   None       |
|    Mac.    : 2385   0      2.08    78.70   11.34    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:     2.078 -  11.868: 1666   |   5:    51.027 -  60.816:   69        |
|      1:    11.868 -  21.657:  631   |   6:    60.816 -  70.606:   37        |
|      2:    21.657 -  31.447:  169   |   7:    70.606 -  80.396:   15        |
|      3:    31.447 -  41.237:  117   |   8:    80.396 -  90.186:    2        |
|      4:    41.237 -  51.027:  115   |   9:    90.186 -  99.975:    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)= 335         
Filter by distance & map next to the model:
   mapped sites are within: 0.598 - 5.205
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 335
   mapped sites are within: 0.703 - 5.205

peak=    7.586 closest distance to " O   HOH Z 120 " =    1.787
peak=    6.551 closest distance to " CG1 ILE A 234 " =    1.481
peak=    6.222 closest distance to " CG2 VAL A 230 " =    1.253
peak=    6.121 closest distance to " O   HOH Z 210 " =    1.722
peak=    5.789 closest distance to " O   HOH Z 426 " =    1.295
peak=    5.663 closest distance to " CG2 VAL A 296 " =    1.148
peak=    5.511 closest distance to " CG  LEU A   5 " =    1.450
peak=    5.288 closest distance to " OD1 ASN A 301 " =    1.044
peak=    5.240 closest distance to " O   HOH Z 111 " =    2.240
peak=    5.125 closest distance to " O   HOH Z 117 " =    1.400
peak=    5.063 closest distance to " CB  VAL A 230 " =    1.293
peak=    5.054 closest distance to " CB  SER A  63 " =    1.224
peak=    5.033 closest distance to " O   HOH Z 412 " =    3.398
peak=    4.926 closest distance to " N   SER A 164 " =    0.922
peak=    4.911 closest distance to " O   HOH Z  57 " =    0.993
peak=    4.897 closest distance to " O   HOH Z 425 " =    1.852
peak=    4.823 closest distance to " O   HOH Z 422 " =    1.315
peak=    4.794 closest distance to " O  BHOH Z 338 " =    1.117
peak=    4.761 closest distance to " O   HOH Z 388 " =    1.356
peak=    4.726 closest distance to " CD2 LEU A 228 " =    1.271
peak=    4.711 closest distance to " O   GLN A  11 " =    1.008
peak=    4.606 closest distance to " O   HOH Z 139 " =    1.413
peak=    4.521 closest distance to " O   HOH Z 102 " =    1.507
peak=    4.506 closest distance to " CG  PRO A 280 " =    0.936
peak=    4.418 closest distance to " O   HOH Z  54 " =    1.246
peak=    4.359 closest distance to " O   HOH Z 128 " =    1.659
peak=    4.340 closest distance to " O   HOH Z 433 " =    1.998
peak=    4.338 closest distance to " O   HOH Z 394 " =    1.807
peak=    4.317 closest distance to " O   HOH Z  82 " =    0.965
peak=    4.316 closest distance to " O   HOH Z 403 " =    1.975
peak=    4.305 closest distance to " O   HOH Z 248 " =    1.850
peak=    4.273 closest distance to " O   ASP A 124 " =    1.341
peak=    4.271 closest distance to " CD  LYS A 166 " =    1.657
peak=    4.268 closest distance to " CA  ARG A 195 " =    1.196
peak=    4.261 closest distance to " CG AARG A 275 " =    1.207
peak=    4.259 closest distance to " O   HOH Z 377 " =    1.647
peak=    4.255 closest distance to " O   HOH Z 404 " =    1.509
peak=    4.240 closest distance to " O   HOH Z 431 " =    1.739
peak=    4.236 closest distance to " OE1 GLN A  88 " =    1.018
peak=    4.216 closest distance to " CG  PRO A  54 " =    1.279
peak=    4.208 closest distance to " CG  PRO A 198 " =    1.293
peak=    4.183 closest distance to " CB  GLN A 223 " =    1.423
peak=    4.168 closest distance to " O   HOH Z 395 " =    1.532
peak=    4.166 closest distance to " O   HOH Z 139 " =    1.745
peak=    4.159 closest distance to " CB  VAL A 296 " =    1.133
peak=    4.156 closest distance to " CZ  PHE A 218 " =    1.119
peak=    4.151 closest distance to " O   HOH Z  48 " =    2.115
peak=    4.128 closest distance to " O   PRO A 198 " =    1.613
peak=    4.120 closest distance to " O   HOH Z  67 " =    1.955
peak=    4.100 closest distance to " CB  TRP A 266 " =    1.003
peak=    4.074 closest distance to " CB  GLN A 183 " =    1.135
peak=    4.069 closest distance to " CA  TYR A  30 " =    0.951
peak=    4.068 closest distance to " NH2 ARG A 156 " =    1.200
peak=    4.065 closest distance to " CB  PRO A  54 " =    0.959
peak=    4.057 closest distance to " CB  ARG A 275 " =    0.766
peak=    4.051 closest distance to " O   HOH Z 214 " =    1.467
peak=    4.028 closest distance to " O   HOH Z 126 " =    1.624
peak=    4.027 closest distance to " NE2 HIS A 115 " =    1.215
peak=    4.018 closest distance to " CB  VAL A 296 " =    1.540
peak=    4.017 closest distance to " CD2 TRP A 179 " =    2.507
peak=    4.016 closest distance to " O   HOH Z  40 " =    2.090
peak=    4.012 closest distance to " O   HOH Z  49 " =    1.496
peak=    4.011 closest distance to " O   HOH Z  57 " =    2.687
peak=    3.999 closest distance to " O   HOH Z 234 " =    3.575
peak=    3.994 closest distance to " OE1 GLN A  11 " =    2.164
peak=    3.961 closest distance to " NH1AARG A 145 " =    1.305
peak=    3.957 closest distance to " O   HOH Z  63 " =    2.268
peak=    3.944 closest distance to " O   HOH Z 193 " =    1.733
peak=    3.927 closest distance to " CB  TRP A 179 " =    1.344
peak=    3.923 closest distance to " ND2 ASN A 301 " =    0.995
peak=    3.920 closest distance to " O   HOH Z 357 " =    2.185
peak=    3.920 closest distance to " CG  LEU A 228 " =    1.444
peak=    3.917 closest distance to " O   HOH Z 416 " =    1.384
peak=    3.913 closest distance to " O   HOH Z 417 " =    3.221
peak=    3.902 closest distance to " CG1 ILE A 120 " =    1.148
peak=    3.899 closest distance to " O   HOH Z 130 " =    2.825
peak=    3.898 closest distance to " CG  GLN A  11 " =    1.071
peak=    3.884 closest distance to " O   HOH Z  48 " =    1.906
