# Date 2008-01-16 Time 02:57:25 PST -0800 (1200481045.53 s)
#phil __OFF__

Command line arguments: "../1044.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2616
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1044

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.1647, 88.5498, 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: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 2.01241
Completeness in resolution range: 0.960716
Completeness with d_max=infinity: 0.957757

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2591
                             d_min =   2.0124

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 2.01241
Completeness in resolution range: 0.960716
Completeness with d_max=infinity: 0.957757

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2595 -  4.3062 [2147/2171]  1929   218  10.2%
  bin  2:  4.3062 -  3.4307 [2046/2066]  1845   201   9.8%
  bin  3:  3.4307 -  3.0008 [2040/2059]  1834   206  10.1%
  bin  4:  3.0008 -  2.7281 [2005/2035]  1805   200  10.0%
  bin  5:  2.7281 -  2.5335 [2006/2025]  1808   198   9.9%
  bin  6:  2.5335 -  2.3848 [1982/2007]  1779   203  10.2%
  bin  7:  2.3848 -  2.2657 [1986/2014]  1788   198  10.0%
  bin  8:  2.2657 -  2.1674 [1967/2003]  1773   194   9.9%
  bin  9:  2.1674 -  2.0842 [1965/2007]  1771   194   9.9%
  bin 10:  2.0842 -  2.0124 [1445/2003]  1298   147  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1044/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: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 14
        2.42 -     3.04: 2156
        3.04 -     3.66: 4559
        3.66 -     4.28: 8822
        4.28 -     4.90: 12135
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.964 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.998 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.998 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.053 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27681 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_1044/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1044/model_refine_001.geo

CPU time processing inputs: 8.25


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.16465 88.54975 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: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4821   r_free= 0.4771   ksol= 0.00   Bsol= 0.00   scale= 0.775    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.283346                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8029 0.99   1394  154 0.3989 0.3697      6.6141      6.5248|
|  2:  4.8029 -  3.8321 0.99   1335  151 0.4014 0.4390       6.797      6.9066|
|  3:  3.8321 -  3.3536 0.99   1308  143 0.4427 0.4138      6.6854      6.6637|
|  4:  3.3536 -  3.0496 0.99   1305  148 0.4734 0.4158      6.5365        6.44|
|  5:  3.0496 -  2.8325 0.99   1302  145 0.5058 0.4911      6.3762       6.417|
|  6:  2.8325 -  2.6664 0.99   1293  142 0.5091 0.5722      6.2892      6.1994|
|  7:  2.6664 -  2.5335 0.99   1284  140 0.5235 0.5151      6.2386      6.2348|
|  8:  2.5335 -  2.4237 0.98   1273  145 0.5422 0.4518      6.2001      6.1264|
|  9:  2.4237 -  2.3307 0.98   1266  140 0.5086 0.6122      6.1109      6.1864|
| 10:  2.3307 -  2.2506 1.00   1289  143 0.5311 0.5128      6.1221      6.1036|
| 11:  2.2506 -  2.1804 0.97   1256  137 0.5120 0.5130      6.0247      6.0871|
| 12:  2.1804 -  2.1182 0.98   1252  145 0.5234 0.5169      5.9814      5.9945|
| 13:  2.1182 -  2.0626 0.99   1303  133 0.5304 0.5269      5.8825       5.848|
| 14:  2.0626 -  2.0124 0.61    770   93 0.5366 0.5058      5.8718      5.7651|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.8029  1394   154  0.71  33.24   0.78     0.74      67260.43|
|  2:  4.8029 -  3.8321  1335   151  0.71  34.12   0.86     0.76     103085.99|
|  3:  3.8321 -  3.3536  1308   143  0.61  42.79   0.81     0.71     110640.10|
|  4:  3.3536 -  3.0496  1305   148  0.51  51.25   0.79     0.58      99885.28|
|  5:  3.0496 -  2.8325  1302   145  0.41  59.14   0.73     0.48      83362.36|
|  6:  2.8325 -  2.6664  1293   142  0.37  62.13   0.71     0.41      74783.78|
|  7:  2.6664 -  2.5335  1284   140  0.35  63.82   0.71     0.39      67206.19|
|  8:  2.5335 -  2.4237  1273   145  0.35  63.68   0.71     0.40      59513.24|
|  9:  2.4237 -  2.3307  1266   140  0.34  64.21   0.72     0.40      55434.55|
| 10:  2.3307 -  2.2506  1289   143  0.34  64.75   0.72     0.39      50259.43|
| 11:  2.2506 -  2.1804  1256   137  0.32  66.03   0.74     0.39      48371.32|
| 12:  2.1804 -  2.1182  1252   145  0.33  65.74   0.73     0.39      43485.09|
| 13:  2.1182 -  2.0626  1303   133  0.30  68.03   0.69     0.36      38364.85|
| 14:  2.0626 -  2.0124   770    93  0.29  68.64   0.70     0.30      32607.95|
|alpha:            min =        0.30 max =            0.76 mean =         0.49|
|beta:             min =    32607.95 max =       110640.10 mean =     68008.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.09|
|phase err.(test): min =        0.00 max =           89.99 mean =        57.24|
|-----------------------------------------------------------------------------|

