# Date 2008-01-16 Time 03:21:43 PST -0800 (1200482503.47 s)
#phil __OFF__

Command line arguments: "../1209.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2006
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1209

-------------------------------------------------------------------------------
  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: (71.655, 48.1033, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 2.04054
Completeness in resolution range: 0.977495
Completeness with d_max=infinity: 0.974383

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3141
                             d_min =   2.0405

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: (71.655, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 2.04054
Completeness in resolution range: 0.977495
Completeness with d_max=infinity: 0.974383

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3145 -  4.3654 [2105/2129]  1894   211  10.0%
  bin  2:  4.3654 -  3.4783 [2028/2047]  1826   202  10.0%
  bin  3:  3.4783 -  3.0426 [1993/2012]  1794   199  10.0%
  bin  4:  3.0426 -  2.7662 [1972/2002]  1774   198  10.0%
  bin  5:  2.7662 -  2.5689 [1974/1993]  1778   196   9.9%
  bin  6:  2.5689 -  2.4181 [1947/1972]  1749   198  10.2%
  bin  7:  2.4181 -  2.2974 [1947/1975]  1755   192   9.9%
  bin  8:  2.2974 -  2.1977 [1954/1990]  1758   196  10.0%
  bin  9:  2.1977 -  2.1133 [1905/1947]  1712   193  10.1%
  bin 10:  2.1133 -  2.0405 [1764/1973]  1590   174   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1209/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.57 -     2.23: 6
        2.23 -     2.90: 1323
        2.90 -     3.57: 4323
        3.57 -     4.23: 8910
        4.23 -     4.90: 12865
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.565 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.844 3.040 -x+1/2,-y+1,z+1/2
  " OG  SER A 245 " - " O   HOH Z 202 "  2.068 3.040 -x+1/2,-y+1,z-1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27422 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_1209/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1209/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 = 71.655 48.10325 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: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5345   r_free= 0.5228   ksol= 0.00   Bsol= 0.00   scale= 0.729    |
|                                                                             |
| 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:   1.10 A                  |
| x-ray target function (ml) for work reflections: 6.317332                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.8686 0.99   1374  153 0.4481 0.4477      6.6773      6.6578|
|  2:  4.8686 -  3.8851 0.99   1307  146 0.4934 0.5254      6.9213      6.9788|
|  3:  3.8851 -  3.4001 0.99   1293  143 0.5272 0.4773      6.7805      6.7691|
|  4:  3.4001 -  3.0921 0.99   1284  139 0.5376 0.4871      6.6022      6.5352|
|  5:  3.0921 -  2.8720 0.99   1266  144 0.5490 0.5093       6.417      6.4444|
|  6:  2.8720 -  2.7036 0.99   1277  141 0.5565 0.5543      6.3135      6.2303|
|  7:  2.7036 -  2.5689 0.99   1265  140 0.5585 0.4921      6.2718      6.1954|
|  8:  2.5689 -  2.4575 0.98   1251  139 0.5600 0.5128       6.208      6.2139|
|  9:  2.4575 -  2.3633 0.98   1252  143 0.5529 0.6471      6.1381      6.1637|
| 10:  2.3633 -  2.2820 0.99   1247  136 0.5788 0.6135      6.1358      6.1587|
| 11:  2.2820 -  2.2109 0.98   1252  137 0.5592 0.5687      6.0588      6.0837|
| 12:  2.2109 -  2.1478 0.97   1240  142 0.5577 0.5140      6.0019      6.0658|
| 13:  2.1478 -  2.0914 1.00   1246  136 0.5482 0.4974      5.9058      5.8605|
| 14:  2.0914 -  2.0405 0.85   1076  120 0.5584 0.5559      5.8551      5.7798|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.8686  1374   153  0.60  42.66   0.75     0.64     103599.04|
|  2:  4.8686 -  3.8851  1307   146  0.58  45.56   0.81     0.63     155635.95|
|  3:  3.8851 -  3.4001  1293   143  0.46  54.83   0.74     0.56     162060.25|
|  4:  3.4001 -  3.0921  1284   139  0.35  63.90   0.74     0.43     138129.75|
|  5:  3.0921 -  2.8720  1266   144  0.29  68.11   0.68     0.35     100964.86|
|  6:  2.8720 -  2.7036  1277   141  0.27  69.64   0.66     0.31      83672.96|
|  7:  2.7036 -  2.5689  1265   140  0.26  70.75   0.67     0.28      74335.80|
|  8:  2.5689 -  2.4575  1251   139  0.19  75.99   0.70     0.21      70455.74|
|  9:  2.4575 -  2.3633  1252   143  0.11  82.14   0.67     0.12      67488.40|
| 10:  2.3633 -  2.2820  1247   136  0.04  86.84   0.66     0.05      62933.55|
| 11:  2.2820 -  2.2109  1252   137  0.08  83.94   0.70     0.10      57808.88|
| 12:  2.2109 -  2.1478  1240   142  0.13  80.59   0.70     0.15      51493.17|
| 13:  2.1478 -  2.0914  1246   136  0.13  80.63   0.69     0.15      43292.48|
| 14:  2.0914 -  2.0405  1076   120  0.14  79.92   0.67     0.15      35444.32|
|alpha:            min =        0.05 max =            0.64 mean =         0.30|
|beta:             min =    35444.32 max =       162060.25 mean =     87396.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.26|
|phase err.(work): min =        0.00 max =           90.00 mean =        69.96|
|phase err.(test): min =        0.00 max =           89.99 mean =        70.03|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 33.272001             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.201   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.553872              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 86.298   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      668 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1463 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2549 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3792 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4896 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6369 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7510 |
|-----------------------------------------------------------------------------|
|-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 |       55.087 |
| 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 |       1.728 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.681)------------------------------------------|
|    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 = 12.681)------------------------------------------|
|    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: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5379   r_free= 0.5276   ksol= 0.00   Bsol= 0.00   scale= 0.704    |
|                                                                             |