peak=    3.881 closest distance to " OE1 GLU A   2 " =    1.421
peak=    3.871 closest distance to " O   HOH Z 155 " =    1.561
peak=    3.859 closest distance to " O   HOH Z  80 " =    2.121
peak=    3.850 closest distance to " CB  ALA A 100 " =    1.467
peak=    3.849 closest distance to " CB  MET A  40 " =    0.836
peak=    3.847 closest distance to " O   HOH Z 343 " =    2.699
peak=    3.846 closest distance to " CG  GLN A  77 " =    0.890
peak=    3.843 closest distance to " O   HOH Z 261 " =    2.120
peak=    3.840 closest distance to " CD ALYS A 290 " =    1.193
peak=    3.834 closest distance to " O   HOH Z 350 " =    1.359
peak=    3.826 closest distance to " O   HOH Z 389 " =    2.177
peak=    3.820 closest distance to " O   HOH Z 418 " =    1.887
peak=    3.805 closest distance to " CA  ILE A 106 " =    0.764
peak=    3.801 closest distance to " CE  LYS A 119 " =    1.464
peak=    3.796 closest distance to " O   HOH Z 246 " =    1.531
peak=    3.793 closest distance to " O   HOH Z 146 " =    1.869
peak=    3.781 closest distance to " CA  ARG A  66 " =    0.889
peak=    3.777 closest distance to " CB  ALA A 299 " =    1.028
peak=    3.772 closest distance to " O   HOH Z 130 " =    1.181
peak=    3.772 closest distance to " O   HOH Z 124 " =    1.237
peak=    3.750 closest distance to " CB  SER A 141 " =    1.085
peak=    3.750 closest distance to " O   HOH Z 176 " =    2.283
peak=    3.742 closest distance to " CE1 HIS A 108 " =    1.150
peak=    3.734 closest distance to " O   SER A  87 " =    2.400
peak=    3.731 closest distance to " CG2 THR A 221 " =    1.044
peak=    3.728 closest distance to " O   ALA A 165 " =    1.300
peak=    3.723 closest distance to " O   HOH Z 393 " =    3.494
peak=    3.721 closest distance to " CG1 VAL A 153 " =    1.117
peak=    3.706 closest distance to " NE2 GLN A  11 " =    1.083
peak=    3.689 closest distance to " O   HOH Z 435 " =    1.849
peak=    3.667 closest distance to " NE2 GLN A 278 " =    2.360
peak=    3.657 closest distance to " CB  GLN A  88 " =    1.162
peak=    3.657 closest distance to " O   HOH Z 227 " =    1.670
peak=    3.655 closest distance to " CD1 LEU A 222 " =    0.835
peak=    3.650 closest distance to " CB  THR A  31 " =    1.410
peak=    3.641 closest distance to " O   HOH Z  44 " =    2.018
peak=    3.635 closest distance to " O   HOH Z 126 " =    2.569
peak=    3.627 closest distance to " O   HOH Z  47 " =    1.446
peak=    3.621 closest distance to " O   HOH Z 174 " =    1.375
peak=    3.617 closest distance to " CB  ASN A 285 " =    0.866
peak=    3.614 closest distance to " O   HOH Z 134 " =    2.241
peak=    3.606 closest distance to " O   HOH Z 232 " =    2.159
peak=    3.605 closest distance to " O   HOH Z 369 " =    1.746
peak=    3.604 closest distance to " O   HOH Z 265 " =    2.097
peak=    3.599 closest distance to " CB  VAL A 202 " =    1.389
peak=    3.595 closest distance to " CB  GLU A  46 " =    0.985
peak=    3.592 closest distance to " CB  SER A  62 " =    0.970
peak=    3.590 closest distance to " O   HOH Z 234 " =    1.949
peak=    3.587 closest distance to " CG1 ILE A  33 " =    1.269
peak=    3.576 closest distance to " CB  GLU A 152 " =    1.082
peak=    3.565 closest distance to " O   HOH Z 403 " =    1.449
peak=    3.561 closest distance to " NZ  LYS A  48 " =    1.342
peak=    3.561 closest distance to " CZ3 TRP A  85 " =    0.949
peak=    3.561 closest distance to " CG2 THR A  42 " =    0.761
peak=    3.555 closest distance to " CB  GLU A 128 " =    1.120
peak=    3.544 closest distance to " CB  ASP A 124 " =    0.855
peak=    3.543 closest distance to " CB  PRO A 198 " =    1.049
peak=    3.539 closest distance to " O   HOH Z 146 " =    1.765
peak=    3.538 closest distance to " O   HOH Z 368 " =    4.148
peak=    3.538 closest distance to " O   HOH Z   4 " =    1.618
peak=    3.534 closest distance to " OH  TYR A 116 " =    1.425
peak=    3.533 closest distance to " O   HOH Z 415 " =    1.667
peak=    3.526 closest distance to " CB  ASN A 187 " =    1.030
peak=    3.526 closest distance to " OD2 ASP A 298 " =    0.851
peak=    3.521 closest distance to " O   HOH Z 368 " =    3.242
peak=    3.519 closest distance to " CB  ALA A 256 " =    1.446
peak=    3.505 closest distance to " O   HOH Z 415 " =    1.320
peak=    3.504 closest distance to " O   HOH Z 128 " =    2.159
peak=    3.502 closest distance to " O   HOH Z 148 " =    1.999
peak=    3.498 closest distance to " O   HOH Z  95 " =    1.741
peak=    3.492 closest distance to " CA  ALA A  21 " =    1.245
peak=    3.490 closest distance to " OG1 THR A 294 " =    2.396
peak=    3.487 closest distance to " CA  ASP A 191 " =    0.775
peak=    3.483 closest distance to " O   HOH Z 301 " =    1.950
peak=    3.482 closest distance to " CA  GLU A 152 " =    1.011
peak=    3.475 closest distance to " O   HOH Z 257 " =    2.517
peak=    3.473 closest distance to " CA  ALA A   9 " =    1.182
peak=    3.472 closest distance to " CB  ALA A   1 " =    1.359
peak=    3.472 closest distance to " N   ASN A  39 " =    1.201
peak=    3.467 closest distance to " N   ASP A 298 " =    0.914
peak=    3.463 closest distance to " CG  PRO A 213 " =    1.272
peak=    3.456 closest distance to " O   HOH Z 280 " =    2.875
peak=    3.456 closest distance to " CG  GLN A 205 " =    1.047
peak=    3.451 closest distance to " CB  GLN A  73 " =    1.083
peak=    3.451 closest distance to " CA  THR A 246 " =    1.061
peak=    3.451 closest distance to " O   HOH Z  88 " =    3.085
peak=    3.450 closest distance to " CB  SER A  28 " =    1.065
peak=    3.447 closest distance to " O   HOH Z  38 " =    2.628
peak=    3.446 closest distance to " CB  LEU A  83 " =    0.703
peak=    3.444 closest distance to " O   HOH Z 273 " =    3.034