============================== 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 = 15.629015             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.188   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.436177              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.658   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      669 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1478 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2566 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3818 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4955 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6489 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7535 |
|-----------------------------------------------------------------------------|
|-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 |       54.671 |
| 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 |       1.662 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.405)------------------------------------------|
|    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 = 12.405)------------------------------------------|
|    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: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4868   r_free= 0.4785   ksol= 0.00   Bsol= 0.00   scale= 0.748    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.284782                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4741   r_free= 0.4643   ksol= 0.32   Bsol= 42.90   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.31,6.62,11.44,0.00,0.00,0.00); trace/3= 8.46                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.278047                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.784831             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.889   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.290323              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.791   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4741      final r-factor (work) = 0.3896          |
| start r-factor (free) = 0.4643      final r-factor (free) = 0.4207          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 97.9715 = 13.78 * 0.50 * 6.2823 + 1.00 * 54.6714                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.8188 = 13.78 * 0.50 * 6.1903 + 1.00 * 0.1528                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3896      final r-factor (work) = 0.3447          |
| start r-factor (free) = 0.4207      final r-factor (free) = 0.3989          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0019 = 1.29 * 1.00 * 6.1903 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8993 = 1.29 * 1.00 * 6.1079 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.86   13.28    None  None   None       |
|    all(noH): 2823   0      0.00    70.86   13.28    None  None   None       |
|    Sol.    : 438    0      0.00    67.85   26.49    None  None   None       |
|    Mac.    : 2385   0      0.00    70.86   10.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.086: 1067   |   5:    35.429 -  42.515:   74        |
|      1:     7.086 -  14.172:  715   |   6:    42.515 -  49.600:   50        |
|      2:    14.172 -  21.257:  468   |   7:    49.600 -  56.686:   32        |
|      3:    21.257 -  28.343:  257   |   8:    56.686 -  63.772:   17        |
|      4:    28.343 -  35.429:  138   |   9:    63.772 -  70.858:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3447 r_free = 0.3989             target_work(ml) = 6.085         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3444 r_free = 0.4000             target_work(ml) = 6.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3444   r_free= 0.4000   ksol= 0.32   Bsol= 42.90   scale= 1.070   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.31,6.62,11.44,0.00,0.00,0.00); trace/3= 8.46                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.084657                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3434   r_free= 0.3977   ksol= 0.30   Bsol= 42.90   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.51,4.21,8.31,0.00,0.00,0.00); trace/3= 5.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.086327                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.173613              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.390   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.575575              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.674  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3434      final r-factor (work) = 0.2694          |
| start r-factor (free) = 0.3977      final r-factor (free) = 0.3261          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9886 = 6.17 * 0.50 * 6.1020 + 1.00 * 0.1528                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.5690 = 6.17 * 0.50 * 5.9869 + 1.00 * 0.0886                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2694      final r-factor (work) = 0.2487          |
| start r-factor (free) = 0.3261      final r-factor (free) = 0.3054          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5317 = 0.58 * 1.00 * 5.9869 + 1.00 * 0.0858                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6947 = 0.58 * 1.00 * 5.8501 + 1.00 * 0.3276                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.38   13.18    None  None   None       |
|    all(noH): 2823   0      0.00    72.38   13.18    None  None   None       |
|    Sol.    : 438    0      0.00    71.01   30.91    None  None   None       |
|    Mac.    : 2385   0      0.00    72.38   9.92     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.239: 1188   |   5:    36.192 -  43.431:   83        |
|      1:     7.239 -  14.477:  735   |   6:    43.431 -  50.669:   57        |
|      2:    14.477 -  21.715:  364   |   7:    50.669 -  57.907:   37        |
|      3:    21.715 -  28.954:  207   |   8:    57.907 -  65.146:    9        |
|      4:    28.954 -  36.192:  138   |   9:    65.146 -  72.384:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2487 r_free = 0.3054             target_work(ml) = 5.825         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2484 r_free = 0.3051             target_work(ml) = 5.824         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2484   r_free= 0.3051   ksol= 0.30   Bsol= 42.90   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.51,4.21,8.31,0.00,0.00,0.00); trace/3= 5.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.824348                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2472   r_free= 0.3039   ksol= 0.31   Bsol= 61.57   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.64,2.80,5.47,0.00,0.00,0.00); trace/3= 3.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.825723                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.894571              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.588   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 10.648453             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.299   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2472      final r-factor (work) = 0.1834          |
| start r-factor (free) = 0.3039      final r-factor (free) = 0.2388          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4120 = 4.89 * 0.50 * 5.8527 + 1.00 * 0.0886                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0504 = 4.89 * 0.50 * 5.7076 + 1.00 * 0.0824                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1834      final r-factor (work) = 0.1603          |
| start r-factor (free) = 0.2388      final r-factor (free) = 0.2191          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 60.7952 = 10.65 * 1.00 * 5.7076 + 1.00 * 0.0183                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 58.6375 = 10.65 * 1.00 * 5.5048 + 1.00 * 0.0202                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.77  14.69    None  None   None       |
|    all(noH): 2823   0      0.00    100.77  14.69    None  None   None       |
|    Sol.    : 438    0      0.21    100.77  42.59    None  None   None       |
|    Mac.    : 2385   0      0.00    96.86   9.57     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 -  10.077: 1640   |   5:    50.384 -  60.461:   89        |
|      1:    10.077 -  20.154:  606   |   6:    60.461 -  70.538:   67        |
|      2:    20.154 -  30.231:  174   |   7:    70.538 -  80.615:   29        |
|      3:    30.231 -  40.307:  103   |   8:    80.615 -  90.692:   11        |
|      4:    40.307 -  50.384:   97   |   9:    90.692 - 100.768:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1603 r_free = 0.2191             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1601 r_free = 0.2192             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1601   r_free= 0.2192   ksol= 0.31   Bsol= 61.57   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.64,2.80,5.47,0.00,0.00,0.00); trace/3= 3.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.465238                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1603   r_free= 0.2192   ksol= 0.34   Bsol= 87.25   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.07,2.18,4.21,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.464726                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.877806              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.700   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.366166              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.591  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1603      final r-factor (work) = 0.1401          |
| start r-factor (free) = 0.2192      final r-factor (free) = 0.1948          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0091 = 2.88 * 0.50 * 5.5089 + 1.00 * 0.0824                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8605 = 2.88 * 0.50 * 5.4131 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1401      final r-factor (work) = 0.1362          |