| 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:   1.10 A                  |
| x-ray target function (ml) for work reflections: 6.317633                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5302   r_free= 0.5193   ksol= 0.27   Bsol= 20.00   scale= 0.902   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.17,9.42,9.38,0.00,0.00,0.00); trace/3= 8.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.46 A                  |
| x-ray target function (ml) for work reflections: 5.524184                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 28.005603             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.804   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.910090              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.632   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5302      final r-factor (work) = 0.4860          |
| start r-factor (free) = 0.5193      final r-factor (free) = 0.4938          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 143.5279 = 28.01 * 0.50 * 6.3159 + 1.00 * 55.0872                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.0708 = 28.01 * 0.50 * 5.4921 + 1.00 * 0.1660                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4860      final r-factor (work) = 0.4416          |
| start r-factor (free) = 0.4938      final r-factor (free) = 0.4899          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.9973 = 2.91 * 1.00 * 5.4921 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.2174 = 2.91 * 1.00 * 6.2474 + 1.00 * 0.0368                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    149.37  22.07    None  None   None       |
|    all(noH): 2823   0      0.00    149.37  22.07    None  None   None       |
|    Sol.    : 438    0      0.00    149.37  30.86    None  None   None       |
|    Mac.    : 2385   0      0.00    103.79  20.46    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 -  14.938: 1234   |   5:    74.687 -  89.625:   37        |
|      1:    14.938 -  29.875:  832   |   6:    89.625 - 104.562:   16        |
|      2:    29.875 -  44.812:  415   |   7:   104.562 - 119.500:    4        |
|      3:    44.812 -  59.750:  198   |   8:   119.500 - 134.437:    0        |
|      4:    59.750 -  74.687:   85   |   9:   134.437 - 149.374:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4416 r_free = 0.4899             target_work(ml) = 5.883         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4406 r_free = 0.4924             target_work(ml) = 5.884         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4406   r_free= 0.4924   ksol= 0.27   Bsol= 20.00   scale= 1.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.17,9.42,9.38,0.00,0.00,0.00); trace/3= 8.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.99 A                  |
| x-ray target function (ml) for work reflections: 5.883666                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4394   r_free= 0.4878   ksol= 0.33   Bsol= 80.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,5.30,5.98,0.00,0.00,0.00); trace/3= 4.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.99 A                  |
| x-ray target function (ml) for work reflections: 5.884993                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.337146             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.297  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.792165              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.959  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4394      final r-factor (work) = 0.3941          |
| start r-factor (free) = 0.4878      final r-factor (free) = 0.4629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.4124 = 18.34 * 0.50 * 6.2438 + 1.00 * 0.1658                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.6861 = 18.34 * 0.50 * 5.8425 + 1.00 * 0.1189                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3941      final r-factor (work) = 0.3903          |
| start r-factor (free) = 0.4629      final r-factor (free) = 0.4540          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6690 = 0.79 * 1.00 * 5.8425 + 1.00 * 0.0408                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6236 = 0.79 * 1.00 * 5.8208 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    151.64  18.14    None  None   None       |
|    all(noH): 2823   0      0.00    151.64  18.14    None  None   None       |
|    Sol.    : 438    0      0.00    151.64  26.93    None  None   None       |
|    Mac.    : 2385   0      0.00    91.03   16.52    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 -  15.164: 1493   |   5:    75.818 -  90.982:   10        |
|      1:    15.164 -  30.327:  888   |   6:    90.982 - 106.146:    3        |
|      2:    30.327 -  45.491:  303   |   7:   106.146 - 121.309:    3        |
|      3:    45.491 -  60.655:   94   |   8:   121.309 - 136.473:    0        |
|      4:    60.655 -  75.818:   28   |   9:   136.473 - 151.636:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3903 r_free = 0.4540             target_work(ml) = 6.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3903 r_free = 0.4541             target_work(ml) = 6.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3903   r_free= 0.4541   ksol= 0.33   Bsol= 80.00   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,5.30,5.98,0.00,0.00,0.00); trace/3= 4.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.169499                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3904   r_free= 0.4518   ksol= 0.33   Bsol= 92.63   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.89,3.91,4.06,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.169800                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.797083             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.524  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.667362              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.262   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3904      final r-factor (work) = 0.3419          |
| start r-factor (free) = 0.4518      final r-factor (free) = 0.4090          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.4515 = 11.80 * 0.50 * 5.8205 + 1.00 * 0.1189                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.2157 = 11.80 * 0.50 * 6.1210 + 1.00 * 0.1107                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3419      final r-factor (work) = 0.3282          |