peak=    3.442 closest distance to " O   HOH Z  44 " =    1.701
peak=    3.435 closest distance to " CB  ASN A 142 " =    1.036
peak=    3.431 closest distance to " CD  ARG A  36 " =    1.019
peak=    3.429 closest distance to " CB  GLU A 277 " =    0.772
peak=    3.429 closest distance to " O   HOH Z   9 " =    2.305
peak=    3.424 closest distance to " CB  ALA A 226 " =    1.190
peak=    3.421 closest distance to " O   HOH Z 139 " =    5.066
peak=    3.419 closest distance to " CA  VAL A  41 " =    0.819
peak=    3.418 closest distance to " CB  ARG A  79 " =    1.211
peak=    3.414 closest distance to " CG2 ILE A 234 " =    1.192
peak=    3.412 closest distance to " O   ALA A 292 " =    1.530
peak=    3.404 closest distance to " CD  ARG A 159 " =    0.794
peak=    3.402 closest distance to " CA  SER A  12 " =    1.307
peak=    3.401 closest distance to " C   VAL A 265 " =    1.058
peak=    3.393 closest distance to " O   HOH Z 154 " =    2.382
peak=    3.386 closest distance to " CD2 TRP A 179 " =    1.240
peak=    3.383 closest distance to " CB  ARG A 269 " =    1.452
peak=    3.382 closest distance to " O   HOH Z  90 " =    3.629
peak=    3.377 closest distance to " O   HOH Z 423 " =    1.731
peak=    3.376 closest distance to " O   HOH Z  59 " =    1.930
peak=    3.374 closest distance to " O  BHOH Z  74 " =    1.368
peak=    3.374 closest distance to " CB  MET A  47 " =    1.014
peak=    3.370 closest distance to " O   HOH Z 359 " =    1.815
peak=    3.370 closest distance to " CA  GLY A  23 " =    0.885
peak=    3.358 closest distance to " CD  PRO A  54 " =    1.093
peak=    3.356 closest distance to " CG  PRO A 243 " =    1.318
peak=    3.356 closest distance to " CA  ASN A 217 " =    1.378
peak=    3.353 closest distance to " O   HOH Z 214 " =    2.276
peak=    3.351 closest distance to " CB  ALA A 248 " =    1.295
peak=    3.349 closest distance to " O   HOH Z 359 " =    1.485
peak=    3.348 closest distance to " CB  TYR A 169 " =    0.774
peak=    3.345 closest distance to " O   HOH Z  85 " =    2.077
peak=    3.345 closest distance to " O   HOH Z 200 " =    1.423
peak=    3.344 closest distance to " O   HOH Z 353 " =    2.852
peak=    3.336 closest distance to " NH2 ARG A  79 " =    1.268
peak=    3.335 closest distance to " O   HOH Z 272 " =    1.970
peak=    3.328 closest distance to " O   HOH Z 282 " =    1.454
peak=    3.328 closest distance to " CA  SER A  87 " =    0.929
peak=    3.327 closest distance to " O   HOH Z 155 " =    2.914
peak=    3.327 closest distance to " O   HOH Z 432 " =    1.669
peak=    3.325 closest distance to " OG  SER A 245 " =    1.669
peak=    3.325 closest distance to " CB  VAL A 265 " =    1.351
peak=    3.323 closest distance to " N   SER A 271 " =    1.079
peak=    3.321 closest distance to " ND1 HIS A  81 " =    1.609
peak=    3.320 closest distance to " N   LYS A 166 " =    0.861
peak=    3.319 closest distance to " CD2 LEU A   5 " =    1.196
peak=    3.316 closest distance to " CG1 ILE A 106 " =    1.136
peak=    3.316 closest distance to " O   HOH Z 133 " =    2.143
peak=    3.316 closest distance to " N   THR A  52 " =    1.098
peak=    3.315 closest distance to " CG2 VAL A 197 " =    1.119
peak=    3.313 closest distance to " O   HOH Z 383 " =    2.045
peak=    3.312 closest distance to " CG1BVAL A 121 " =    1.242
peak=    3.311 closest distance to " C   GLY A  80 " =    1.285
peak=    3.309 closest distance to " O   GLU A   2 " =    1.764
peak=    3.308 closest distance to " CA  ALA A 295 " =    1.081
peak=    3.307 closest distance to " NH1 ARG A  14 " =    1.077
peak=    3.303 closest distance to " CB  LEU A 281 " =    0.790
peak=    3.299 closest distance to " CD1 LEU A 228 " =    1.575
peak=    3.298 closest distance to " CE3 TRP A  85 " =    1.177
peak=    3.297 closest distance to " CB  MET A 105 " =    1.264
peak=    3.296 closest distance to " O   HOH Z  56 " =    1.861
peak=    3.291 closest distance to " CB  PHE A 283 " =    0.939
peak=    3.288 closest distance to " O   HOH Z 420 " =    5.205
peak=    3.276 closest distance to " O   HOH Z 193 " =    1.780
peak=    3.275 closest distance to " CB  TRP A 179 " =    1.422
peak=    3.271 closest distance to " OD2 ASP A 298 " =    3.534
peak=    3.268 closest distance to " O   HOH Z 223 " =    1.602
peak=    3.267 closest distance to " O   HOH Z 316 " =    3.205
peak=    3.267 closest distance to " O   HOH Z 332 " =    1.623
peak=    3.264 closest distance to " N   ALA A 256 " =    1.020
peak=    3.262 closest distance to " CB  GLN A  89 " =    1.036
peak=    3.259 closest distance to " CB  ASN A 148 " =    1.473
peak=    3.259 closest distance to " OD1 ASN A 217 " =    1.711
peak=    3.258 closest distance to " N   ILE A  33 " =    0.999
peak=    3.257 closest distance to " CB  ARG A 190 " =    1.814
peak=    3.256 closest distance to " CA  GLY A 196 " =    0.747
peak=    3.255 closest distance to " O   ASP A 200 " =    1.652
peak=    3.254 closest distance to " CB AVAL A  41 " =    1.221
peak=    3.254 closest distance to " OH  TYR A 169 " =    0.902
peak=    3.252 closest distance to " CG  ASN A 252 " =    1.260
peak=    3.251 closest distance to " O   HOH Z 346 " =    1.596
peak=    3.250 closest distance to " N   GLY A  75 " =    1.616
peak=    3.250 closest distance to " O   HOH Z  68 " =    2.430
peak=    3.250 closest distance to " O   HOH Z 196 " =    1.935
peak=    3.249 closest distance to " N   CYS A 260 " =    0.844
peak=    3.247 closest distance to " O   HOH Z 189 " =    2.983
peak=    3.245 closest distance to " CA  THR A 264 " =    0.913
peak=    3.239 closest distance to " CD ALYS A 290 " =    1.316
peak=    3.238 closest distance to " CB  THR A 235 " =    1.316
peak=    3.235 closest distance to " O   HOH Z 394 " =    4.327