| start r-factor (free) = 0.1948      final r-factor (free) = 0.1848          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0021 = 0.37 * 1.00 * 5.4131 + 1.00 * 0.0200                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9721 = 0.37 * 1.00 * 5.3419 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.23   13.68    None  None   None       |
|    all(noH): 2823   0      0.00    99.23   13.68    None  None   None       |
|    Sol.    : 438    0      0.90    99.23   39.78    None  None   None       |
|    Mac.    : 2385   0      0.00    82.61   8.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.923: 1719   |   5:    49.617 -  59.540:   84        |
|      1:     9.923 -  19.847:  574   |   6:    59.540 -  69.463:   47        |
|      2:    19.847 -  29.770:  147   |   7:    69.463 -  79.386:   23        |
|      3:    29.770 -  39.693:  123   |   8:    79.386 -  89.310:    7        |
|      4:    39.693 -  49.617:   94   |   9:    89.310 -  99.233:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1362 r_free = 0.1848             target_work(ml) = 5.313         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1360 r_free = 0.1848             target_work(ml) = 5.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1360   r_free= 0.1848   ksol= 0.34   Bsol= 87.25   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.07,2.18,4.21,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.311960                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1359   r_free= 0.1848   ksol= 0.33   Bsol= 74.09   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.13,3.89,0.00,0.00,0.00); trace/3= 2.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.311415                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.515148              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.493  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.483246              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.344   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1359      final r-factor (work) = 0.1226          |
| start r-factor (free) = 0.1848      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4588 = 3.52 * 0.50 * 5.3410 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3511 = 3.52 * 0.50 * 5.2693 + 1.00 * 0.0898                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1226      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1719      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5608 = 0.48 * 1.00 * 5.2693 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5513 = 0.48 * 1.00 * 5.2271 + 1.00 * 0.0253                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.37   13.62    None  None   None       |
|    all(noH): 2823   0      0.00    99.37   13.62    None  None   None       |
|    Sol.    : 438    0      1.27    99.37   39.67    None  None   None       |
|    Mac.    : 2385   0      0.00    81.91   8.84     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 -   9.937: 1747   |   5:    49.687 -  59.625:   84        |
|      1:     9.937 -  19.875:  551   |   6:    59.625 -  69.562:   47        |
|      2:    19.875 -  29.812:  140   |   7:    69.562 -  79.499:   24        |
|      3:    29.812 -  39.750:  129   |   8:    79.499 -  89.437:    6        |
|      4:    39.750 -  49.687:   90   |   9:    89.437 -  99.374:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1215 r_free = 0.1709             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1213 r_free = 0.1710             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1710   ksol= 0.33   Bsol= 74.09   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.13,3.89,0.00,0.00,0.00); trace/3= 2.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.222537                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8029 0.99   1394  154 0.1022 0.1408      5.4347      5.5994|
|  2:  4.8029 -  3.8321 0.99   1335  151 0.0858 0.1192      5.4651      5.6917|
|  3:  3.8321 -  3.3536 0.99   1308  143 0.1118 0.1554      5.5317      5.8671|
|  4:  3.3536 -  3.0496 0.99   1305  148 0.1306 0.1852      5.5128      5.7058|
|  5:  3.0496 -  2.8325 0.99   1302  145 0.1494 0.1778      5.4306      5.6233|
|  6:  2.8325 -  2.6664 0.99   1293  142 0.1366 0.2365       5.308      5.6229|
|  7:  2.6664 -  2.5335 0.99   1284  140 0.1407 0.1657      5.2711       5.403|
|  8:  2.5335 -  2.4237 0.98   1273  145 0.1318 0.1789      5.1805      5.4215|
|  9:  2.4237 -  2.3307 0.98   1266  140 0.1309 0.1885      5.1257      5.3527|
| 10:  2.3307 -  2.2506 1.00   1289  143 0.1250 0.1844      5.0405      5.2622|
| 11:  2.2506 -  2.1804 0.97   1256  137 0.1270 0.1911      5.0127      5.3136|
| 12:  2.1804 -  2.1182 0.98   1252  145 0.1205 0.1981      4.9453      5.3082|
| 13:  2.1182 -  2.0626 0.99   1303  133 0.1256 0.1851      4.8635      5.0862|
| 14:  2.0626 -  2.0124 0.61    770   93 0.1138 0.1707      4.7585      4.9804|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.8029  1394   154  0.93   9.97   0.97     0.94       8509.07|
|  2:  4.8029 -  3.8321  1335   151  0.95   8.60   1.00     0.98      10080.47|
|  3:  3.8321 -  3.3536  1308   143  0.93  12.03   1.02     1.02      11594.99|
|  4:  3.3536 -  3.0496  1305   148  0.91  14.67   1.00     0.98      11592.26|
|  5:  3.0496 -  2.8325  1302   145  0.89  17.55   1.00     0.98      10070.94|
|  6:  2.8325 -  2.6664  1293   142  0.88  18.10   0.97     0.95       8631.00|
|  7:  2.6664 -  2.5335  1284   140  0.89  17.84   0.98     0.94       7708.66|
|  8:  2.5335 -  2.4237  1273   145  0.89  17.31   0.98     0.95       6617.79|
|  9:  2.4237 -  2.3307  1266   140  0.90  16.84   1.00     0.95       6016.25|
| 10:  2.3307 -  2.2506  1289   143  0.89  17.24   0.99     0.95       5119.91|
| 11:  2.2506 -  2.1804  1256   137  0.89  17.65   0.98     0.93       4953.87|
| 12:  2.1804 -  2.1182  1252   145  0.90  16.87   0.99     0.99       4590.26|
| 13:  2.1182 -  2.0626  1303   133  0.88  18.08   0.98     0.96       3914.68|
| 14:  2.0626 -  2.0124   770    93  0.91  15.25   0.96     0.92       2975.47|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2975.47 max =        11594.99 mean =      7475.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.52|
|phase err.(test): min =        0.00 max =           89.34 mean =        14.75|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1702   ksol= 0.32   Bsol= 72.16   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,-0.55,1.18,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.219343                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1702   ksol= 0.32   Bsol= 72.16   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,-0.55,1.18,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.219343                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8029 0.99   1394  154 0.1007 0.1328      5.4025      5.5579|
|  2:  4.8029 -  3.8321 0.99   1335  151 0.0859 0.1179      5.4557      5.6803|
|  3:  3.8321 -  3.3536 0.99   1308  143 0.1118 0.1550      5.5296      5.8691|
|  4:  3.3536 -  3.0496 0.99   1305  148 0.1307 0.1859      5.5141      5.7096|
|  5:  3.0496 -  2.8325 0.99   1302  145 0.1493 0.1780      5.4325      5.6236|
|  6:  2.8325 -  2.6664 0.99   1293  142 0.1366 0.2367      5.3086      5.6248|
|  7:  2.6664 -  2.5335 0.99   1284  140 0.1406 0.1657      5.2717      5.4033|
|  8:  2.5335 -  2.4237 0.98   1273  145 0.1318 0.1792       5.181      5.4218|
|  9:  2.4237 -  2.3307 0.98   1266  140 0.1308 0.1885      5.1254      5.3529|
| 10:  2.3307 -  2.2506 1.00   1289  143 0.1250 0.1844      5.0403      5.2629|
| 11:  2.2506 -  2.1804 0.97   1256  137 0.1270 0.1909      5.0121      5.3124|
| 12:  2.1804 -  2.1182 0.98   1252  145 0.1205 0.1979      4.9448      5.3072|
| 13:  2.1182 -  2.0626 0.99   1303  133 0.1255 0.1851      4.8632      5.0862|
| 14:  2.0626 -  2.0124 0.61    770   93 0.1139 0.1707      4.7584      4.9804|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.8029  1394   154  0.94   9.68   0.96     0.94       7852.07|
|  2:  4.8029 -  3.8321  1335   151  0.95   8.34   1.00     0.98       9661.45|
|  3:  3.8321 -  3.3536  1308   143  0.93  11.93   1.02     1.02      11467.70|
|  4:  3.3536 -  3.0496  1305   148  0.91  14.71   1.00     0.98      11634.21|
|  5:  3.0496 -  2.8325  1302   145  0.89  17.58   1.00     0.98      10132.22|
|  6:  2.8325 -  2.6664  1293   142  0.88  18.13   0.97     0.95       8655.26|
|  7:  2.6664 -  2.5335  1284   140  0.89  17.86   0.98     0.94       7726.62|
|  8:  2.5335 -  2.4237  1273   145  0.89  17.33   0.98     0.95       6626.47|
|  9:  2.4237 -  2.3307  1266   140  0.90  16.85   1.00     0.95       6022.84|
| 10:  2.3307 -  2.2506  1289   143  0.89  17.23   0.99     0.95       5114.85|
| 11:  2.2506 -  2.1804  1256   137  0.89  17.63   0.98     0.93       4944.69|
| 12:  2.1804 -  2.1182  1252   145  0.90  16.86   0.99     0.99       4583.48|
| 13:  2.1182 -  2.0626  1303   133  0.88  18.07   0.98     0.96       3911.23|
| 14:  2.0626 -  2.0124   770    93  0.91  15.24   0.96     0.92       2973.79|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2973.79 max =        11634.21 mean =      7391.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.47|
|phase err.(test): min =        0.00 max =           89.19 mean =        14.71|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.66    102.04  16.29    None  None   None       |
|    all(noH): 2823   0      2.66    102.04  16.29    None  None   None       |
|    Sol.    : 438    0      3.94    102.04  42.33    None  None   None       |
|    Mac.    : 2385   0      2.66    84.57   11.51    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:     2.665 -  12.602: 1747   |   5:    52.352 -  62.289:   84        |
|      1:    12.602 -  22.540:  551   |   6:    62.289 -  72.227:   47        |
|      2:    22.540 -  32.477:  140   |   7:    72.227 -  82.164:   24        |
|      3:    32.477 -  42.415:  129   |   8:    82.164 -  92.102:    6        |
|      4:    42.415 -  52.352:   90   |   9:    92.102 - 102.039:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 343         
Filter by distance & map next to the model:
   mapped sites are within: 0.352 - 4.867
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 343
   mapped sites are within: 0.722 - 4.867