| start r-factor (free) = 0.4090      final r-factor (free) = 0.4005          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0964 = 0.67 * 1.00 * 6.1210 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0874 = 0.67 * 1.00 * 6.0612 + 1.00 * 0.0424                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    174.35  17.69    None  None   None       |
|    all(noH): 2823   0      0.00    174.35  17.69    None  None   None       |
|    Sol.    : 438    0      0.00    151.05  29.20    None  None   None       |
|    Mac.    : 2385   0      0.00    174.35  15.57    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 -  17.435: 1681   |   5:    87.177 - 104.612:    3        |
|      1:    17.435 -  34.871:  847   |   6:   104.612 - 122.048:    3        |
|      2:    34.871 -  52.306:  222   |   7:   122.048 - 139.483:    0        |
|      3:    52.306 -  69.742:   46   |   8:   139.483 - 156.919:    1        |
|      4:    69.742 -  87.177:   19   |   9:   156.919 - 174.354:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3282 r_free = 0.4005             target_work(ml) = 6.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3280 r_free = 0.4009             target_work(ml) = 6.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3280   r_free= 0.4009   ksol= 0.33   Bsol= 92.63   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.89,3.91,4.06,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.055005                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3278   r_free= 0.3996   ksol= 0.33   Bsol= 80.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.49,3.30,3.08,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.054024                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.072238             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.791  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.232927              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.963   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3278      final r-factor (work) = 0.2723          |
| start r-factor (free) = 0.3996      final r-factor (free) = 0.3427          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.6901 = 12.07 * 0.50 * 6.0601 + 1.00 * 0.1107                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.2666 = 12.07 * 0.50 * 5.9890 + 1.00 * 0.1160                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2723      final r-factor (work) = 0.2409          |
| start r-factor (free) = 0.3427      final r-factor (free) = 0.3101          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4335 = 1.23 * 1.00 * 5.9890 + 1.00 * 0.0495                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2425 = 1.23 * 1.00 * 5.8587 + 1.00 * 0.0191                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    147.25  17.13    None  None   None       |
|    all(noH): 2823   0      0.00    147.25  17.13    None  None   None       |
|    Sol.    : 438    0      0.00    147.25  39.99    None  None   None       |
|    Mac.    : 2385   0      0.00    113.16  12.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  14.725: 1705   |   5:    73.625 -  88.350:   21        |
|      1:    14.725 -  29.450:  640   |   6:    88.350 - 103.075:    8        |
|      2:    29.450 -  44.175:  246   |   7:   103.075 - 117.800:    4        |
|      3:    44.175 -  58.900:  123   |   8:   117.800 - 132.525:    0        |
|      4:    58.900 -  73.625:   75   |   9:   132.525 - 147.250:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2409 r_free = 0.3101             target_work(ml) = 5.818         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2407 r_free = 0.3107             target_work(ml) = 5.818         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2407   r_free= 0.3107   ksol= 0.33   Bsol= 80.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.49,3.30,3.08,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.817813                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2405   r_free= 0.3102   ksol= 0.34   Bsol= 90.77   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.06,2.05,2.33,0.00,0.00,0.00); trace/3= 1.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.817139                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.890717              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.880  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.402178              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.797  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2405      final r-factor (work) = 0.2056          |
| start r-factor (free) = 0.3102      final r-factor (free) = 0.2629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4416 = 4.89 * 0.50 * 5.8583 + 1.00 * 0.1160                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1478 = 4.89 * 0.50 * 5.7542 + 1.00 * 0.0766                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2056      final r-factor (work) = 0.1938          |
| start r-factor (free) = 0.2629      final r-factor (free) = 0.2469          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3333 = 0.40 * 1.00 * 5.7542 + 1.00 * 0.0191                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2841 = 0.40 * 1.00 * 5.6443 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    132.78  15.92    None  None   None       |
|    all(noH): 2823   0      0.00    132.78  15.92    None  None   None       |
|    Sol.    : 438    0      0.72    132.78  41.69    None  None   None       |
|    Mac.    : 2385   0      0.00    101.76  11.18    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 -  13.278: 1793   |   5:    66.390 -  79.668:   54        |
|      1:    13.278 -  26.556:  541   |   6:    79.668 -  92.946:   10        |
|      2:    26.556 -  39.834:  202   |   7:    92.946 - 106.224:    4        |
|      3:    39.834 -  53.112:  142   |   8:   106.224 - 119.502:    0        |
|      4:    53.112 -  66.390:   76   |   9:   119.502 - 132.780:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1938 r_free = 0.2469             target_work(ml) = 5.618         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1935 r_free = 0.2471             target_work(ml) = 5.617         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1935   r_free= 0.2471   ksol= 0.34   Bsol= 90.77   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.06,2.05,2.33,0.00,0.00,0.00); trace/3= 1.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.617254                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.8686 0.99   1374  153 0.1269 0.1814      5.6474      5.8527|
|  2:  4.8686 -  3.8851 0.99   1307  146 0.1312 0.1692      5.8361      6.0362|