peak=    3.234 closest distance to " CZ3 TRP A  92 " =    1.428
peak=    3.234 closest distance to " O   HOH Z 250 " =    1.284
peak=    3.234 closest distance to " O   HOH Z 387 " =    2.936
peak=    3.233 closest distance to " CB  ALA A 291 " =    1.215
peak=    3.229 closest distance to " CZ3 TRP A 274 " =    4.300
peak=    3.224 closest distance to " O   HOH Z 294 " =    1.724
peak=    3.222 closest distance to " O   HOH Z  58 " =    1.671
peak=    3.219 closest distance to " CB  PHE A  16 " =    1.315
peak=    3.215 closest distance to " NZ  LYS A  76 " =    1.107
peak=    3.214 closest distance to " O   GLY A  91 " =    1.160
peak=    3.213 closest distance to " CA  TYR A 116 " =    1.556
peak=    3.209 closest distance to " O   HOH Z 285 " =    2.651
peak=    3.208 closest distance to " O   HOH Z 130 " =    2.146
peak=    3.205 closest distance to " O   HOH Z 183 " =    1.626
peak=    3.196 closest distance to " CG1 ILE A  49 " =    1.778
peak=    3.192 closest distance to " CB  GLU A 277 " =    3.911
peak=    3.187 closest distance to " O   HOH Z 417 " =    1.274
peak=    3.187 closest distance to " CB  ALA A  34 " =    0.763
peak=    3.186 closest distance to " O   HOH Z  54 " =    1.390
peak=    3.185 closest distance to " O   HOH Z  64 " =    2.461
peak=    3.184 closest distance to " CB  ARG A 219 " =    1.536
peak=    3.183 closest distance to " O   HOH Z  27 " =    1.088
peak=    3.179 closest distance to " CA  GLN A 223 " =    0.759
peak=    3.176 closest distance to " CA  GLY A 241 " =    0.883
peak=    3.175 closest distance to " CA  LEU A 282 " =    1.037
peak=    3.172 closest distance to " CZ3 TRP A 266 " =    1.159
peak=    3.172 closest distance to " N   ARG A 190 " =    0.942
peak=    3.171 closest distance to " O   HOH Z  30 " =    1.456
peak=    3.170 closest distance to " N   TYR A  15 " =    0.799
peak=    3.169 closest distance to " CA  CYS A 254 " =    1.402
peak=    3.169 closest distance to " C   ALA A 295 " =    1.893
peak=    3.168 closest distance to " O   HOH Z 380 " =    2.030
peak=    3.167 closest distance to " CB  ASP A 140 " =    0.815
peak=    3.166 closest distance to " O   HOH Z 419 " =    2.288
peak=    3.165 closest distance to " CG  GLU A  37 " =    0.990
peak=    3.154 closest distance to " O   TYR A 116 " =    1.251
peak=    3.154 closest distance to " CA  ALA A  51 " =    1.081
peak=    3.153 closest distance to " O   HOH Z 134 " =    2.217
peak=    3.152 closest distance to " CG2AVAL A 121 " =    1.918
peak=    3.152 closest distance to " O   HOH Z   5 " =    1.965
peak=    3.151 closest distance to " CE1 TYR A 186 " =    1.135
peak=    3.148 closest distance to " CA  ALA A 100 " =    1.135
peak=    3.146 closest distance to " NH1 ARG A 269 " =    0.748
peak=    3.142 closest distance to " CD  ARG A 269 " =    0.870
peak=    3.140 closest distance to " CA  ALA A 248 " =    1.298
peak=    3.137 closest distance to " O   HOH Z 141 " =    1.694
peak=    3.132 closest distance to " CE3 TRP A 274 " =    2.563
peak=    3.130 closest distance to " O   HOH Z 336 " =    1.961
peak=    3.123 closest distance to " O   HOH Z 281 " =    2.597
peak=    3.117 closest distance to " O   HOH Z 371 " =    2.895
peak=    3.115 closest distance to " CZ  PHE A 192 " =    0.979
peak=    3.112 closest distance to " CB  VAL A 257 " =    0.797
peak=    3.107 closest distance to " N   VAL A 126 " =    1.799
peak=    3.107 closest distance to " N   ALA A   1 " =    1.414
peak=    3.105 closest distance to " N   PHE A 130 " =    1.202
peak=    3.102 closest distance to " CD  ARG A  24 " =    1.383
peak=    3.099 closest distance to " O   SER A 273 " =    1.787
peak=    3.099 closest distance to " CB  LEU A 143 " =    1.137
peak=    3.097 closest distance to " N   ASP A 162 " =    1.367
peak=    3.090 closest distance to " CG1 ILE A  20 " =    1.277
peak=    3.088 closest distance to " O   HOH Z 236 " =    1.922
peak=    3.088 closest distance to " CB  TYR A  30 " =    0.958
peak=    3.087 closest distance to " O   HOH Z 427 " =    3.079
peak=    3.083 closest distance to " CA  CYS A 260 " =    0.842
peak=    3.079 closest distance to " OG  SER A  62 " =    2.862
peak=    3.075 closest distance to " CD1 LEU A 101 " =    1.057
peak=    3.066 closest distance to " OD1 ASN A  69 " =    2.366
peak=    3.060 closest distance to " O   HOH Z 184 " =    1.647
peak=    3.045 closest distance to " O   HOH Z 261 " =    1.157
peak=    3.029 closest distance to " O   HOH Z 130 " =    2.358

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.412 - 5.696
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 221
   mapped sites are within: 0.707 - 5.696

peak=   -5.009 closest distance to " CG2 VAL A 230 " =    0.872
peak=   -4.829 closest distance to " O   HOH Z 166 " =    1.403
peak=   -4.823 closest distance to " O   HOH Z 400 " =    0.807
peak=   -4.598 closest distance to " CB  ALA A 291 " =    2.516
peak=   -4.533 closest distance to " CD1 PHE A  59 " =    1.972
peak=   -4.486 closest distance to " CD  GLN A 223 " =    1.311
peak=   -4.425 closest distance to " OD1 ASN A 301 " =    0.873
peak=   -4.340 closest distance to " O   HOH Z 426 " =    0.791
peak=   -4.300 closest distance to " CG2BVAL A  41 " =    2.575
peak=   -4.183 closest distance to " CA  TYR A  68 " =    2.894
peak=   -4.155 closest distance to " CD  GLN A  58 " =    0.933
peak=   -4.133 closest distance to " OXT GLY A 302 " =    2.923
peak=   -4.131 closest distance to " O   HOH Z 198 " =    1.097
peak=   -4.114 closest distance to " O   SER A 135 " =    2.016
peak=   -4.097 closest distance to " CA  TRP A 274 " =    1.090
peak=   -4.083 closest distance to " O   HOH Z 184 " =    1.131
peak=   -4.074 closest distance to " CG  ARG A 269 " =    2.426
peak=   -4.061 closest distance to " O   HOH Z 103 " =    2.402