peak=   10.359 closest distance to " CB  VAL A 230 " =    1.465
peak=    5.408 closest distance to " CG  LEU A   5 " =    1.240
peak=    5.250 closest distance to " CB  GLN A 223 " =    1.541
peak=    5.206 closest distance to " CG  LEU A 228 " =    1.218
peak=    4.951 closest distance to " O   HOH Z 369 " =    2.093
peak=    4.941 closest distance to " CD2 LEU A   5 " =    1.166
peak=    4.860 closest distance to " O   HOH Z 425 " =    1.605
peak=    4.838 closest distance to " O   HOH Z 142 " =    1.878
peak=    4.816 closest distance to " NE2 GLN A  11 " =    1.091
peak=    4.813 closest distance to " CB  VAL A 296 " =    1.090
peak=    4.785 closest distance to " CZ  PHE A 218 " =    1.195
peak=    4.758 closest distance to " O   HOH Z 111 " =    2.161
peak=    4.709 closest distance to " CB  GLN A 183 " =    1.261
peak=    4.678 closest distance to " CG2 VAL A 296 " =    0.987
peak=    4.666 closest distance to " O   HOH Z 232 " =    2.241
peak=    4.526 closest distance to " OE1 GLN A  55 " =    1.093
peak=    4.491 closest distance to " CA  ALA A  51 " =    1.024
peak=    4.467 closest distance to " O   HOH Z   9 " =    1.507
peak=    4.456 closest distance to " CB  SER A  63 " =    1.247
peak=    4.437 closest distance to " CB  ASP A 124 " =    0.815
peak=    4.421 closest distance to " O   HOH Z 207 " =    1.340
peak=    4.400 closest distance to " O   HOH Z 368 " =    2.399
peak=    4.374 closest distance to " O   HOH Z 126 " =    1.719
peak=    4.363 closest distance to " CG2 ILE A 234 " =    1.028
peak=    4.344 closest distance to " CB  TYR A 169 " =    0.731
peak=    4.306 closest distance to " O   HOH Z 303 " =    2.156
peak=    4.306 closest distance to " O   SER A  87 " =    2.382
peak=    4.289 closest distance to " CD1AILE A 234 " =    0.967
peak=    4.280 closest distance to " O   HOH Z 359 " =    1.835
peak=    4.257 closest distance to " CG  MET A 185 " =    1.310
peak=    4.239 closest distance to " CB  ARG A 190 " =    1.481
peak=    4.227 closest distance to " NH1 ARG A 138 " =    1.079
peak=    4.222 closest distance to " O   HOH Z 183 " =    1.298
peak=    4.221 closest distance to " O   HOH Z 261 " =    1.741
peak=    4.217 closest distance to " CB  ASN A 148 " =    1.427
peak=    4.174 closest distance to " CZ3 TRP A 266 " =    1.104
peak=    4.156 closest distance to " CA  TYR A  30 " =    1.009
peak=    4.136 closest distance to " O   HOH Z 214 " =    1.282
peak=    4.122 closest distance to " O   HOH Z 265 " =    2.084
peak=    4.121 closest distance to " O   HOH Z 411 " =    3.638
peak=    4.110 closest distance to " CG  PRO A 243 " =    1.164
peak=    4.110 closest distance to " CG1 VAL A 296 " =    1.214
peak=    4.084 closest distance to " CB  GLU A 277 " =    3.771
peak=    4.076 closest distance to " O   HOH Z 427 " =    3.007
peak=    4.073 closest distance to " O   HOH Z 287 " =    2.047
peak=    4.053 closest distance to " CB  VAL A 202 " =    1.588
peak=    4.039 closest distance to " O   HOH Z  49 " =    1.248
peak=    4.029 closest distance to " CD  LYS A 166 " =    1.413
peak=    4.022 closest distance to " CD2 LEU A 228 " =    1.235
peak=    4.008 closest distance to " CD  ARG A 159 " =    0.749
peak=    4.006 closest distance to " O   HOH Z 193 " =    2.123
peak=    3.990 closest distance to " CB  ARG A 275 " =    0.977
peak=    3.984 closest distance to " O   HOH Z 298 " =    2.007
peak=    3.960 closest distance to " CG  PRO A 198 " =    1.283
peak=    3.957 closest distance to " CB  GLU A 128 " =    1.021
peak=    3.950 closest distance to " CA  ALA A 295 " =    1.068
peak=    3.931 closest distance to " CG2 THR A 221 " =    1.046
peak=    3.923 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.912 closest distance to " CG  PRO A 213 " =    1.194
peak=    3.908 closest distance to " ND2 ASN A 187 " =    1.602
peak=    3.907 closest distance to " CB  VAL A 230 " =    1.224
peak=    3.885 closest distance to " CB  ASN A 142 " =    1.097
peak=    3.884 closest distance to " O   HOH Z 346 " =    1.579
peak=    3.879 closest distance to " O   HOH Z 290 " =    1.218
peak=    3.875 closest distance to " O   HOH Z 188 " =    3.027
peak=    3.871 closest distance to " CB  TRP A 266 " =    1.050
peak=    3.848 closest distance to " O   HOH Z 248 " =    1.439
peak=    3.844 closest distance to " CD1 LEU A   5 " =    1.386
peak=    3.835 closest distance to " CD2 TRP A 179 " =    1.287
peak=    3.835 closest distance to " CB  ARG A  79 " =    1.508
peak=    3.835 closest distance to " CA  TYR A 116 " =    1.431
peak=    3.833 closest distance to " O   HOH Z 422 " =    2.602
peak=    3.831 closest distance to " CB  VAL A 265 " =    1.327
peak=    3.825 closest distance to " O   HOH Z 158 " =    3.106
peak=    3.817 closest distance to " CA  ARG A 195 " =    1.277
peak=    3.792 closest distance to " O   HOH Z 406 " =    1.576
peak=    3.791 closest distance to " O   PRO A 198 " =    1.559
peak=    3.788 closest distance to " CB  ASP A 140 " =    0.859
peak=    3.780 closest distance to " NH1AARG A 145 " =    1.275
peak=    3.778 closest distance to " O   HOH Z 130 " =    1.033
peak=    3.773 closest distance to " CA  ALA A 291 " =    0.913
peak=    3.772 closest distance to " O   HOH Z 251 " =    1.582
peak=    3.771 closest distance to " CA  TYR A  30 " =    1.072
peak=    3.769 closest distance to " CA  GLY A 267 " =    0.790
peak=    3.767 closest distance to " CG AARG A 275 " =    1.411
peak=    3.763 closest distance to " O   HOH Z 214 " =    2.873
peak=    3.754 closest distance to " O   HOH Z 234 " =    3.715
peak=    3.745 closest distance to " O   HOH Z  19 " =    2.304
peak=    3.743 closest distance to " O   HOH Z  80 " =    1.811
peak=    3.739 closest distance to " O   HOH Z 227 " =    1.868
peak=    3.725 closest distance to " O   HOH Z 313 " =    1.774
peak=    3.717 closest distance to " O   HOH Z 184 " =    1.516
peak=    3.714 closest distance to " O   HOH Z 246 " =    1.216
peak=    3.711 closest distance to " O   ASP A 200 " =    1.623
peak=    3.709 closest distance to " O   HOH Z 272 " =    1.877
peak=    3.708 closest distance to " O   HOH Z 199 " =    1.601
peak=    3.706 closest distance to " O   HOH Z 213 " =    1.893
peak=    3.703 closest distance to " CD  ARG A 269 " =    0.898
peak=    3.699 closest distance to " CB  GLU A 152 " =    1.168
peak=    3.685 closest distance to " O   HOH Z 365 " =    2.930
peak=    3.680 closest distance to " CG  LEU A 167 " =    1.170
peak=    3.676 closest distance to " O   HOH Z  76 " =    1.293
peak=    3.671 closest distance to " O   ASP A 124 " =    1.166
peak=    3.671 closest distance to " CB  TRP A 150 " =    1.413
peak=    3.654 closest distance to " CA  VAL A 125 " =    1.172
peak=    3.653 closest distance to " O   HOH Z 145 " =    1.454
peak=    3.648 closest distance to " CD  ARG A  66 " =    2.421
peak=    3.644 closest distance to " O   HOH Z 357 " =    2.802
peak=    3.618 closest distance to " CB  ASN A  39 " =    0.900
peak=    3.606 closest distance to " O   HOH Z 112 " =    0.793
peak=    3.601 closest distance to " CA  LEU A 282 " =    1.109
peak=    3.592 closest distance to " CG1 VAL A 153 " =    0.909
peak=    3.591 closest distance to " CG  ARG A 269 " =    1.812
peak=    3.590 closest distance to " CB  LEU A  83 " =    0.742
peak=    3.585 closest distance to " CA  ARG A  36 " =    1.153
peak=    3.584 closest distance to " CB  SER A  62 " =    0.923
peak=    3.580 closest distance to " OG  SER A 276 " =    1.431
peak=    3.580 closest distance to " CB  GLN A  88 " =    1.254
peak=    3.575 closest distance to " CG  MET A 113 " =    1.713
peak=    3.570 closest distance to " O   HOH Z  30 " =    1.322
peak=    3.567 closest distance to " O   HOH Z  59 " =    2.424
peak=    3.565 closest distance to " CB  TRP A 179 " =    1.415
peak=    3.565 closest distance to " CB  GLN A  89 " =    1.155
peak=    3.552 closest distance to " CG1 ILE A  49 " =    1.542
peak=    3.533 closest distance to " O   HOH Z 258 " =    1.946
peak=    3.531 closest distance to " CG  GLU A  37 " =    0.985
peak=    3.529 closest distance to " CA  ASN A 127 " =    1.038
peak=    3.526 closest distance to " O   HOH Z   4 " =    1.769
peak=    3.524 closest distance to " O   HOH Z  43 " =    2.044
peak=    3.519 closest distance to " CB  GLU A  46 " =    0.948
peak=    3.518 closest distance to " CE3 TRP A 150 " =    1.103
peak=    3.518 closest distance to " CZ  PHE A  38 " =    1.233
peak=    3.518 closest distance to " CB  SER A 212 " =    1.336
peak=    3.517 closest distance to " CB AVAL A  41 " =    1.338
peak=    3.513 closest distance to " O   HOH Z 155 " =    3.444
peak=    3.511 closest distance to " CA  SER A  87 " =    0.960
peak=    3.509 closest distance to " CA  ASP A 124 " =    0.787
peak=    3.506 closest distance to " NE2 HIS A 207 " =    1.188
peak=    3.499 closest distance to " CD1 LEU A 300 " =    1.137
peak=    3.492 closest distance to " O   HOH Z 368 " =    4.090
peak=    3.490 closest distance to " O   ALA A 165 " =    1.432
peak=    3.484 closest distance to " CD ALYS A 290 " =    1.039
peak=    3.484 closest distance to " O   ALA A 158 " =    1.436
peak=    3.482 closest distance to " CA  ALA A 160 " =    1.075
peak=    3.481 closest distance to " CA  ASP A 162 " =    0.951
peak=    3.472 closest distance to " ND2BASN A 224 " =    0.854
peak=    3.466 closest distance to " O   HOH Z  88 " =    3.187
peak=    3.466 closest distance to " N   PHE A 130 " =    1.273
peak=    3.464 closest distance to " O   HOH Z  10 " =    1.858
peak=    3.463 closest distance to " O   HOH Z 316 " =    3.073
peak=    3.462 closest distance to " O   HOH Z 126 " =    2.029
peak=    3.456 closest distance to " CB  ALA A   9 " =    1.729
peak=    3.454 closest distance to " ND1 HIS A  81 " =    1.823
peak=    3.451 closest distance to " CA  ARG A 102 " =    1.154
peak=    3.450 closest distance to " O   HOH Z 128 " =    1.139
peak=    3.446 closest distance to " O   HOH Z 148 " =    3.392
peak=    3.443 closest distance to " O  BHOH Z 338 " =    2.287
peak=    3.440 closest distance to " CD1 ILE A  33 " =    1.862
peak=    3.433 closest distance to " CG  PHE A 204 " =    0.903
peak=    3.432 closest distance to " OD1 ASN A  69 " =    2.601
peak=    3.424 closest distance to " N   ALA A 256 " =    1.185
peak=    3.422 closest distance to " O   HOH Z 133 " =    2.914
peak=    3.419 closest distance to " CB  PRO A 243 " =    1.387
peak=    3.419 closest distance to " CD1 LEU A  96 " =    1.028
peak=    3.413 closest distance to " CE3 TRP A  85 " =    1.152
peak=    3.413 closest distance to " CB  ALA A 242 " =    0.777
peak=    3.411 closest distance to " CA  ALA A 100 " =    0.920