|  3:  3.8851 -  3.4001 0.99   1293  143 0.1767 0.2284      5.9541      6.2451|
|  4:  3.4001 -  3.0921 0.99   1284  139 0.2112 0.2597      5.9252       6.078|
|  5:  3.0921 -  2.8720 0.99   1266  144 0.2300 0.2579         5.8      5.9387|
|  6:  2.8720 -  2.7036 0.99   1277  141 0.2162 0.2929      5.6914      5.8421|
|  7:  2.7036 -  2.5689 0.99   1265  140 0.2189 0.2765      5.6338      5.8362|
|  8:  2.5689 -  2.4575 0.98   1251  139 0.2211 0.2303      5.6078      5.7169|
|  9:  2.4575 -  2.3633 0.98   1252  143 0.2227 0.3269      5.5441      5.8139|
| 10:  2.3633 -  2.2820 0.99   1247  136 0.2128 0.2987      5.4984      5.6495|
| 11:  2.2820 -  2.2109 0.98   1252  137 0.2284 0.2524      5.4874       5.612|
| 12:  2.2109 -  2.1478 0.97   1240  142 0.2093 0.2911      5.3754      5.7634|
| 13:  2.1478 -  2.0914 1.00   1246  136 0.2158 0.2809      5.3178      5.4428|
| 14:  2.0914 -  2.0405 0.85   1076  120 0.2074 0.2840      5.2286      5.4195|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.8686  1374   153  0.90  14.71   0.95     0.92      14527.27|
|  2:  4.8686 -  3.8851  1307   146  0.90  14.70   1.01     0.98      21128.05|
|  3:  3.8851 -  3.4001  1293   143  0.86  20.31   1.01     0.98      27423.91|
|  4:  3.4001 -  3.0921  1284   139  0.83  23.75   1.00     0.93      26517.86|
|  5:  3.0921 -  2.8720  1266   144  0.80  26.59   1.00     0.97      21536.77|
|  6:  2.8720 -  2.7036  1277   141  0.80  26.68   0.96     0.88      17379.07|
|  7:  2.7036 -  2.5689  1265   140  0.80  26.25   0.99     0.94      15921.50|
|  8:  2.5689 -  2.4575  1251   139  0.79  27.60   0.98     0.89      15386.76|
|  9:  2.4575 -  2.3633  1252   143  0.78  28.74   1.00     0.90      14072.53|
| 10:  2.3633 -  2.2820  1247   136  0.79  27.86   1.01     0.90      12381.26|
| 11:  2.2820 -  2.2109  1252   137  0.79  28.06   0.99     0.89      12025.48|
| 12:  2.2109 -  2.1478  1240   142  0.80  26.87   1.01     0.94      10458.80|
| 13:  2.1478 -  2.0914  1246   136  0.79  27.97   0.98     0.90       9531.31|
| 14:  2.0914 -  2.0405  1076   120  0.78  28.34   0.94     0.86       7968.16|
|alpha:            min =        0.86 max =            0.98 mean =         0.92|
|beta:             min =     7968.16 max =        27423.91 mean =     16305.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.81|
|phase err.(work): min =        0.00 max =           89.95 mean =        24.74|
|phase err.(test): min =        0.00 max =           89.82 mean =        23.36|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1940   r_free= 0.2472   ksol= 0.34   Bsol= 86.26   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,0.06,0.73,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.617767                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1940   r_free= 0.2472   ksol= 0.34   Bsol= 86.26   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,0.06,0.73,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.617767                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.8686 0.99   1374  153 0.1280 0.1833       5.649      5.8486|
|  2:  4.8686 -  3.8851 0.99   1307  146 0.1326 0.1693       5.838      6.0391|
|  3:  3.8851 -  3.4001 0.99   1293  143 0.1768 0.2267      5.9558      6.2407|
|  4:  3.4001 -  3.0921 0.99   1284  139 0.2116 0.2604       5.926      6.0798|
|  5:  3.0921 -  2.8720 0.99   1266  144 0.2305 0.2584       5.801      5.9396|
|  6:  2.8720 -  2.7036 0.99   1277  141 0.2163 0.2922      5.6913      5.8406|
|  7:  2.7036 -  2.5689 0.99   1265  140 0.2189 0.2768      5.6338      5.8367|
|  8:  2.5689 -  2.4575 0.98   1251  139 0.2210 0.2304      5.6073       5.716|
|  9:  2.4575 -  2.3633 0.98   1252  143 0.2229 0.3267      5.5442      5.8141|
| 10:  2.3633 -  2.2820 0.99   1247  136 0.2127 0.2986       5.499      5.6499|
| 11:  2.2820 -  2.2109 0.98   1252  137 0.2280 0.2531      5.4875      5.6136|
| 12:  2.2109 -  2.1478 0.97   1240  142 0.2093 0.2918      5.3754      5.7648|
| 13:  2.1478 -  2.0914 1.00   1246  136 0.2158 0.2805      5.3177      5.4426|
| 14:  2.0914 -  2.0405 0.85   1076  120 0.2074 0.2836      5.2286      5.4189|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.8686  1374   153  0.90  14.52   0.94     0.91      14081.00|
|  2:  4.8686 -  3.8851  1307   146  0.90  14.68   1.01     0.98      20941.92|
|  3:  3.8851 -  3.4001  1293   143  0.86  20.32   1.01     0.98      27532.72|
|  4:  3.4001 -  3.0921  1284   139  0.83  23.74   1.00     0.93      26477.15|
|  5:  3.0921 -  2.8720  1266   144  0.80  26.61   0.99     0.97      21545.01|
|  6:  2.8720 -  2.7036  1277   141  0.80  26.68   0.96     0.87      17388.02|
|  7:  2.7036 -  2.5689  1265   140  0.80  26.21   0.99     0.94      15885.54|
|  8:  2.5689 -  2.4575  1251   139  0.79  27.58   0.98     0.89      15371.66|
|  9:  2.4575 -  2.3633  1252   143  0.78  28.74   1.00     0.89      14064.27|
| 10:  2.3633 -  2.2820  1247   136  0.79  27.89   1.00     0.89      12405.24|
| 11:  2.2820 -  2.2109  1252   137  0.78  28.11   0.98     0.88      12065.09|
| 12:  2.2109 -  2.1478  1240   142  0.80  26.89   1.00     0.94      10466.42|
| 13:  2.1478 -  2.0914  1246   136  0.79  27.97   0.97     0.90       9538.85|
| 14:  2.0914 -  2.0405  1076   120  0.78  28.35   0.94     0.85       7972.47|
|alpha:            min =        0.85 max =            0.98 mean =         0.92|
|beta:             min =     7972.47 max =        27532.72 mean =     16264.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.81|
|phase err.(work): min =        0.00 max =           89.95 mean =        24.73|
|phase err.(test): min =        0.00 max =           89.80 mean =        23.31|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.681)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    134.47  17.61    None  None   None       |
|    all(noH): 2823   0      1.69    134.47  17.61    None  None   None       |
|    Sol.    : 438    0      2.41    134.47  43.38    None  None   None       |
|    Mac.    : 2385   0      1.69    103.45  12.88    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:     1.691 -  14.969: 1793   |   5:    68.082 -  81.360:   54        |
|      1:    14.969 -  28.247:  541   |   6:    81.360 -  94.638:   10        |
|      2:    28.247 -  41.525:  202   |   7:    94.638 - 107.916:    4        |
|      3:    41.525 -  54.803:  142   |   8:   107.916 - 121.194:    0        |
|      4:    54.803 -  68.082:   76   |   9:   121.194 - 134.472:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 350         
Filter by distance & map next to the model:
   mapped sites are within: 0.578 - 4.933