peak=   -4.060 closest distance to " CG1 VAL A 112 " =    2.585
peak=   -4.042 closest distance to " CD  GLN A  58 " =    1.043
peak=   -4.041 closest distance to " O   HOH Z 151 " =    1.131
peak=   -4.028 closest distance to " O   HOH Z 290 " =    0.997
peak=   -4.020 closest distance to " O   GLN A  11 " =    1.063
peak=   -4.016 closest distance to " O   HOH Z 351 " =    1.717
peak=   -3.975 closest distance to " CD  GLN A  73 " =    0.707
peak=   -3.959 closest distance to " CD  GLN A 223 " =    0.773
peak=   -3.915 closest distance to " CA  ASP A 298 " =    1.105
peak=   -3.894 closest distance to " CD  GLN A  11 " =    0.730
peak=   -3.861 closest distance to " O   HOH Z 216 " =    1.495
peak=   -3.834 closest distance to " O   HOH Z 411 " =    5.201
peak=   -3.819 closest distance to " CG  LEU A   5 " =    0.880
peak=   -3.816 closest distance to " CB  SER A 146 " =    2.110
peak=   -3.815 closest distance to " CG1 VAL A 197 " =    2.419
peak=   -3.809 closest distance to " O   HOH Z  37 " =    1.341
peak=   -3.807 closest distance to " CZ  ARG A 259 " =    0.825
peak=   -3.798 closest distance to " CA  VAL A 197 " =    0.958
peak=   -3.797 closest distance to " CA  SER A 164 " =    2.023
peak=   -3.795 closest distance to " O   HOH Z  10 " =    1.769
peak=   -3.787 closest distance to " O   HOH Z  13 " =    1.601
peak=   -3.787 closest distance to " CD  ARG A  14 " =    3.206
peak=   -3.769 closest distance to " OE2 GLU A 277 " =    2.884
peak=   -3.769 closest distance to " CG  ASP A  50 " =    2.288
peak=   -3.742 closest distance to " OD1 ASN A 148 " =    1.438
peak=   -3.719 closest distance to " O   HOH Z 238 " =    0.939
peak=   -3.714 closest distance to " O   HOH Z 265 " =    1.129
peak=   -3.710 closest distance to " CG  PRO A 243 " =    1.786
peak=   -3.708 closest distance to " O   HOH Z 388 " =    1.794
peak=   -3.686 closest distance to " CB  ALA A 161 " =    2.628
peak=   -3.685 closest distance to " O   SER A 276 " =    1.717
peak=   -3.684 closest distance to " O   HOH Z 422 " =    1.233
peak=   -3.679 closest distance to " CG1 VAL A 250 " =    2.515
peak=   -3.677 closest distance to " CD  GLN A  88 " =    1.137
peak=   -3.669 closest distance to " O   HOH Z 407 " =    1.362
peak=   -3.667 closest distance to " O   HOH Z 231 " =    1.575
peak=   -3.666 closest distance to " O   PRO A 198 " =    1.288
peak=   -3.665 closest distance to " CD2 PHE A  61 " =    2.071
peak=   -3.664 closest distance to " O   HOH Z 120 " =    1.749
peak=   -3.650 closest distance to " N   THR A  52 " =    1.602
peak=   -3.640 closest distance to " O   HOH Z  19 " =    2.130
peak=   -3.639 closest distance to " O   HOH Z  52 " =    2.217
peak=   -3.637 closest distance to " NH2 ARG A  66 " =    1.258
peak=   -3.636 closest distance to " O   HOH Z  60 " =    1.440
peak=   -3.629 closest distance to " N   ALA A   1 " =    2.677
peak=   -3.626 closest distance to " N   VAL A 230 " =    1.009
peak=   -3.623 closest distance to " N   ALA A 226 " =    2.184
peak=   -3.598 closest distance to " O   HOH Z   7 " =    1.312
peak=   -3.590 closest distance to " O   HOH Z 109 " =    3.462
peak=   -3.572 closest distance to " OD1 ASP A 171 " =    1.652
peak=   -3.572 closest distance to " CG  ASP A 231 " =    0.743
peak=   -3.567 closest distance to " O   HOH Z 435 " =    1.233
peak=   -3.564 closest distance to " O   TYR A  15 " =    1.694
peak=   -3.561 closest distance to " O   HOH Z 137 " =    1.542
peak=   -3.553 closest distance to " CG1 VAL A 112 " =    2.789
peak=   -3.540 closest distance to " OG  SER A 245 " =    0.921
peak=   -3.539 closest distance to " CE  MET A 105 " =    2.206
peak=   -3.537 closest distance to " O   HOH Z  54 " =    1.213
peak=   -3.534 closest distance to " N   SER A   3 " =    2.501
peak=   -3.533 closest distance to " O   HOH Z 183 " =    1.341
peak=   -3.532 closest distance to " CD  PRO A 243 " =    1.876
peak=   -3.532 closest distance to " O   HOH Z 394 " =    1.749
peak=   -3.516 closest distance to " CG2 THR A 221 " =    2.513
peak=   -3.512 closest distance to " O   HOH Z 196 " =    1.902
peak=   -3.508 closest distance to " N   ARG A 275 " =    1.295
peak=   -3.503 closest distance to " N   ASP A 272 " =    1.244
peak=   -3.499 closest distance to " C   ALA A 158 " =    1.488
peak=   -3.495 closest distance to " C   ASN A 285 " =    2.451
peak=   -3.493 closest distance to " CD1 LEU A 167 " =    2.056
peak=   -3.488 closest distance to " O  BHOH Z 338 " =    1.146
peak=   -3.481 closest distance to " O   HOH Z 136 " =    0.716
peak=   -3.476 closest distance to " CD1 TYR A 247 " =    2.441
peak=   -3.464 closest distance to " OD2 ASP A 298 " =    0.883
peak=   -3.459 closest distance to " O   HOH Z 301 " =    2.443
peak=   -3.452 closest distance to " O   SER A  95 " =    2.150
peak=   -3.452 closest distance to " CB  ALA A  10 " =    2.083
peak=   -3.451 closest distance to " O   HOH Z 109 " =    3.561
peak=   -3.448 closest distance to " O   HOH Z 174 " =    1.740
peak=   -3.447 closest distance to " CB  PRO A 243 " =    2.892
peak=   -3.447 closest distance to " O   HOH Z  57 " =    0.909
peak=   -3.447 closest distance to " CA  SER A 271 " =    2.302
peak=   -3.444 closest distance to " CB  ALA A 291 " =    2.368
peak=   -3.441 closest distance to " ND2 ASN A  60 " =    1.590
peak=   -3.438 closest distance to " CZ  ARG A  36 " =    1.123
peak=   -3.437 closest distance to " CA  GLY A 203 " =    2.274
peak=   -3.436 closest distance to " O   ALA A   7 " =    1.524
peak=   -3.433 closest distance to " O   HOH Z 150 " =    1.557
peak=   -3.427 closest distance to " O   HOH Z 313 " =    1.423
peak=   -3.424 closest distance to " N   SER A 134 " =    1.291
peak=   -3.414 closest distance to " O   HOH Z 311 " =    3.287