peak=    3.408 closest distance to " O   HOH Z  78 " =    1.596
peak=    3.407 closest distance to " CD1 LEU A 101 " =    1.257
peak=    3.405 closest distance to " O   HOH Z 403 " =    1.500
peak=    3.403 closest distance to " O   PRO A 198 " =    1.338
peak=    3.400 closest distance to " O   HOH Z 171 " =    4.080
peak=    3.397 closest distance to " O   HOH Z 353 " =    2.642
peak=    3.396 closest distance to " O   HOH Z 193 " =    1.654
peak=    3.396 closest distance to " O   HOH Z 394 " =    1.895
peak=    3.396 closest distance to " O   HOH Z 102 " =    1.310
peak=    3.392 closest distance to " O   HOH Z 133 " =    1.374
peak=    3.386 closest distance to " CB  SER A   3 " =    1.583
peak=    3.384 closest distance to " O   HOH Z 211 " =    1.429
peak=    3.379 closest distance to " ND2 ASN A 249 " =    1.906
peak=    3.378 closest distance to " O   MET A 105 " =    1.653
peak=    3.374 closest distance to " CB  SER A 216 " =    0.961
peak=    3.374 closest distance to " CB  ALA A 248 " =    1.086
peak=    3.372 closest distance to " O   HOH Z  88 " =    3.366
peak=    3.370 closest distance to " O   HOH Z 146 " =    1.559
peak=    3.369 closest distance to " CA  VAL A 112 " =    1.198
peak=    3.367 closest distance to " O   HOH Z 124 " =    2.110
peak=    3.367 closest distance to " O   HOH Z 222 " =    0.944
peak=    3.365 closest distance to " CD2 LEU A 255 " =    1.596
peak=    3.364 closest distance to " O   PHE A 192 " =    1.454
peak=    3.363 closest distance to " NH2 ARG A  56 " =    0.962
peak=    3.360 closest distance to " O   HOH Z 298 " =    2.282
peak=    3.359 closest distance to " O   HOH Z 313 " =    1.513
peak=    3.358 closest distance to " O   GLU A   2 " =    1.611
peak=    3.358 closest distance to " CZ3 TRP A  85 " =    1.069
peak=    3.355 closest distance to " N   VAL A 126 " =    1.434
peak=    3.350 closest distance to " CZ  PHE A 192 " =    1.001
peak=    3.348 closest distance to " CZ3 TRP A 274 " =    4.708
peak=    3.345 closest distance to " CA  ALA A 184 " =    1.111
peak=    3.345 closest distance to " O   HOH Z  21 " =    1.745
peak=    3.344 closest distance to " O   HOH Z 148 " =    2.106
peak=    3.344 closest distance to " O   HOH Z 423 " =    1.736
peak=    3.343 closest distance to " O   HOH Z 280 " =    2.931
peak=    3.342 closest distance to " O   HOH Z 299 " =    4.403
peak=    3.340 closest distance to " OG  SER A  62 " =    3.030
peak=    3.340 closest distance to " CG BARG A 275 " =    1.552
peak=    3.340 closest distance to " CA  GLN A  94 " =    0.807
peak=    3.335 closest distance to " O   HOH Z 273 " =    2.847
peak=    3.331 closest distance to " CB  GLU A  37 " =    0.946
peak=    3.327 closest distance to " CB  SER A  26 " =    1.830
peak=    3.327 closest distance to " OD1 ASN A 217 " =    1.571
peak=    3.318 closest distance to " N   ASN A  39 " =    1.219
peak=    3.317 closest distance to " CB  THR A  82 " =    1.296
peak=    3.316 closest distance to " CG AARG A 102 " =    1.067
peak=    3.315 closest distance to " CB  ASP A 298 " =    1.164
peak=    3.314 closest distance to " CG  MET A 185 " =    1.002
peak=    3.312 closest distance to " CD1 ILE A 199 " =    1.058
peak=    3.310 closest distance to " CB  ALA A   1 " =    4.867
peak=    3.306 closest distance to " OG  SER A 135 " =    1.297
peak=    3.306 closest distance to " CA  ALA A  21 " =    1.153
peak=    3.304 closest distance to " CA  THR A 264 " =    0.722
peak=    3.302 closest distance to " O   THR A 182 " =    1.425
peak=    3.301 closest distance to " O   HOH Z 361 " =    3.744
peak=    3.297 closest distance to " OG  SER A 245 " =    1.716
peak=    3.295 closest distance to " OE2 GLU A   2 " =    1.996
peak=    3.293 closest distance to " O   HOH Z 116 " =    1.828
peak=    3.290 closest distance to " O   PRO A 213 " =    1.455
peak=    3.290 closest distance to " O   HOH Z 291 " =    1.562
peak=    3.290 closest distance to " O   HOH Z 172 " =    3.890
peak=    3.288 closest distance to " CG2 VAL A 257 " =    0.867
peak=    3.285 closest distance to " CB  ASN A 187 " =    1.022
peak=    3.284 closest distance to " CB  LYS A 117 " =    1.166
peak=    3.284 closest distance to " O   HOH Z  40 " =    1.759
peak=    3.282 closest distance to " CB  SER A 288 " =    1.492
peak=    3.279 closest distance to " CA  ASP A 191 " =    1.273
peak=    3.278 closest distance to " CB  THR A 235 " =    1.351
peak=    3.273 closest distance to " CB  TYR A  30 " =    1.160
peak=    3.271 closest distance to " CA  ILE A 106 " =    0.799
peak=    3.270 closest distance to " O  BHOH Z  74 " =    1.370
peak=    3.269 closest distance to " O   HOH Z 261 " =    1.849
peak=    3.269 closest distance to " O   HOH Z  57 " =    1.264
peak=    3.267 closest distance to " CB  PRO A  90 " =    1.210
peak=    3.267 closest distance to " CB  THR A  52 " =    0.863
peak=    3.266 closest distance to " O   HOH Z 180 " =    2.089
peak=    3.265 closest distance to " CZ3 TRP A  92 " =    1.356
peak=    3.262 closest distance to " CB  PRO A  54 " =    0.840
peak=    3.259 closest distance to " CA  GLY A 211 " =    1.397
peak=    3.259 closest distance to " CA  ARG A 139 " =    1.164
peak=    3.257 closest distance to " O   ASN A  74 " =    1.356
peak=    3.256 closest distance to " OD2 ASP A  65 " =    2.845
peak=    3.253 closest distance to " CE1 TYR A 186 " =    1.188
peak=    3.252 closest distance to " OE2 GLU A  53 " =    2.151
peak=    3.249 closest distance to " O   HOH Z 391 " =    2.915
peak=    3.249 closest distance to " CB  ALA A 227 " =    1.044
peak=    3.248 closest distance to " O   HOH Z 343 " =    2.865
peak=    3.247 closest distance to " CB  PHE A 283 " =    0.741
peak=    3.244 closest distance to " O   HOH Z 383 " =    1.840
peak=    3.239 closest distance to " CA  MET A 105 " =    0.952
peak=    3.238 closest distance to " CA  ALA A 129 " =    1.457
peak=    3.237 closest distance to " CB  LEU A 228 " =    1.266
peak=    3.236 closest distance to " CG2 ILE A 151 " =    0.885
peak=    3.236 closest distance to " CA  ALA A 158 " =    1.135
peak=    3.231 closest distance to " O   HOH Z 417 " =    3.204
peak=    3.229 closest distance to " CG2 ILE A 120 " =    1.144
peak=    3.228 closest distance to " O   HOH Z 163 " =    1.443
peak=    3.226 closest distance to " O   HOH Z 329 " =    4.264
peak=    3.224 closest distance to " O   HOH Z 200 " =    3.356
peak=    3.224 closest distance to " OG BSER A 258 " =    3.530
peak=    3.222 closest distance to " CG1AVAL A 121 " =    0.773
peak=    3.216 closest distance to " CG2 ILE A  20 " =    1.552
peak=    3.214 closest distance to " CB  ALA A 291 " =    1.188
peak=    3.211 closest distance to " CB  TYR A 116 " =    1.136
peak=    3.209 closest distance to " N   ARG A 156 " =    1.543
peak=    3.205 closest distance to " N   ASP A 162 " =    1.265
peak=    3.205 closest distance to " CA  ASP A 140 " =    1.543
peak=    3.205 closest distance to " CG  GLN A  58 " =    1.224
peak=    3.201 closest distance to " CG2 VAL A 197 " =    1.162
peak=    3.200 closest distance to " O   HOH Z 203 " =    1.680
peak=    3.199 closest distance to " O   HOH Z 171 " =    4.017
peak=    3.196 closest distance to " CB  VAL A 268 " =    0.894
peak=    3.195 closest distance to " CB  THR A  31 " =    1.515
peak=    3.194 closest distance to " CB  SER A 146 " =    0.996
peak=    3.192 closest distance to " NZ  LYS A 117 " =    3.184
peak=    3.190 closest distance to " O   HOH Z 128 " =    2.149
peak=    3.186 closest distance to " O   HOH Z 371 " =    3.055
peak=    3.184 closest distance to " O   THR A 251 " =    1.280
peak=    3.179 closest distance to " CB  ASN A 173 " =    0.976
peak=    3.179 closest distance to " CD  ARG A 219 " =    1.048
peak=    3.178 closest distance to " CG2AVAL A 121 " =    2.267
peak=    3.174 closest distance to " CB  GLN A 205 " =    1.142
peak=    3.173 closest distance to " O   TYR A 116 " =    1.274
peak=    3.169 closest distance to " CA  GLU A 152 " =    0.920
peak=    3.165 closest distance to " O   HOH Z 141 " =    1.583
peak=    3.161 closest distance to " CA  ASN A 217 " =    1.386
peak=    3.157 closest distance to " CB  ALA A 100 " =    1.287
peak=    3.156 closest distance to " O   HOH Z 188 " =    1.960
peak=    3.154 closest distance to " O   PHE A  61 " =    1.455
peak=    3.153 closest distance to " O   HOH Z 350 " =    1.670
peak=    3.152 closest distance to " O   HOH Z 263 " =    1.687
peak=    3.150 closest distance to " O   THR A 220 " =    1.278
peak=    3.149 closest distance to " O   HOH Z 394 " =    3.719
peak=    3.148 closest distance to " N   ARG A  66 " =    1.527
peak=    3.142 closest distance to " CG  ARG A 159 " =    0.954
peak=    3.141 closest distance to " CB  ARG A 138 " =    1.018
peak=    3.141 closest distance to " O   HOH Z 368 " =    3.484
peak=    3.139 closest distance to " O   HOH Z 201 " =    2.875
peak=    3.133 closest distance to " OH  TYR A 247 " =    1.228
peak=    3.133 closest distance to " CA  GLY A 241 " =    0.937
peak=    3.122 closest distance to " CG2AVAL A  72 " =    1.794
peak=    3.114 closest distance to " CD  LYS A 119 " =    2.109
peak=    3.103 closest distance to " NZ  LYS A  48 " =    1.252
peak=    3.102 closest distance to " C   ALA A 299 " =    0.935
peak=    3.102 closest distance to " O   HOH Z  85 " =    2.293
peak=    3.097 closest distance to " CB  ASN A 215 " =    1.203
peak=    3.096 closest distance to " CB  ALA A  43 " =    0.909
peak=    3.095 closest distance to " O   HOH Z  59 " =    2.105
peak=    3.094 closest distance to " CG BARG A 102 " =    1.877
peak=    3.093 closest distance to " CG1 ILE A  33 " =    1.297
peak=    3.091 closest distance to " CG  GLN A  89 " =    1.473
peak=    3.091 closest distance to " CG1 ILE A  20 " =    1.340
peak=    3.087 closest distance to " O   HOH Z 345 " =    3.851
peak=    3.083 closest distance to " CA  GLN A 223 " =    0.975
peak=    3.078 closest distance to " O   HOH Z 303 " =    1.817
peak=    3.078 closest distance to " CD  LYS A  76 " =    1.918
peak=    3.073 closest distance to " O   HOH Z 393 " =    3.073
peak=    3.071 closest distance to " CE3 TRP A  85 " =    1.720
peak=    3.065 closest distance to " O   HOH Z 132 " =    2.703
peak=    3.059 closest distance to " NE1 TRP A  85 " =    1.431
peak=    3.053 closest distance to " CG  GLN A  11 " =    1.581
peak=    3.048 closest distance to " CD  ARG A 195 " =    1.056
peak=    3.040 closest distance to " NH1 ARG A  56 " =    1.052
peak=    3.039 closest distance to " O   HOH Z 409 " =    2.917
peak=    3.035 closest distance to " O   HOH Z 285 " =    2.114
peak=    2.864 closest distance to " CE2 TYR A 169 " =    1.537