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 342 from: 350
   mapped sites are within: 0.702 - 4.933

peak=    6.618 closest distance to " O   HOH Z 103 " =    1.239
peak=    6.583 closest distance to " OD1 ASP A 107 " =    1.261
peak=    6.532 closest distance to " O   HOH Z 159 " =    1.551
peak=    6.486 closest distance to " O   HOH Z  84 " =    1.381
peak=    6.209 closest distance to " O   HOH Z 342 " =    1.811
peak=    6.115 closest distance to " C   THR A  29 " =    1.197
peak=    5.944 closest distance to " O   HOH Z 138 " =    1.255
peak=    5.839 closest distance to " O   HOH Z 390 " =    1.711
peak=    5.797 closest distance to " O   HOH Z  57 " =    1.381
peak=    5.774 closest distance to " NH1 ARG A 269 " =    1.248
peak=    5.717 closest distance to " O   HOH Z  53 " =    1.535
peak=    5.657 closest distance to " OD1 ASN A 301 " =    1.269
peak=    5.608 closest distance to " O   HOH Z  70 " =    1.564
peak=    5.589 closest distance to " CG1 ILE A 120 " =    1.137
peak=    5.573 closest distance to " O   HOH Z 426 " =    1.434
peak=    5.544 closest distance to " N   SER A 164 " =    1.058
peak=    5.424 closest distance to " O   SER A   3 " =    1.265
peak=    5.343 closest distance to " O   HOH Z  41 " =    1.442
peak=    5.338 closest distance to " NH1 ARG A 138 " =    1.144
peak=    5.280 closest distance to " CD  ARG A  36 " =    1.266
peak=    5.257 closest distance to " ND2 ASN A  74 " =    0.993
peak=    5.223 closest distance to " CA  VAL A 230 " =    1.377
peak=    5.213 closest distance to " CD  ARG A 138 " =    1.503
peak=    5.192 closest distance to " O   GLN A  11 " =    1.132
peak=    5.160 closest distance to " O   LEU A  25 " =    1.043
peak=    5.078 closest distance to " CG  GLN A  77 " =    1.165
peak=    5.054 closest distance to " CD  ARG A  36 " =    1.279
peak=    5.050 closest distance to " CB  SER A  26 " =    1.039
peak=    5.020 closest distance to " CD  ARG A 269 " =    1.062
peak=    5.008 closest distance to " N   THR A  29 " =    1.047
peak=    5.002 closest distance to " O   HOH Z 102 " =    1.840
peak=    4.968 closest distance to " CG1BVAL A 121 " =    1.657
peak=    4.910 closest distance to " NH1BARG A 275 " =    1.449
peak=    4.851 closest distance to " C   TYR A  30 " =    1.017
peak=    4.834 closest distance to " CG2 THR A  31 " =    1.307
peak=    4.817 closest distance to " O   VAL A 121 " =    0.959
peak=    4.791 closest distance to " CG1 ILE A 234 " =    1.569
peak=    4.785 closest distance to " O   HOH Z 117 " =    2.361
peak=    4.747 closest distance to " O   ALA A 299 " =    0.926
peak=    4.746 closest distance to " O   GLN A  58 " =    1.343
peak=    4.725 closest distance to " CB  SER A  63 " =    1.332
peak=    4.723 closest distance to " O   GLN A  73 " =    1.368
peak=    4.723 closest distance to " CG1 VAL A 296 " =    1.333
peak=    4.671 closest distance to " OG1 THR A  29 " =    1.130
peak=    4.634 closest distance to " OG1 THR A  31 " =    0.948
peak=    4.602 closest distance to " ND2 ASN A 301 " =    1.091
peak=    4.574 closest distance to " N   PHE A  59 " =    1.141
peak=    4.536 closest distance to " CG  LEU A   5 " =    1.473
peak=    4.530 closest distance to " N   SER A   3 " =    0.803
peak=    4.511 closest distance to " O   HOH Z  67 " =    1.874
peak=    4.481 closest distance to " O   HOH Z 120 " =    1.882
peak=    4.439 closest distance to " CG BARG A 275 " =    1.521
peak=    4.380 closest distance to " CG2 VAL A 230 " =    1.224
peak=    4.328 closest distance to " CG1 VAL A 230 " =    1.217
peak=    4.307 closest distance to " OH  TYR A  68 " =    1.281
peak=    4.295 closest distance to " O   HOH Z 411 " =    2.992
peak=    4.228 closest distance to " O   HOH Z 139 " =    1.280
peak=    4.206 closest distance to " CG  ASN A  69 " =    1.237
peak=    4.179 closest distance to " CB AVAL A  41 " =    0.713
peak=    4.146 closest distance to " CG  GLN A  11 " =    1.174
peak=    4.134 closest distance to " NE2 HIS A 115 " =    1.293
peak=    4.116 closest distance to " O   GLN A  58 " =    1.214
peak=    4.116 closest distance to " O   ARG A 275 " =    0.796
peak=    4.107 closest distance to " CG2 THR A 157 " =    1.078
peak=    4.097 closest distance to " O   HOH Z 279 " =    1.363
peak=    4.083 closest distance to " N   ASN A 187 " =    0.827
peak=    4.082 closest distance to " CB  LEU A  25 " =    1.056
peak=    4.078 closest distance to " O   HOH Z 407 " =    2.440
peak=    4.078 closest distance to " O   HOH Z 107 " =    1.752
peak=    4.070 closest distance to " CD BLYS A 290 " =    1.228
peak=    4.052 closest distance to " N   SER A  28 " =    1.145
peak=    4.027 closest distance to " O   HOH Z 132 " =    3.478
peak=    4.019 closest distance to " CB  GLN A  88 " =    1.380
peak=    4.018 closest distance to " O   HOH Z 335 " =    1.145
peak=    4.008 closest distance to " O   VAL A  72 " =    1.047
peak=    3.995 closest distance to " N   THR A  31 " =    0.761
peak=    3.994 closest distance to " O   HOH Z 206 " =    0.980
peak=    3.978 closest distance to " CA  HIS A 115 " =    1.060
peak=    3.963 closest distance to " CB  TYR A  30 " =    1.033
peak=    3.957 closest distance to " O   HOH Z 379 " =    1.853
peak=    3.936 closest distance to " CB  SER A 288 " =    1.295
peak=    3.934 closest distance to " O   TYR A  30 " =    0.989
peak=    3.929 closest distance to " CA  TRP A 274 " =    1.031
peak=    3.926 closest distance to " OD2 ASP A 270 " =    0.979
peak=    3.923 closest distance to " CD1 ILE A 263 " =    1.300
peak=    3.922 closest distance to " O   HOH Z 248 " =    1.807
peak=    3.918 closest distance to " CB  ASN A  39 " =    0.754
peak=    3.913 closest distance to " O   HOH Z 377 " =    2.027
peak=    3.911 closest distance to " O   HOH Z 149 " =    1.552
peak=    3.910 closest distance to " N   TYR A  30 " =    0.748
peak=    3.900 closest distance to " NH2 ARG A 269 " =    0.971
peak=    3.897 closest distance to " CD1 LEU A 297 " =    1.360
peak=    3.873 closest distance to " O   GLU A   2 " =    1.678
peak=    3.866 closest distance to " O   HOH Z 137 " =    1.298
peak=    3.862 closest distance to " O   HOH Z 152 " =    2.502
peak=    3.861 closest distance to " O   HOH Z  57 " =    2.513
peak=    3.835 closest distance to " CD  ARG A 269 " =    1.333
peak=    3.830 closest distance to " CZ3 TRP A 266 " =    1.106
peak=    3.804 closest distance to " CD2 TYR A  68 " =    1.126
peak=    3.802 closest distance to " CB  TRP A 179 " =    1.184
peak=    3.799 closest distance to " CB  SER A 273 " =    0.895
peak=    3.793 closest distance to " CB  ALA A 137 " =    1.274