peak=   -3.413 closest distance to " CD2 PHE A  59 " =    2.552
peak=   -3.410 closest distance to " O   HOH Z 234 " =    4.193
peak=   -3.409 closest distance to " CG  GLN A 103 " =    2.323
peak=   -3.404 closest distance to " CD1 LEU A  25 " =    2.538
peak=   -3.394 closest distance to " CB  ALA A 248 " =    2.277
peak=   -3.379 closest distance to " O   HOH Z  31 " =    2.284
peak=   -3.369 closest distance to " O   HOH Z 401 " =    0.783
peak=   -3.364 closest distance to " O   HOH Z 403 " =    0.924
peak=   -3.364 closest distance to " CZ  ARG A  79 " =    1.694
peak=   -3.360 closest distance to " CD  PRO A 213 " =    2.252
peak=   -3.351 closest distance to " O   HOH Z 200 " =    1.369
peak=   -3.345 closest distance to " O   HOH Z  90 " =    1.933
peak=   -3.344 closest distance to " O   HOH Z  33 " =    1.582
peak=   -3.336 closest distance to " O   HOH Z 244 " =    2.034
peak=   -3.333 closest distance to " O   HOH Z  17 " =    1.319
peak=   -3.324 closest distance to " NH2 ARG A 159 " =    2.322
peak=   -3.321 closest distance to " O   HOH Z 414 " =    2.108
peak=   -3.319 closest distance to " O   HOH Z 252 " =    3.825
peak=   -3.317 closest distance to " O   VAL A 121 " =    0.901
peak=   -3.316 closest distance to " O   HOH Z 131 " =    0.756
peak=   -3.305 closest distance to " CA  ASN A 127 " =    1.031
peak=   -3.304 closest distance to " O   HOH Z 124 " =    1.736
peak=   -3.300 closest distance to " CB  GLU A 277 " =    1.320
peak=   -3.299 closest distance to " NH2 ARG A  36 " =    2.695
peak=   -3.298 closest distance to " CG2 ILE A  49 " =    2.603
peak=   -3.297 closest distance to " O   SER A 164 " =    1.887
peak=   -3.295 closest distance to " O   HOH Z 384 " =    1.958
peak=   -3.293 closest distance to " NE2 GLN A 103 " =    1.966
peak=   -3.285 closest distance to " CD  GLN A  88 " =    0.750
peak=   -3.280 closest distance to " O   HOH Z 368 " =    2.053
peak=   -3.279 closest distance to " NH2 ARG A 269 " =    2.398
peak=   -3.278 closest distance to " OD2 ASP A 231 " =    1.705
peak=   -3.278 closest distance to " CE2 PHE A  61 " =    2.546
peak=   -3.277 closest distance to " O   HOH Z 144 " =    1.764
peak=   -3.276 closest distance to " O   HOH Z 259 " =    1.140
peak=   -3.276 closest distance to " CE2 PHE A 218 " =    2.427
peak=   -3.274 closest distance to " OG1 THR A  82 " =    1.554
peak=   -3.268 closest distance to " O   HOH Z 222 " =    1.419
peak=   -3.268 closest distance to " CG  MET A  93 " =    2.530
peak=   -3.262 closest distance to " CD  GLN A  77 " =    1.257
peak=   -3.261 closest distance to " O   SER A 206 " =    1.318
peak=   -3.260 closest distance to " CB  PRO A 243 " =    2.925
peak=   -3.254 closest distance to " O   HOH Z  50 " =    0.964
peak=   -3.254 closest distance to " N   ILE A 120 " =    1.316
peak=   -3.253 closest distance to " CD1 ILE A 151 " =    2.234
peak=   -3.252 closest distance to " CG1 VAL A 296 " =    1.228
peak=   -3.248 closest distance to " N   THR A 235 " =    1.222
peak=   -3.247 closest distance to " O   HOH Z 171 " =    2.400
peak=   -3.246 closest distance to " OG  SER A  97 " =    2.415
peak=   -3.242 closest distance to " NZ  LYS A 119 " =    1.848
peak=   -3.238 closest distance to " O   HOH Z 185 " =    2.578
peak=   -3.237 closest distance to " OD2 ASP A 171 " =    1.922
peak=   -3.232 closest distance to " O   HOH Z 308 " =    1.253
peak=   -3.227 closest distance to " O  BHOH Z  74 " =    1.513
peak=   -3.227 closest distance to " C   THR A 264 " =    1.408
peak=   -3.220 closest distance to " CD2 HIS A 115 " =    1.079
peak=   -3.218 closest distance to " CG2 VAL A 189 " =    2.190
peak=   -3.214 closest distance to " O   HOH Z 108 " =    2.065
peak=   -3.213 closest distance to " CB  PHE A 130 " =    1.285
peak=   -3.208 closest distance to " CG  ARG A 259 " =    2.448
peak=   -3.208 closest distance to " OH  TYR A 172 " =    1.766
peak=   -3.204 closest distance to " O   HOH Z 150 " =    1.191
peak=   -3.203 closest distance to " O   HOH Z 412 " =    2.370
peak=   -3.202 closest distance to " CZ2 TRP A  92 " =    2.798
peak=   -3.200 closest distance to " O   HOH Z 413 " =    0.914
peak=   -3.194 closest distance to " O   HOH Z 418 " =    1.381
peak=   -3.191 closest distance to " O   HOH Z  64 " =    1.572
peak=   -3.189 closest distance to " O   LEU A 282 " =    2.160
peak=   -3.183 closest distance to " O   HOH Z 259 " =    1.586
peak=   -3.183 closest distance to " O   HOH Z  39 " =    2.489
peak=   -3.182 closest distance to " O   HOH Z  91 " =    2.168
peak=   -3.180 closest distance to " C   THR A 279 " =    1.145
peak=   -3.180 closest distance to " C   LEU A 228 " =    2.177
peak=   -3.179 closest distance to " CB  HIS A  86 " =    2.360
peak=   -3.178 closest distance to " CD  ARG A  36 " =    1.023
peak=   -3.173 closest distance to " O   HOH Z 165 " =    1.593
peak=   -3.168 closest distance to " CA  GLY A 241 " =    3.382
peak=   -3.168 closest distance to " O   HOH Z 156 " =    3.653
peak=   -3.162 closest distance to " CD  GLN A  55 " =    0.785
peak=   -3.161 closest distance to " OH  TYR A 247 " =    2.235
peak=   -3.155 closest distance to " C   VAL A 265 " =    1.027
peak=   -3.150 closest distance to " CD2 PHE A 192 " =    2.139
peak=   -3.150 closest distance to " O   HOH Z 205 " =    0.914
peak=   -3.148 closest distance to " OG BSER A 210 " =    1.188
peak=   -3.144 closest distance to " O   HOH Z 252 " =    1.490
peak=   -3.137 closest distance to " O   HOH Z 117 " =    1.036
peak=   -3.135 closest distance to " O   HOH Z  38 " =    1.046
peak=   -3.135 closest distance to " OG  SER A  87 " =    1.741
peak=   -3.132 closest distance to " CG  ARG A 259 " =    1.448
peak=   -3.127 closest distance to " O   HOH Z 307 " =    2.069