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 219         
Filter by distance & map next to the model:
   mapped sites are within: 0.475 - 5.671
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 219
   mapped sites are within: 0.746 - 5.671

peak=   -5.419 closest distance to " CG2 VAL A 230 " =    0.746
peak=   -4.444 closest distance to " CG1 VAL A 296 " =    1.232
peak=   -4.426 closest distance to " O   HOH Z 162 " =    2.728
peak=   -4.296 closest distance to " CD  ARG A  14 " =    3.287
peak=   -4.236 closest distance to " O   HOH Z 196 " =    2.374
peak=   -4.221 closest distance to " CD  GLN A  58 " =    0.977
peak=   -4.218 closest distance to " CG1 VAL A 112 " =    2.627
peak=   -4.191 closest distance to " CD  ARG A 156 " =    2.156
peak=   -4.130 closest distance to " CZ2 TRP A  92 " =    2.811
peak=   -4.128 closest distance to " CG1 VAL A 250 " =    2.757
peak=   -4.121 closest distance to " O   HOH Z 411 " =    5.343
peak=   -4.108 closest distance to " O   PRO A 198 " =    1.286
peak=   -3.980 closest distance to " CA  ASP A 298 " =    1.121
peak=   -3.973 closest distance to " O   HOH Z 103 " =    1.721
peak=   -3.962 closest distance to " CD1 LEU A 101 " =    2.417
peak=   -3.957 closest distance to " CG  GLN A 223 " =    2.339
peak=   -3.954 closest distance to " O   HOH Z 166 " =    1.853
peak=   -3.935 closest distance to " O   HOH Z 133 " =    1.036
peak=   -3.907 closest distance to " O   HOH Z 231 " =    2.092
peak=   -3.896 closest distance to " O   VAL A 189 " =    2.701
peak=   -3.887 closest distance to " C   ALA A 158 " =    1.310
peak=   -3.874 closest distance to " O   HOH Z 216 " =    1.024
peak=   -3.866 closest distance to " OG  SER A  97 " =    2.288
peak=   -3.861 closest distance to " CE2 TYR A  30 " =    2.671
peak=   -3.855 closest distance to " CE3 TRP A  70 " =    1.796
peak=   -3.815 closest distance to " CA  ASN A 110 " =    2.683
peak=   -3.801 closest distance to " O   HOH Z 359 " =    2.958
peak=   -3.794 closest distance to " CD  GLN A  55 " =    1.173
peak=   -3.793 closest distance to " O   HOH Z 193 " =    1.317
peak=   -3.786 closest distance to " O   HOH Z 351 " =    1.678
peak=   -3.772 closest distance to " O   HOH Z  52 " =    1.554
peak=   -3.769 closest distance to " CA  GLY A 241 " =    2.355
peak=   -3.748 closest distance to " CG  GLN A  88 " =    0.895
peak=   -3.746 closest distance to " O   HOH Z  73 " =    2.550
peak=   -3.741 closest distance to " O   HOH Z 232 " =    1.855
peak=   -3.740 closest distance to " C   HIS A 108 " =    1.221
peak=   -3.732 closest distance to " CG  ARG A 269 " =    2.280
peak=   -3.725 closest distance to " O   HOH Z 115 " =    1.807
peak=   -3.690 closest distance to " CD2 TYR A 293 " =    1.942
peak=   -3.679 closest distance to " O   HOH Z 183 " =    1.137
peak=   -3.679 closest distance to " CG2 VAL A 202 " =    2.800
peak=   -3.667 closest distance to " CG1 VAL A 112 " =    2.635
peak=   -3.664 closest distance to " CG  PRO A 163 " =    2.301
peak=   -3.652 closest distance to " CB  HIS A  86 " =    1.181
peak=   -3.648 closest distance to " O   HOH Z  68 " =    1.490
peak=   -3.640 closest distance to " CE3 TRP A 150 " =    2.282
peak=   -3.626 closest distance to " O   PRO A 163 " =    2.165
peak=   -3.623 closest distance to " CA  GLY A 133 " =    2.294
peak=   -3.618 closest distance to " C   ARG A  79 " =    2.700
peak=   -3.617 closest distance to " O   HOH Z 295 " =    1.560
peak=   -3.613 closest distance to " O   VAL A  67 " =    2.707
peak=   -3.604 closest distance to " O   HOH Z 251 " =    4.905
peak=   -3.603 closest distance to " CD2 LEU A 167 " =    1.867
peak=   -3.600 closest distance to " CG2 VAL A 189 " =    1.986
peak=   -3.596 closest distance to " CA  GLY A 241 " =    3.175
peak=   -3.595 closest distance to " CB  VAL A 230 " =    1.174
peak=   -3.592 closest distance to " O   SER A 271 " =    2.113
peak=   -3.590 closest distance to " O   HOH Z 128 " =    2.719
peak=   -3.586 closest distance to " O   HOH Z 394 " =    1.540
peak=   -3.571 closest distance to " OE1 GLN A  88 " =    1.262
peak=   -3.570 closest distance to " N   ASP A 171 " =    2.510
peak=   -3.565 closest distance to " OG BSER A 134 " =    1.444
peak=   -3.563 closest distance to " CE2 TRP A  70 " =    2.310
peak=   -3.560 closest distance to " O   HOH Z 149 " =    2.078
peak=   -3.557 closest distance to " CD1 ILE A  33 " =    2.607
peak=   -3.554 closest distance to " OG ASER A 134 " =    1.340
peak=   -3.546 closest distance to " OG  SER A 141 " =    1.600
peak=   -3.532 closest distance to " O   HOH Z  10 " =    1.581
peak=   -3.527 closest distance to " CG  TRP A 274 " =    1.106
peak=   -3.524 closest distance to " O   HOH Z  17 " =    1.450
peak=   -3.513 closest distance to " O   HOH Z 177 " =    1.875
peak=   -3.512 closest distance to " CD1 ILE A 151 " =    2.536
peak=   -3.508 closest distance to " N   ALA A  43 " =    2.810
peak=   -3.507 closest distance to " OG  SER A  62 " =    4.380
peak=   -3.502 closest distance to " O   HOH Z 236 " =    1.470
peak=   -3.500 closest distance to " CE BMET A  47 " =    1.501
peak=   -3.495 closest distance to " O   HOH Z  70 " =    2.161
peak=   -3.493 closest distance to " CG1 VAL A 265 " =    2.460
peak=   -3.491 closest distance to " CD2 PHE A  61 " =    2.045
peak=   -3.486 closest distance to " CH2 TRP A 179 " =    1.169
peak=   -3.485 closest distance to " C   MET A 188 " =    1.474
peak=   -3.482 closest distance to " O   HOH Z 145 " =    0.766
peak=   -3.480 closest distance to " O   HOH Z  93 " =    2.097
peak=   -3.477 closest distance to " O   TYR A 186 " =    1.857
peak=   -3.477 closest distance to " SD  MET A 105 " =    0.999
peak=   -3.476 closest distance to " O   HOH Z 431 " =    1.926
peak=   -3.465 closest distance to " OD1 ASP A 171 " =    1.651
peak=   -3.463 closest distance to " O   VAL A  67 " =    2.724
peak=   -3.460 closest distance to " CD  LYS A 289 " =    2.378
peak=   -3.457 closest distance to " O   GLY A  17 " =    1.268
peak=   -3.454 closest distance to " N   PHE A  59 " =    1.953
peak=   -3.453 closest distance to " NE2 GLN A  88 " =    1.080
peak=   -3.446 closest distance to " CB  VAL A 189 " =    2.398
peak=   -3.444 closest distance to " CA  GLY A  98 " =    2.116
peak=   -3.441 closest distance to " O   HOH Z 407 " =    3.070
peak=   -3.438 closest distance to " ND2 ASN A  45 " =    2.312
peak=   -3.434 closest distance to " OG  SER A  87 " =    1.533
peak=   -3.433 closest distance to " O   HOH Z 411 " =    1.755
peak=   -3.431 closest distance to " CD1 PHE A  59 " =    2.052
peak=   -3.429 closest distance to " CG  TRP A 266 " =    1.753
peak=   -3.422 closest distance to " CB  TRP A  85 " =    2.762
peak=   -3.416 closest distance to " O   GLY A 211 " =    1.416
peak=   -3.415 closest distance to " N   LYS A 166 " =    1.952
peak=   -3.415 closest distance to " CA  GLY A 203 " =    2.556
peak=   -3.414 closest distance to " O   MET A  40 " =    2.843
peak=   -3.409 closest distance to " CG1 VAL A 125 " =    1.875
peak=   -3.405 closest distance to " C   LEU A 143 " =    1.096