peak=    3.789 closest distance to " OD1 ASN A  60 " =    1.076
peak=    3.783 closest distance to " ND2 ASN A 249 " =    0.821
peak=    3.775 closest distance to " OG ASER A  12 " =    1.140
peak=    3.775 closest distance to " CA  ASP A  27 " =    0.831
peak=    3.775 closest distance to " O   HOH Z 425 " =    2.151
peak=    3.769 closest distance to " CD1 PHE A  16 " =    0.986
peak=    3.760 closest distance to " CA  ALA A 160 " =    1.296
peak=    3.756 closest distance to " O   HOH Z 272 " =    1.794
peak=    3.755 closest distance to " N   GLN A  11 " =    0.953
peak=    3.752 closest distance to " O   HOH Z   2 " =    3.679
peak=    3.745 closest distance to " O   THR A 220 " =    1.539
peak=    3.735 closest distance to " O   HOH Z 417 " =    1.485
peak=    3.735 closest distance to " O   ASN A  74 " =    1.129
peak=    3.723 closest distance to " O   HOH Z 131 " =    1.220
peak=    3.722 closest distance to " OE1 GLN A  73 " =    1.516
peak=    3.714 closest distance to " CB  PHE A 283 " =    1.015
peak=    3.712 closest distance to " O   HOH Z 422 " =    1.182
peak=    3.710 closest distance to " O   HOH Z 158 " =    3.043
peak=    3.702 closest distance to " O   HOH Z 174 " =    1.954
peak=    3.699 closest distance to " O   ASN A  60 " =    1.093
peak=    3.697 closest distance to " NE2 HIS A 108 " =    0.759
peak=    3.685 closest distance to " ND2 ASN A 110 " =    1.145
peak=    3.682 closest distance to " CB  GLU A   2 " =    0.891
peak=    3.681 closest distance to " O   HOH Z 146 " =    1.788
peak=    3.677 closest distance to " CA  VAL A 296 " =    1.247
peak=    3.674 closest distance to " OG  SER A  62 " =    2.817
peak=    3.665 closest distance to " CD  PRO A  54 " =    1.231
peak=    3.645 closest distance to " N   ARG A 275 " =    0.922
peak=    3.643 closest distance to " O   HOH Z 174 " =    1.878
peak=    3.641 closest distance to " CG  ARG A 269 " =    1.279
peak=    3.640 closest distance to " CA  CYS A 260 " =    0.961
peak=    3.638 closest distance to " O   HOH Z 286 " =    1.804
peak=    3.637 closest distance to " NH1 ARG A  36 " =    1.440
peak=    3.632 closest distance to " OE1 GLN A  58 " =    1.473
peak=    3.631 closest distance to " O   HOH Z 139 " =    4.933
peak=    3.629 closest distance to " CA  GLY A 196 " =    0.855
peak=    3.623 closest distance to " ND2 ASN A 215 " =    0.951
peak=    3.614 closest distance to " O   HOH Z 146 " =    2.448
peak=    3.612 closest distance to " CD2 LEU A 228 " =    1.385
peak=    3.609 closest distance to " O   HOH Z 223 " =    1.463
peak=    3.596 closest distance to " CD1 ILE A  33 " =    1.715
peak=    3.592 closest distance to " O   HOH Z 203 " =    1.012
peak=    3.588 closest distance to " O   HOH Z  54 " =    2.239
peak=    3.585 closest distance to " O   HOH Z  14 " =    1.280
peak=    3.574 closest distance to " O   ARG A  56 " =    1.723
peak=    3.572 closest distance to " O   THR A  31 " =    1.217
peak=    3.572 closest distance to " OD1 ASN A 215 " =    0.961
peak=    3.563 closest distance to " N   ASP A 298 " =    0.857
peak=    3.562 closest distance to " O   GLU A 152 " =    1.071
peak=    3.561 closest distance to " CG  PRO A 198 " =    1.558
peak=    3.558 closest distance to " NH2AARG A 145 " =    1.368
peak=    3.551 closest distance to " NH1BARG A 102 " =    1.320
peak=    3.548 closest distance to " CG  GLU A 277 " =    3.782
peak=    3.547 closest distance to " O   HOH Z 403 " =    1.503
peak=    3.540 closest distance to " O   THR A 157 " =    1.251
peak=    3.538 closest distance to " OG  SER A  97 " =    1.301
peak=    3.530 closest distance to " CB  SER A  97 " =    1.407
peak=    3.530 closest distance to " O   HOH Z 207 " =    1.731
peak=    3.530 closest distance to " O  BHOH Z  74 " =    1.215
peak=    3.529 closest distance to " O   HOH Z 258 " =    3.502
peak=    3.529 closest distance to " O   HOH Z 124 " =    1.576
peak=    3.526 closest distance to " NH2 ARG A  56 " =    1.520
peak=    3.525 closest distance to " CE1 TYR A 186 " =    1.117
peak=    3.524 closest distance to " O   HOH Z 128 " =    2.085
peak=    3.521 closest distance to " CZ  PHE A 218 " =    1.302
peak=    3.521 closest distance to " O   HOH Z  90 " =    2.901
peak=    3.519 closest distance to " N   SER A 271 " =    1.094
peak=    3.518 closest distance to " NE1 TRP A  92 " =    1.064
peak=    3.508 closest distance to " CA  THR A 246 " =    1.132
peak=    3.508 closest distance to " CG1 VAL A 153 " =    1.279
peak=    3.501 closest distance to " CB  ALA A 114 " =    0.922
peak=    3.501 closest distance to " O   HOH Z  28 " =    1.932
peak=    3.494 closest distance to " O   HOH Z 277 " =    1.500
peak=    3.494 closest distance to " CA  ARG A 195 " =    1.264
peak=    3.491 closest distance to " CG2 VAL A  67 " =    1.004
peak=    3.488 closest distance to " CB  PRO A 243 " =    1.377
peak=    3.484 closest distance to " CD  LYS A  48 " =    1.172
peak=    3.480 closest distance to " CB  SER A   3 " =    1.110
peak=    3.478 closest distance to " N   GLY A  75 " =    0.857
peak=    3.471 closest distance to " OG ASER A 134 " =    1.265
peak=    3.471 closest distance to " OE1 GLU A   2 " =    1.114
peak=    3.464 closest distance to " CA  ARG A  66 " =    1.021
peak=    3.462 closest distance to " CZ AARG A 145 " =    1.410
peak=    3.461 closest distance to " CB  ASN A  69 " =    0.844
peak=    3.451 closest distance to " N   LYS A 119 " =    0.908
peak=    3.451 closest distance to " O   HOH Z 272 " =    2.014
peak=    3.451 closest distance to " CG2 ILE A 120 " =    1.359
peak=    3.450 closest distance to " O   PRO A 198 " =    1.556
peak=    3.448 closest distance to " CG  GLN A 183 " =    1.234
peak=    3.446 closest distance to " O   HOH Z 301 " =    2.180
peak=    3.445 closest distance to " O   SER A 273 " =    0.995
peak=    3.443 closest distance to " O   TYR A 116 " =    1.222
peak=    3.442 closest distance to " CE3 TRP A  85 " =    1.130
peak=    3.435 closest distance to " O   HOH Z  61 " =    1.338
peak=    3.428 closest distance to " N   ASP A 132 " =    0.835
peak=    3.427 closest distance to " O   HOH Z 296 " =    1.858
peak=    3.426 closest distance to " O   SER A  26 " =    1.641
peak=    3.424 closest distance to " CB  ALA A  34 " =    0.939
peak=    3.422 closest distance to " O   HOH Z 424 " =    1.076
peak=    3.416 closest distance to " CA  ALA A 100 " =    1.211
peak=    3.413 closest distance to " OG  SER A  28 " =    0.881
peak=    3.408 closest distance to " CB  ASN A 142 " =    1.109
peak=    3.402 closest distance to " O   THR A 251 " =    1.189
peak=    3.402 closest distance to " O   HOH Z 100 " =    1.543