peak=   -3.123 closest distance to " O   PHE A  59 " =    2.276
peak=   -3.117 closest distance to " CA  GLY A  98 " =    2.094
peak=   -3.114 closest distance to " O   HOH Z 331 " =    1.219
peak=   -3.111 closest distance to " O   HOH Z 100 " =    0.782
peak=   -3.087 closest distance to " ND2 ASN A  45 " =    1.190
peak=   -3.079 closest distance to " CG1BVAL A  72 " =    5.696
peak=   -3.064 closest distance to " CG  TRP A 266 " =    1.831
peak=   -3.053 closest distance to " OE1 GLN A  88 " =    1.114
peak=   -3.042 closest distance to " OE1 GLU A  44 " =    0.823
peak=   -3.041 closest distance to " ND2 ASN A  60 " =    1.797
peak=   -3.041 closest distance to " CB  MET A 188 " =    1.656
peak=   -3.038 closest distance to " CG2 VAL A 296 " =    1.132

================= 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    :  0.5041 0.4876   6.301498e+00   6.282508e+00
   1_bss:  0.4980 0.4799   6.297166e+00   6.277313e+00
   1_xyz:  0.4311 0.4392   6.229700e+00   6.234803e+00
   1_adp:  0.3890 0.4310   6.167598e+00   6.222846e+00
   1_occ:  0.3880 0.4296   6.166622e+00   6.222907e+00
   2_bss:  0.3863 0.4247   6.167473e+00   6.221973e+00
   2_xyz:  0.3279 0.3965   6.061708e+00   6.172822e+00
   2_adp:  0.3199 0.3815   6.046037e+00   6.152997e+00
   2_occ:  0.3198 0.3819   6.045957e+00   6.153347e+00
   3_bss:  0.3202 0.3808   6.047173e+00   6.153399e+00
   3_xyz:  0.2751 0.3227   5.912748e+00   6.038664e+00
   3_adp:  0.2615 0.3080   5.877544e+00   6.006621e+00
   3_occ:  0.2613 0.3079   5.876992e+00   6.006749e+00
   4_bss:  0.2610 0.3084   5.877720e+00   6.007221e+00
   4_xyz:  0.1897 0.2360   5.588999e+00   5.767058e+00
   4_adp:  0.1673 0.2162   5.486923e+00   5.688464e+00
   4_occ:  0.1670 0.2163   5.486300e+00   5.689025e+00
   5_bss:  0.1667 0.2161   5.484894e+00   5.687162e+00
   5_xyz:  0.1426 0.1897   5.349454e+00   5.565461e+00
   5_adp:  0.1400 0.1846   5.325918e+00   5.535551e+00
   5_occ:  0.1397 0.1846   5.324966e+00   5.535336e+00
   5_bss:  0.1400 0.1848   5.325716e+00   5.536035e+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:  0.297  24.534   5.964  11.570   7.994   0.000   0.000   0.000
   1_xyz:  0.297  24.534   5.964  11.570   7.994   0.000   0.000   0.000
   1_adp:  0.297  24.534   5.964  11.570   7.994   0.000   0.000   0.000
   1_occ:  0.297  24.534   5.964  11.570   7.994   0.000   0.000   0.000
   2_bss:  0.312  52.158   2.940   7.454   4.827   0.000   0.000   0.000
   2_xyz:  0.312  52.158   2.940   7.454   4.827   0.000   0.000   0.000
   2_adp:  0.312  52.158   2.940   7.454   4.827   0.000   0.000   0.000
   2_occ:  0.312  52.158   2.940   7.454   4.827   0.000   0.000   0.000
   3_bss:  0.312  52.158   2.565   5.828   3.722   0.000   0.000   0.000
   3_xyz:  0.312  52.158   2.565   5.828   3.722   0.000   0.000   0.000
   3_adp:  0.312  52.158   2.565   5.828   3.722   0.000   0.000   0.000
   3_occ:  0.312  52.158   2.565   5.828   3.722   0.000   0.000   0.000
   4_bss:  0.318  62.170   1.687   4.435   2.855   0.000   0.000   0.000
   4_xyz:  0.318  62.170   1.687   4.435   2.855   0.000   0.000   0.000
   4_adp:  0.318  62.170   1.687   4.435   2.855   0.000   0.000   0.000
   4_occ:  0.318  62.170   1.687   4.435   2.855   0.000   0.000   0.000
   5_bss:  0.320  62.170   1.424   2.905   2.805   0.000   0.000   0.000
   5_xyz:  0.320  62.170   1.424   2.905   2.805   0.000   0.000   0.000
   5_adp:  0.320  62.170   1.424   2.905   2.805   0.000   0.000   0.000
   5_occ:  0.320  62.170   1.424   2.905   2.805   0.000   0.000   0.000
   5_bss:  0.324  66.279  -0.867   0.275   0.593   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.089 0.3797  0.4295    74225.197
   1_bss:  60.084 0.3921  0.5659    72634.761
   1_xyz:  52.045 0.4943  0.6977    57849.125
   1_adp:  49.309 0.5290  0.8097    54346.171
   1_occ:  49.237 0.5299  0.8096    54298.371
   2_bss:  48.917 0.5338  0.7278    53719.621
   2_xyz:  45.052 0.5807  0.7919    45596.073
   2_adp:  42.974 0.6066  0.8105    42538.014
   2_occ:  42.984 0.6065  0.8103    42597.098
   3_bss:  42.898 0.6075  0.7841    42438.110
   3_xyz:  34.814 0.7036  0.8928    29568.528
   3_adp:  32.868 0.7263  0.9078    26960.155
   3_occ:  32.852 0.7265  0.9073    26930.429
   4_bss:  32.837 0.7267  0.8753    26943.904
   4_xyz:  23.383 0.8280  0.9591    14364.471
   4_adp:  21.212 0.8498  0.9596    12098.159
   4_occ:  21.207 0.8499  0.9597    12123.024
   5_bss:  21.129 0.8506  0.9405    12043.960
   5_xyz:  17.956 0.8809  0.9603     9142.421
   5_adp:  17.058 0.8895  0.9623     8695.268
   5_occ:  17.049 0.8896  0.9624     8696.289
   5_bss:  17.035 0.8897  0.9523     8691.224
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4651e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4651e+01
   1_xyz:   1.715  0.013  0.109 18.156  0.007  4.126   1.4661e-01
   1_adp:   1.715  0.013  0.109 18.156  0.007  4.126   1.4661e-01
   1_occ:   1.715  0.013  0.109 18.156  0.007  4.126   1.4661e-01
   2_bss:   1.715  0.013  0.109 18.156  0.007  4.126   1.4661e-01
   2_xyz:   1.286  0.009  0.088 16.966  0.005  4.110   9.8996e-02
   2_adp:   1.286  0.009  0.088 16.966  0.005  4.110   9.8996e-02
   2_occ:   1.286  0.009  0.088 16.966  0.005  4.110   9.8996e-02
   3_bss:   1.286  0.009  0.088 16.966  0.005  4.110   9.8996e-02
   3_xyz:   1.210  0.008  0.088 15.586  0.004  4.133   7.9295e-02
   3_adp:   1.210  0.008  0.088 15.586  0.004  4.133   7.9295e-02
   3_occ:   1.210  0.008  0.088 15.586  0.004  4.133   7.9295e-02
   4_bss:   1.210  0.008  0.088 15.586  0.004  4.133   7.9295e-02
   4_xyz:   1.343  0.013  0.094 16.215  0.005  4.128   1.1542e-01
   4_adp:   1.343  0.013  0.094 16.215  0.005  4.128   1.1542e-01
   4_occ:   1.343  0.013  0.094 16.215  0.005  4.128   1.1542e-01