peak=   -3.403 closest distance to " O   HOH Z 290 " =    1.319
peak=   -3.401 closest distance to " O   ALA A 227 " =    1.434
peak=   -3.401 closest distance to " O   HOH Z 377 " =    1.893
peak=   -3.399 closest distance to " N   ALA A 226 " =    2.131
peak=   -3.392 closest distance to " O   HOH Z  60 " =    2.121
peak=   -3.383 closest distance to " CD  PRO A 243 " =    1.982
peak=   -3.380 closest distance to " OD1 ASN A 148 " =    1.460
peak=   -3.376 closest distance to " O   HOH Z 111 " =    1.677
peak=   -3.374 closest distance to " CG  ARG A 259 " =    2.423
peak=   -3.371 closest distance to " O   HOH Z 275 " =    1.657
peak=   -3.370 closest distance to " CG  GLN A 103 " =    2.493
peak=   -3.367 closest distance to " O   HOH Z 325 " =    1.898
peak=   -3.361 closest distance to " CD1 ILE A 239 " =    2.155
peak=   -3.357 closest distance to " O   HOH Z  64 " =    1.740
peak=   -3.356 closest distance to " O   HOH Z 140 " =    1.891
peak=   -3.356 closest distance to " NE2 GLN A  55 " =    2.310
peak=   -3.348 closest distance to " O   ASP A  27 " =    1.915
peak=   -3.346 closest distance to " CG2 VAL A 296 " =    1.268
peak=   -3.343 closest distance to " N   THR A  52 " =    1.642
peak=   -3.341 closest distance to " O   HOH Z 252 " =    3.639
peak=   -3.338 closest distance to " NE  ARG A  66 " =    4.039
peak=   -3.337 closest distance to " CB  ALA A 248 " =    2.172
peak=   -3.335 closest distance to " CG  GLU A 277 " =    1.295
peak=   -3.333 closest distance to " CG2 THR A 178 " =    2.351
peak=   -3.331 closest distance to " O   HOH Z 100 " =    1.256
peak=   -3.330 closest distance to " O   HOH Z 110 " =    1.468
peak=   -3.326 closest distance to " O   HOH Z 198 " =    2.493
peak=   -3.325 closest distance to " O   HOH Z 434 " =    1.723
peak=   -3.321 closest distance to " CG  GLU A  53 " =    1.550
peak=   -3.318 closest distance to " CB  ALA A  43 " =    2.677
peak=   -3.310 closest distance to " CD2 LEU A 237 " =    2.803
peak=   -3.309 closest distance to " O   HOH Z 371 " =    1.314
peak=   -3.308 closest distance to " CB  TYR A  15 " =    2.224
peak=   -3.306 closest distance to " O   HOH Z 435 " =    2.850
peak=   -3.303 closest distance to " CD1 LEU A   5 " =    2.623
peak=   -3.303 closest distance to " CE  LYS A  76 " =    2.608
peak=   -3.298 closest distance to " C   LEU A 222 " =    0.989
peak=   -3.289 closest distance to " CD2 PHE A 225 " =    1.145
peak=   -3.289 closest distance to " CG  LEU A   5 " =    0.915
peak=   -3.288 closest distance to " CZ  PHE A  38 " =    2.547
peak=   -3.282 closest distance to " O   HOH Z  30 " =    1.807
peak=   -3.279 closest distance to " O   HOH Z 368 " =    1.885
peak=   -3.275 closest distance to " CG  GLN A  11 " =    1.573
peak=   -3.275 closest distance to " O   HOH Z  11 " =    1.779
peak=   -3.272 closest distance to " CG  LEU A 281 " =    1.899
peak=   -3.267 closest distance to " ND2 ASN A 249 " =    2.431
peak=   -3.266 closest distance to " O   HOH Z 285 " =    2.042
peak=   -3.264 closest distance to " O   HOH Z 368 " =    1.587
peak=   -3.261 closest distance to " ND2 ASN A  60 " =    1.430
peak=   -3.258 closest distance to " O   HOH Z 106 " =    2.019
peak=   -3.256 closest distance to " O   GLN A 240 " =    2.598
peak=   -3.250 closest distance to " O   HOH Z   9 " =    1.603
peak=   -3.247 closest distance to " O   HOH Z 377 " =    1.190
peak=   -3.246 closest distance to " ND2 ASN A  69 " =    1.907
peak=   -3.246 closest distance to " O   HOH Z  19 " =    2.197
peak=   -3.243 closest distance to " CB  PRO A 163 " =    2.439
peak=   -3.242 closest distance to " CB  ALA A 256 " =    2.935
peak=   -3.238 closest distance to " O   HOH Z 259 " =    3.958
peak=   -3.238 closest distance to " NE2 GLN A 240 " =    1.586
peak=   -3.237 closest distance to " O   HOH Z 185 " =    2.385
peak=   -3.234 closest distance to " CD  GLN A 223 " =    1.377
peak=   -3.232 closest distance to " CD1 TYR A 247 " =    2.359
peak=   -3.231 closest distance to " O   HOH Z 298 " =    2.887
peak=   -3.230 closest distance to " O   HOH Z 191 " =    5.671
peak=   -3.229 closest distance to " OG1 THR A  82 " =    1.857
peak=   -3.226 closest distance to " CG  ASP A 231 " =    0.807
peak=   -3.225 closest distance to " O   PHE A 218 " =    1.691
peak=   -3.224 closest distance to " O   HOH Z 165 " =    1.977
peak=   -3.220 closest distance to " OD1 ASN A 173 " =    1.438
peak=   -3.218 closest distance to " O   LYS A 117 " =    1.923
peak=   -3.210 closest distance to " OD2 ASP A 171 " =    1.900
peak=   -3.205 closest distance to " CB  ASN A 148 " =    1.941
peak=   -3.204 closest distance to " O   HOH Z 134 " =    3.065
peak=   -3.201 closest distance to " O   HOH Z 286 " =    1.977
peak=   -3.200 closest distance to " O   GLY A  80 " =    2.663
peak=   -3.199 closest distance to " O   HOH Z 174 " =    2.403
peak=   -3.192 closest distance to " O   HOH Z 405 " =    4.362
peak=   -3.190 closest distance to " O   HOH Z 234 " =    4.475
peak=   -3.189 closest distance to " O   HOH Z 426 " =    1.761
peak=   -3.186 closest distance to " O   HOH Z 231 " =    1.219
peak=   -3.180 closest distance to " CG2BVAL A  41 " =    1.841
peak=   -3.178 closest distance to " OG  SER A  87 " =    1.384
peak=   -3.178 closest distance to " NE2 GLN A 103 " =    1.784
peak=   -3.176 closest distance to " O   HOH Z 105 " =    3.334
peak=   -3.172 closest distance to " O   HOH Z 438 " =    3.189
peak=   -3.172 closest distance to " O   HOH Z 244 " =    1.584
peak=   -3.170 closest distance to " CD1 ILE A 199 " =    2.542
peak=   -3.157 closest distance to " O   HOH Z  43 " =    1.679
peak=   -3.153 closest distance to " CE1 TYR A 247 " =    2.646
peak=   -3.147 closest distance to " CD2 TYR A 247 " =    2.430
peak=   -3.147 closest distance to " CA  GLY A 241 " =    2.920
peak=   -3.146 closest distance to " O   HOH Z  78 " =    2.114
peak=   -3.144 closest distance to " N   TYR A  68 " =    2.931
peak=   -3.141 closest distance to " CZ  TYR A 169 " =    1.797
peak=   -3.140 closest distance to " CB  PHE A  16 " =    2.428
peak=   -3.140 closest distance to " O   HOH Z 136 " =    0.847
peak=   -3.132 closest distance to " O   HOH Z  44 " =    1.008
peak=   -3.124 closest distance to " O   HOH Z 390 " =    2.018
peak=   -3.123 closest distance to " O   HOH Z 112 " =    1.314
peak=   -3.120 closest distance to " C   GLU A 236 " =    1.003
peak=   -3.116 closest distance to " NH2AARG A 275 " =    5.328
peak=   -3.111 closest distance to " NE2 GLN A 194 " =    1.968
peak=   -3.104 closest distance to " O   HOH Z 323 " =    1.356
peak=   -3.104 closest distance to " CD2 PHE A  61 " =    2.524
peak=   -3.083 closest distance to " C   ASP A 270 " =    1.453
peak=   -3.068 closest distance to " OE1 GLU A  44 " =    0.974
peak=   -3.057 closest distance to " O   HOH Z 166 " =    1.916
peak=   -3.057 closest distance to " OG BSER A 134 " =    1.980
peak=   -3.049 closest distance to " N   SER A 276 " =    1.478
peak=   -3.024 closest distance to " O   HOH Z   6 " =    1.652