peak=    3.402 closest distance to " N   ALA A   1 " =    2.228
peak=    3.401 closest distance to " O   HOH Z 415 " =    1.459
peak=    3.399 closest distance to " CB  LEU A 281 " =    0.981
peak=    3.396 closest distance to " NH1 ARG A 159 " =    1.064
peak=    3.396 closest distance to " O   HOH Z  54 " =    1.840
peak=    3.393 closest distance to " N   ASN A 142 " =    0.867
peak=    3.390 closest distance to " CA  SER A  62 " =    0.863
peak=    3.389 closest distance to " O   HOH Z  56 " =    2.289
peak=    3.388 closest distance to " O   LYS A 119 " =    0.964
peak=    3.388 closest distance to " CB  ASN A 187 " =    1.320
peak=    3.386 closest distance to " CE2 TYR A  68 " =    0.866
peak=    3.386 closest distance to " CG2 VAL A 257 " =    0.785
peak=    3.384 closest distance to " OD2 ASP A  65 " =    1.135
peak=    3.383 closest distance to " OD2 ASP A 286 " =    1.210
peak=    3.381 closest distance to " O   HOH Z 141 " =    1.575
peak=    3.381 closest distance to " N   SER A  26 " =    0.938
peak=    3.380 closest distance to " OD1 ASP A 272 " =    0.954
peak=    3.380 closest distance to " O   HOH Z 125 " =    2.258
peak=    3.371 closest distance to " O   HOH Z 215 " =    1.597
peak=    3.370 closest distance to " O   HOH Z  32 " =    1.132
peak=    3.366 closest distance to " CG  PRO A 280 " =    1.093
peak=    3.363 closest distance to " ND2 ASN A 148 " =    0.858
peak=    3.362 closest distance to " O   HOH Z 201 " =    2.998
peak=    3.361 closest distance to " CB  SER A  62 " =    1.223
peak=    3.358 closest distance to " O   HOH Z 247 " =    1.678
peak=    3.350 closest distance to " O   HOH Z 324 " =    1.875
peak=    3.342 closest distance to " CG2 VAL A 153 " =    0.702
peak=    3.341 closest distance to " O   HOH Z  85 " =    2.190
peak=    3.338 closest distance to " O   HOH Z  40 " =    1.665
peak=    3.337 closest distance to " O   HOH Z 343 " =    1.505
peak=    3.334 closest distance to " O   HOH Z 427 " =    3.158
peak=    3.328 closest distance to " CG  GLU A  37 " =    1.370
peak=    3.327 closest distance to " O   HOH Z 193 " =    2.603
peak=    3.325 closest distance to " O   VAL A 189 " =    1.029
peak=    3.321 closest distance to " O   HOH Z 343 " =    2.276
peak=    3.321 closest distance to " ND2 ASN A  45 " =    1.387
peak=    3.319 closest distance to " OH  TYR A 293 " =    0.718
peak=    3.318 closest distance to " CA  ALA A 154 " =    0.981
peak=    3.315 closest distance to " OH  TYR A 169 " =    0.972
peak=    3.314 closest distance to " CZ2 TRP A  70 " =    1.160
peak=    3.312 closest distance to " O   HOH Z 156 " =    4.440
peak=    3.309 closest distance to " CG2BVAL A  41 " =    1.602
peak=    3.305 closest distance to " CD2 PHE A  38 " =    0.879
peak=    3.303 closest distance to " O   HOH Z 285 " =    2.985
peak=    3.300 closest distance to " CG  PRO A  54 " =    1.389
peak=    3.300 closest distance to " O   HOH Z 222 " =    1.263
peak=    3.298 closest distance to " CB  MET A  47 " =    1.042
peak=    3.295 closest distance to " CA  ASN A  74 " =    1.040
peak=    3.291 closest distance to " CA  GLY A  35 " =    0.798
peak=    3.285 closest distance to " NE2 GLN A  89 " =    1.276
peak=    3.284 closest distance to " OE1 GLU A  37 " =    0.882
peak=    3.284 closest distance to " CD2 LEU A 255 " =    1.455
peak=    3.284 closest distance to " O   HOH Z 326 " =    2.149
peak=    3.282 closest distance to " CG2 THR A 221 " =    1.072
peak=    3.282 closest distance to " O   VAL A  78 " =    0.759
peak=    3.281 closest distance to " O   ASP A 200 " =    1.329
peak=    3.281 closest distance to " CB  ASN A 176 " =    0.984
peak=    3.279 closest distance to " ND1 HIS A  81 " =    1.477
peak=    3.270 closest distance to " N   LEU A  25 " =    0.856
peak=    3.269 closest distance to " N   TYR A 169 " =    1.051
peak=    3.266 closest distance to " O   ALA A 180 " =    1.604
peak=    3.265 closest distance to " CG  ASP A 231 " =    0.977
peak=    3.264 closest distance to " O   HOH Z 361 " =    3.329
peak=    3.260 closest distance to " CA  TYR A 116 " =    1.367
peak=    3.259 closest distance to " CG2 THR A  42 " =    1.384
peak=    3.258 closest distance to " CG  GLN A 278 " =    1.085
peak=    3.254 closest distance to " CB  TRP A  70 " =    0.868
peak=    3.251 closest distance to " CA  PRO A 198 " =    1.236
peak=    3.249 closest distance to " O   TRP A 177 " =    1.468
peak=    3.244 closest distance to " O   HOH Z 221 " =    2.023
peak=    3.242 closest distance to " CA  THR A 235 " =    0.985
peak=    3.242 closest distance to " O   HOH Z 107 " =    1.535
peak=    3.239 closest distance to " CA  GLY A 133 " =    3.936
peak=    3.238 closest distance to " O   GLN A  77 " =    0.728
peak=    3.235 closest distance to " CB  ARG A 156 " =    1.084
peak=    3.234 closest distance to " CB  ALA A 158 " =    1.468
peak=    3.233 closest distance to " CB  VAL A 296 " =    1.405
peak=    3.232 closest distance to " O   HOH Z 401 " =    1.572
peak=    3.230 closest distance to " O   HOH Z 344 " =    3.201
peak=    3.230 closest distance to " CA  GLY A   6 " =    0.835
peak=    3.226 closest distance to " ND2 ASN A  45 " =    4.101
peak=    3.226 closest distance to " O   MET A 105 " =    1.457
peak=    3.224 closest distance to " CA  THR A 279 " =    0.914
peak=    3.221 closest distance to " O   HOH Z 119 " =    1.541
peak=    3.213 closest distance to " O   HOH Z 145 " =    1.765
peak=    3.208 closest distance to " O   HOH Z 395 " =    1.824
peak=    3.206 closest distance to " CE1 HIS A 108 " =    1.743
peak=    3.202 closest distance to " O   THR A 294 " =    1.735
peak=    3.201 closest distance to " CB  VAL A 202 " =    1.203
peak=    3.201 closest distance to " CG2 THR A   4 " =    1.339
peak=    3.200 closest distance to " CA  GLU A 277 " =    1.071
peak=    3.197 closest distance to " CD1 ILE A 109 " =    1.017
peak=    3.194 closest distance to " CG2 THR A 220 " =    1.563
peak=    3.192 closest distance to " CD1 TRP A 274 " =    0.987
peak=    3.188 closest distance to " CG1 ILE A  20 " =    1.249
peak=    3.185 closest distance to " CA  ARG A  36 " =    1.043
peak=    3.182 closest distance to " CB  ALA A 161 " =    0.864
peak=    3.181 closest distance to " OG BSER A 164 " =    1.814
peak=    3.179 closest distance to " O   HOH Z 394 " =    2.335
peak=    3.174 closest distance to " CB  GLN A 183 " =    1.136
peak=    3.173 closest distance to " CZ2 TRP A 150 " =    1.285
peak=    3.171 closest distance to " O   HOH Z 435 " =    2.086
peak=    3.169 closest distance to " O   GLU A  53 " =    0.870
peak=    3.166 closest distance to " O   HOH Z 196 " =    2.018