   5_bss:   1.343  0.013  0.094 16.215  0.005  4.128   1.1542e-01
   5_xyz:   1.141  0.010  0.089 15.575  0.004  4.117   8.0019e-02
   5_adp:   1.141  0.010  0.089 15.575  0.004  4.117   8.0019e-02
   5_occ:   1.141  0.010  0.089 15.575  0.004  4.117   8.0019e-02
   5_bss:   1.141  0.010  0.089 15.575  0.004  4.117   8.0019e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0852e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0852e+00
   1_xyz:  14.309  0.124  0.459 88.597  0.042  2.160   1.0451e-01
   1_adp:  14.309  0.124  0.459 88.597  0.042  2.160   1.0451e-01
   1_occ:  14.309  0.124  0.459 88.597  0.042  2.160   1.0451e-01
   2_bss:  14.309  0.124  0.459 88.597  0.042  2.160   1.0451e-01
   2_xyz:   8.175  0.070  0.303 84.861  0.034  2.069   6.5662e-02
   2_adp:   8.175  0.070  0.303 84.861  0.034  2.069   6.5662e-02
   2_occ:   8.175  0.070  0.303 84.861  0.034  2.069   6.5662e-02
   3_bss:   8.175  0.070  0.303 84.861  0.034  2.069   6.5662e-02
   3_xyz:   7.586  0.089  0.339 89.191  0.038  2.248   8.7280e-02
   3_adp:   7.586  0.089  0.339 89.191  0.038  2.248   8.7280e-02
   3_occ:   7.586  0.089  0.339 89.191  0.038  2.248   8.7280e-02
   4_bss:   7.586  0.089  0.339 89.191  0.038  2.248   8.7280e-02
   4_xyz:   9.883  0.074  0.314 84.214  0.049  2.000   1.6257e-01
   4_adp:   9.883  0.074  0.314 84.214  0.049  2.000   1.6257e-01
   4_occ:   9.883  0.074  0.314 84.214  0.049  2.000   1.6257e-01
   5_bss:   9.883  0.074  0.314 84.214  0.049  2.000   1.6257e-01
   5_xyz:   7.645  0.050  0.553 81.963  0.042  2.099   5.9599e-02
   5_adp:   7.645  0.050  0.553 81.963  0.042  2.099   5.9599e-02
   5_occ:   7.645  0.050  0.553 81.963  0.042  2.099   5.9599e-02
   5_bss:   7.645  0.050  0.553 81.963  0.042  2.099   5.9599e-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: 128.03   0.00  15.70  86.65   0.00  13.50 128.03   0.00  27.72
   1_occ: 128.03   0.00  15.70  86.65   0.00  13.50 128.03   0.00  27.72
   2_bss: 128.03   0.00  15.70  86.65   0.00  13.50 128.03   0.00  27.72
   2_xyz: 128.03   0.00  15.70  86.65   0.00  13.50 128.03   0.00  27.72
   2_adp: 127.03   0.00  14.11  71.04   0.00  11.58 127.03   0.00  27.89
   2_occ: 127.03   0.00  14.11  71.04   0.00  11.58 127.03   0.00  27.89
   3_bss: 127.03   0.00  14.11  71.04   0.00  11.58 127.03   0.00  27.89
   3_xyz: 127.03   0.00  14.11  71.04   0.00  11.58 127.03   0.00  27.89
   3_adp: 118.25   0.00  13.87  67.97   0.00  10.73 118.25   0.62  30.96
   3_occ: 118.25   0.00  13.87  67.97   0.00  10.73 118.25   0.62  30.96
   4_bss: 118.25   0.00  13.87  67.97   0.00  10.73 118.25   0.62  30.96
   4_xyz: 118.25   0.00  13.87  67.97   0.00  10.73 118.25   0.62  30.96
   4_adp: 105.12   0.00  14.38  79.12   0.00   9.86 105.12   0.00  38.98
   4_occ: 105.12   0.00  14.38  79.12   0.00   9.86 105.12   0.00  38.98
   5_bss: 105.12   0.00  14.38  79.12   0.00   9.86 105.12   0.00  38.98
   5_xyz: 105.12   0.00  14.38  79.12   0.00   9.86 105.12   0.00  38.98
   5_adp:  97.90   0.00  13.51  76.62   0.00   9.27  97.90   1.74  36.59
   5_occ:  97.90   0.00  13.51  76.62   0.00   9.27  97.90   1.74  36.59
   5_bss:  99.98   2.08  15.58  78.70   2.08  11.34  99.98   3.82  38.67
------------------------------------------------------------------------
 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:    1.124    0.030    0.409
   1_adp:    1.124    0.030    0.409
   1_occ:    1.124    0.030    0.409
   2_bss:    1.124    0.030    0.409
   2_xyz:    1.607    0.056    0.568
   2_adp:    1.607    0.056    0.568
   2_occ:    1.607    0.056    0.568
   3_bss:    1.607    0.056    0.568
   3_xyz:    1.601    0.048    0.665
   3_adp:    1.601    0.048    0.665
   3_occ:    1.601    0.048    0.665
   4_bss:    1.601    0.048    0.665
   4_xyz:    2.010    0.059    0.856
   4_adp:    2.010    0.059    0.856
   4_occ:    2.010    0.059    0.856
   5_bss:    2.010    0.059    0.856
   5_xyz:    2.066    0.054    0.887
   5_adp:    2.066    0.054    0.887
   5_occ:    2.066    0.054    0.887
   5_bss:    2.066    0.054    0.887
------------------------------------------------------------------------

CPU time actual refinement: 334.57


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_964/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_964/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_964/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_964/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_964/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.41 
  Macro-tasks:
    bulk solvent and scale       = 41.95  
    individual site refinement   = 136.54 
    weights calculation          = 32.64  
    collect and process          = 6.40   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 217.68 
  Micro-tasks:
    mask                            = 3.03   
    f_calc                          = 102.23 
    alpha_beta                      = 8.33   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 112.34 
    fmodel                         = 7.27   
    r_factors                      = 0.31   
    phase_errors                   = 9.82   
    foms                           = 0.35   
    TOTAL for micro-tasks          = 244.85 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.769 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    634 calls, 101.90 s
gradients_fft:          578 calls,  99.59 s

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

# Date 2008-01-16 Time 02:51:11 PST -0800 (1200480671.25 s)
Start R-work = 0.5041, R-free = 0.4876 (no bulk solvent and anisotropic scale)
Final R-work = 0.1554, R-free = 0.2002 (no bulk solvent and anisotropic scale)

Start R-work = 0.4980, R-free = 0.4799
Final R-work = 0.1400, R-free = 0.1848