================= 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    :  0.4821 0.4771   6.283346e+00   6.269384e+00
   1_bss:  0.4741 0.4643   6.278047e+00   6.260943e+00
   1_xyz:  0.3896 0.4207   6.166046e+00   6.200926e+00
   1_adp:  0.3447 0.3989   6.085080e+00   6.169622e+00
   1_occ:  0.3444 0.4000   6.084657e+00   6.171111e+00
   2_bss:  0.3434 0.3977   6.086327e+00   6.170984e+00
   2_xyz:  0.2694 0.3261   5.885943e+00   6.025417e+00
   2_adp:  0.2487 0.3054   5.824804e+00   5.978091e+00
   2_occ:  0.2484 0.3051   5.824348e+00   5.978168e+00
   3_bss:  0.2472 0.3039   5.825723e+00   5.978382e+00
   3_xyz:  0.1834 0.2388   5.567198e+00   5.762171e+00
   3_adp:  0.1603 0.2191   5.464926e+00   5.689488e+00
   3_occ:  0.1601 0.2192   5.465238e+00   5.690551e+00
   4_bss:  0.1603 0.2192   5.464726e+00   5.688473e+00
   4_xyz:  0.1401 0.1948   5.351473e+00   5.586102e+00
   4_adp:  0.1362 0.1848   5.312538e+00   5.534843e+00
   4_occ:  0.1360 0.1848   5.311960e+00   5.534286e+00
   5_bss:  0.1359 0.1848   5.311415e+00   5.533764e+00
   5_xyz:  0.1226 0.1719   5.231195e+00   5.469508e+00
   5_adp:  0.1215 0.1709   5.223082e+00   5.462837e+00
   5_occ:  0.1213 0.1710   5.222537e+00   5.462359e+00
   5_bss:  0.1212 0.1702   5.219343e+00   5.458748e+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:  0.325  42.904   7.308   6.625  11.436   0.000   0.000   0.000
   1_xyz:  0.325  42.904   7.308   6.625  11.436   0.000   0.000   0.000
   1_adp:  0.325  42.904   7.308   6.625  11.436   0.000   0.000   0.000
   1_occ:  0.325  42.904   7.308   6.625  11.436   0.000   0.000   0.000
   2_bss:  0.304  42.904   4.511   4.213   8.307   0.000   0.000   0.000
   2_xyz:  0.304  42.904   4.511   4.213   8.307   0.000   0.000   0.000
   2_adp:  0.304  42.904   4.511   4.213   8.307   0.000   0.000   0.000
   2_occ:  0.304  42.904   4.511   4.213   8.307   0.000   0.000   0.000
   3_bss:  0.312  61.568   2.645   2.799   5.471   0.000   0.000   0.000
   3_xyz:  0.312  61.568   2.645   2.799   5.471   0.000   0.000   0.000
   3_adp:  0.312  61.568   2.645   2.799   5.471   0.000   0.000   0.000
   3_occ:  0.312  61.568   2.645   2.799   5.471   0.000   0.000   0.000
   4_bss:  0.339  87.247   2.073   2.177   4.206   0.000   0.000   0.000
   4_xyz:  0.339  87.247   2.073   2.177   4.206   0.000   0.000   0.000
   4_adp:  0.339  87.247   2.073   2.177   4.206   0.000   0.000   0.000
   4_occ:  0.339  87.247   2.073   2.177   4.206   0.000   0.000   0.000
   5_bss:  0.330  74.095   1.987   2.134   3.889   0.000   0.000   0.000
   5_xyz:  0.330  74.095   1.987   2.134   3.889   0.000   0.000   0.000
   5_adp:  0.330  74.095   1.987   2.134   3.889   0.000   0.000   0.000
   5_occ:  0.330  74.095   1.987   2.134   3.889   0.000   0.000   0.000
   5_bss:  0.324  72.162  -0.632  -0.545   1.177  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.108 0.4307  0.4869    68011.817
   1_bss:  55.552 0.4504  0.6558    65977.689
   1_xyz:  48.600 0.5367  0.7580    50925.908
   1_adp:  44.726 0.5851  0.8581    45510.973
   1_occ:  44.817 0.5840  0.8560    45671.322
   2_bss:  44.725 0.5850  0.7795    45535.573
   2_xyz:  34.382 0.7079  0.9296    28961.596
   2_adp:  31.572 0.7406  0.9649    25350.869
   2_occ:  31.615 0.7400  0.9635    25331.324
   3_bss:  31.540 0.7410  0.8981    25352.510
   3_xyz:  23.322 0.8286  0.9717    14522.690
   3_adp:  21.170 0.8500  0.9758    12241.932
   3_occ:  21.201 0.8497  0.9755    12251.268
   4_bss:  21.137 0.8503  0.9481    12192.268
   4_xyz:  18.504 0.8755  0.9605     9680.563
   4_adp:  17.146 0.8886  0.9597     8750.910
   4_occ:  17.139 0.8886  0.9596     8736.652
   5_bss:  17.125 0.8887  0.9547     8722.377
   5_xyz:  15.627 0.9019  0.9644     7574.458
   5_adp:  15.444 0.9036  0.9624     7489.242
   5_occ:  15.443 0.9036  0.9622     7475.216
   5_bss:  15.397 0.9038  0.9619     7392.072
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4671e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4671e+01
   1_xyz:   1.766  0.015  0.112 18.388  0.007  4.111   1.5279e-01
   1_adp:   1.766  0.015  0.112 18.388  0.007  4.111   1.5279e-01
   1_occ:   1.766  0.015  0.112 18.388  0.007  4.111   1.5279e-01
   2_bss:   1.766  0.015  0.112 18.388  0.007  4.111   1.5279e-01
   2_xyz:   1.237  0.009  0.081 16.820  0.005  4.112   8.8647e-02
   2_adp:   1.237  0.009  0.081 16.820  0.005  4.112   8.8647e-02
   2_occ:   1.237  0.009  0.081 16.820  0.005  4.112   8.8647e-02
   3_bss:   1.237  0.009  0.081 16.820  0.005  4.112   8.8647e-02
   3_xyz:   1.160  0.009  0.086 16.437  0.004  4.137   8.2357e-02
   3_adp:   1.160  0.009  0.086 16.437  0.004  4.137   8.2357e-02
   3_occ:   1.160  0.009  0.086 16.437  0.004  4.137   8.2357e-02
   4_bss:   1.160  0.009  0.086 16.437  0.004  4.137   8.2357e-02
   4_xyz:   1.069  0.009  0.081 16.034  0.004  4.116   7.1598e-02
   4_adp:   1.069  0.009  0.081 16.034  0.004  4.116   7.1598e-02
   4_occ:   1.069  0.009  0.081 16.034  0.004  4.116   7.1598e-02
   5_bss:   1.069  0.009  0.081 16.034  0.004  4.116   7.1598e-02
   5_xyz:   1.204  0.012  0.094 15.847  0.004  4.126   8.9814e-02
   5_adp:   1.204  0.012  0.094 15.847  0.004  4.126   8.9814e-02
   5_occ:   1.204  0.012  0.094 15.847  0.004  4.126   8.9814e-02
   5_bss:   1.204  0.012  0.094 15.847  0.004  4.126   8.9814e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0887e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0887e+00
   1_xyz:  14.847  0.171  0.453 86.604  0.038  2.254   1.1325e-01
   1_adp:  14.847  0.171  0.453 86.604  0.038  2.254   1.1325e-01
   1_occ:  14.847  0.171  0.453 86.604  0.038  2.254   1.1325e-01
   2_bss:  14.847  0.171  0.453 86.604  0.038  2.254   1.1325e-01
   2_xyz:   7.099  0.092  0.304 86.765  0.041  2.109   1.1507e-01
   2_adp:   7.099  0.092  0.304 86.765  0.041  2.109   1.1507e-01
   2_occ:   7.099  0.092  0.304 86.765  0.041  2.109   1.1507e-01
   3_bss:   7.099  0.092  0.304 86.765  0.041  2.109   1.1507e-01
   3_xyz:   8.151  0.061  0.308 85.512  0.038  2.349   1.2745e-01
   3_adp:   8.151  0.061  0.308 85.512  0.038  2.349   1.2745e-01
   3_occ:   8.151  0.061  0.308 85.512  0.038  2.349   1.2745e-01
   4_bss:   8.151  0.061  0.308 85.512  0.038  2.349   1.2745e-01
   4_xyz:   8.281  0.055  0.336 83.627  0.039  2.360   5.3237e-02
   4_adp:   8.281  0.055  0.336 83.627  0.039  2.360   5.3237e-02
   4_occ:   8.281  0.055  0.336 83.627  0.039  2.360   5.3237e-02
   5_bss:   8.281  0.055  0.336 83.627  0.039  2.360   5.3237e-02
   5_xyz:   7.848  0.070  0.503 83.314  0.039  2.266   6.0778e-02
   5_adp:   7.848  0.070  0.503 83.314  0.039  2.266   6.0778e-02
   5_occ:   7.848  0.070  0.503 83.314  0.039  2.266   6.0778e-02
   5_bss:   7.848  0.070  0.503 83.314  0.039  2.266   6.0778e-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:  70.86   0.00  13.28  70.86   0.00  10.85  67.85   0.00  26.49
   1_occ:  70.86   0.00  13.28  70.86   0.00  10.85  67.85   0.00  26.49
   2_bss:  70.86   0.00  13.28  70.86   0.00  10.85  67.85   0.00  26.49
   2_xyz:  70.86   0.00  13.28  70.86   0.00  10.85  67.85   0.00  26.49
   2_adp:  72.38   0.00  13.18  72.38   0.00   9.92  71.01   0.00  30.91
   2_occ:  72.38   0.00  13.18  72.38   0.00   9.92  71.01   0.00  30.91
   3_bss:  72.38   0.00  13.18  72.38   0.00   9.92  71.01   0.00  30.91
   3_xyz:  72.38   0.00  13.18  72.38   0.00   9.92  71.01   0.00  30.91
   3_adp: 100.77   0.00  14.69  96.86   0.00   9.57 100.77   0.21  42.59
   3_occ: 100.77   0.00  14.69  96.86   0.00   9.57 100.77   0.21  42.59
   4_bss: 100.77   0.00  14.69  96.86   0.00   9.57 100.77   0.21  42.59
   4_xyz: 100.77   0.00  14.69  96.86   0.00   9.57 100.77   0.21  42.59
   4_adp:  99.23   0.00  13.68  82.61   0.00   8.89  99.23   0.90  39.78
   4_occ:  99.23   0.00  13.68  82.61   0.00   8.89  99.23   0.90  39.78
   5_bss:  99.23   0.00  13.68  82.61   0.00   8.89  99.23   0.90  39.78
   5_xyz:  99.23   0.00  13.68  82.61   0.00   8.89  99.23   0.90  39.78
   5_adp:  99.37   0.00  13.62  81.91   0.00   8.84  99.37   1.27  39.67
   5_occ:  99.37   0.00  13.62  81.91   0.00   8.84  99.37   1.27  39.67
   5_bss: 102.04   2.66  16.29  84.57   2.66  11.51 102.04   3.94  42.33
------------------------------------------------------------------------
 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:    1.281    0.031    0.417
   1_adp:    1.281    0.031    0.417
   1_occ:    1.281    0.031    0.417
   2_bss:    1.281    0.031    0.417
   2_xyz:    1.869    0.030    0.573
   2_adp:    1.869    0.030    0.573
   2_occ:    1.869    0.030    0.573
   3_bss:    1.869    0.030    0.573
   3_xyz:    1.717    0.028    0.672
   3_adp:    1.717    0.028    0.672
   3_occ:    1.717    0.028    0.672
   4_bss:    1.717    0.028    0.672
   4_xyz:    1.936    0.059    0.711
   4_adp:    1.936    0.059    0.711
   4_occ:    1.936    0.059    0.711
   5_bss:    1.936    0.059    0.711
   5_xyz:    1.945    0.042    0.735
   5_adp:    1.945    0.042    0.735
   5_occ:    1.945    0.042    0.735
   5_bss:    1.945    0.042    0.735
------------------------------------------------------------------------

CPU time actual refinement: 282.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1044/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_1044/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1044/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1044/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1044/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 282.56 
  Macro-tasks:
    bulk solvent and scale       = 34.79  
    individual site refinement   = 117.34 
    weights calculation          = 26.80  
    collect and process          = 5.45   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 184.50 
  Micro-tasks:
    mask                            = 2.01   
    f_calc                          = 86.49  
    alpha_beta                      = 7.02   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 95.66  
    fmodel                         = 6.09   
    r_factors                      = 0.18   
    phase_errors                   = 8.70   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 207.35 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.964 micro seconds
Total CPU time: 4.91 minutes
from_scatterers_fft:    657 calls, 86.21 s
gradients_fft:          601 calls, 84.10 s

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

# Date 2008-01-16 Time 03:02:18 PST -0800 (1200481338.63 s)
Start R-work = 0.4821, R-free = 0.4771 (no bulk solvent and anisotropic scale)
Final R-work = 0.1375, R-free = 0.1861 (no bulk solvent and anisotropic scale)

Start R-work = 0.4741, R-free = 0.4643
Final R-work = 0.1212, R-free = 0.1702