peak=    3.163 closest distance to " OXT GLY A 302 " =    3.718
peak=    3.162 closest distance to " N   ALA A 292 " =    0.975
peak=    3.162 closest distance to " O   HOH Z  65 " =    1.293
peak=    3.160 closest distance to " NE2 GLN A  58 " =    3.736
peak=    3.159 closest distance to " CB  PHE A  59 " =    0.961
peak=    3.156 closest distance to " CB  GLN A  73 " =    0.890
peak=    3.156 closest distance to " NH2 ARG A 195 " =    1.118
peak=    3.155 closest distance to " CA  TRP A 274 " =    1.309
peak=    3.153 closest distance to " O   HOH Z 365 " =    2.993
peak=    3.150 closest distance to " CG1 VAL A 296 " =    1.650
peak=    3.144 closest distance to " CB  GLU A  46 " =    0.829
peak=    3.138 closest distance to " O   ASP A 124 " =    1.083
peak=    3.136 closest distance to " CB  HIS A  81 " =    1.196
peak=    3.134 closest distance to " OG  SER A  22 " =    2.654
peak=    3.132 closest distance to " OG  SER A  32 " =    0.929
peak=    3.127 closest distance to " CZ  PHE A 283 " =    1.093
peak=    3.114 closest distance to " O   HOH Z 214 " =    3.272
peak=    3.114 closest distance to " C   ALA A  10 " =    0.884
peak=    3.113 closest distance to " O   HOH Z 345 " =    3.613
peak=    3.110 closest distance to " N   ILE A  33 " =    1.000
peak=    3.100 closest distance to " O   HOH Z 106 " =    2.181
peak=    3.099 closest distance to " OE1 GLN A 278 " =    1.646
peak=    3.099 closest distance to " CB  SER A  62 " =    4.144
peak=    3.089 closest distance to " CB  ASN A 285 " =    1.011
peak=    3.084 closest distance to " O   HOH Z   5 " =    2.185
peak=    3.079 closest distance to " CB  TRP A 266 " =    0.940
peak=    3.072 closest distance to " N   ALA A  34 " =    1.076
peak=    3.068 closest distance to " CG2 VAL A 268 " =    1.043
peak=    3.054 closest distance to " N   VAL A 265 " =    0.886
peak=    3.048 closest distance to " C   ARG A  79 " =    1.211
peak=    3.028 closest distance to " O   HOH Z   9 " =    2.139
peak=    3.006 closest distance to " CA  SER A  62 " =    1.105

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 223         
Filter by distance & map next to the model:
   mapped sites are within: 0.186 - 5.957
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 223
   mapped sites are within: 0.703 - 5.957

peak=   -5.026 closest distance to " O   SER A  28 " =    1.022
peak=   -4.917 closest distance to " OD1 ASP A 107 " =    0.964
peak=   -4.612 closest distance to " CG  LEU A   5 " =    1.059
peak=   -4.448 closest distance to " O   SER A   3 " =    1.010
peak=   -4.383 closest distance to " OD1 ASN A  69 " =    1.118
peak=   -4.376 closest distance to " CZ  TYR A 116 " =    1.272
peak=   -4.318 closest distance to " OD1 ASP A 107 " =    0.781
peak=   -4.310 closest distance to " O   HOH Z 400 " =    0.774
peak=   -4.293 closest distance to " C   GLN A  58 " =    0.909
peak=   -4.258 closest distance to " O   VAL A 121 " =    0.922
peak=   -4.258 closest distance to " CG  GLN A  73 " =    0.778
peak=   -4.236 closest distance to " O   VAL A  67 " =    2.678
peak=   -4.200 closest distance to " O   HOH Z   2 " =    2.814
peak=   -4.198 closest distance to " O   ARG A  56 " =    4.030
peak=   -4.167 closest distance to " CD  ARG A 138 " =    0.868
peak=   -4.134 closest distance to " NE  ARG A  36 " =    1.148
peak=   -4.118 closest distance to " C   TYR A  30 " =    0.857
peak=   -4.117 closest distance to " CB  THR A  31 " =    0.945
peak=   -4.089 closest distance to " N   ASP A 191 " =    1.326
peak=   -4.071 closest distance to " O   THR A  29 " =    0.804
peak=   -4.002 closest distance to " O   ASP A  27 " =    1.009
peak=   -3.986 closest distance to " N   LEU A  25 " =    1.078
peak=   -3.971 closest distance to " C   TRP A 274 " =    0.898
peak=   -3.954 closest distance to " O   HOH Z 118 " =    1.627
peak=   -3.948 closest distance to " OG1 THR A 251 " =    2.323
peak=   -3.940 closest distance to " CD  GLN A  55 " =    0.802
peak=   -3.925 closest distance to " CB  ALA A 291 " =    2.401
peak=   -3.911 closest distance to " O   HOH Z 114 " =    1.892
peak=   -3.909 closest distance to " NH1 ARG A  56 " =    1.075
peak=   -3.906 closest distance to " NE2 GLN A  58 " =    2.784
peak=   -3.891 closest distance to " O   HOH Z 100 " =    0.984
peak=   -3.884 closest distance to " CD  GLN A 223 " =    1.325
peak=   -3.882 closest distance to " O   HOH Z 141 " =    1.413
peak=   -3.882 closest distance to " O   HOH Z  92 " =    1.588
peak=   -3.855 closest distance to " N   ARG A 275 " =    0.762
peak=   -3.843 closest distance to " O   HOH Z 265 " =    1.715
peak=   -3.842 closest distance to " CE3 TRP A  70 " =    1.244
peak=   -3.829 closest distance to " O   HOH Z 422 " =    1.098
peak=   -3.828 closest distance to " CA  GLY A 241 " =    2.279
peak=   -3.819 closest distance to " CD  GLN A  77 " =    0.790
peak=   -3.816 closest distance to " O   HOH Z 390 " =    2.192
peak=   -3.769 closest distance to " CB  ASP A 286 " =    1.399
peak=   -3.755 closest distance to " OD2 ASP A  50 " =    2.075
peak=   -3.751 closest distance to " O   HOH Z 329 " =    2.048
peak=   -3.750 closest distance to " O   HOH Z 203 " =    0.873
peak=   -3.747 closest distance to " O   HOH Z 411 " =    4.619
peak=   -3.725 closest distance to " CD1 PHE A  59 " =    2.221
peak=   -3.719 closest distance to " O   HOH Z  41 " =    3.078
peak=   -3.700 closest distance to " CD2 LEU A 237 " =    2.609
peak=   -3.696 closest distance to " CZ  ARG A 259 " =    0.729
peak=   -3.687 closest distance to " OG  SER A  32 " =    1.494
peak=   -3.686 closest distance to " CG  ASP A  65 " =    1.154
peak=   -3.683 closest distance to " CD2 PHE A  16 " =    2.272
peak=   -3.672 closest distance to " CE3 TRP A  70 " =    1.056
peak=   -3.663 closest distance to " CG2 THR A 264 " =    2.148
peak=   -3.657 closest distance to " C   THR A 264 " =    1.282
peak=   -3.654 closest distance to " O   HOH Z 207 " =    1.443
peak=   -3.654 closest distance to " N   ARG A 275 " =    1.118
peak=   -3.647 closest distance to " O   HOH Z 407 " =    0.870
peak=   -3.640 closest distance to " O   HOH Z 103 " =    1.029
peak=   -3.635 closest distance to " O   HOH Z 344 " =    1.747
peak=   -3.635 closest distance to " N   THR A  52 " =    1.582
peak=   -3.634 closest distance to " O   GLN A  11 " =    0.880
peak=   -3.633 closest distance to " N   ALA A  34 " =    2.433
peak=   -3.627 closest distance to " N   ASP A 272 " =    1.136
peak=   -3.612 closest distance to " CG1 VAL A 112 " =    2.647
peak=   -3.610 closest distance to " N   GLY A 287 " =    1.479
peak=   -3.606 closest distance to " CG2 VAL A 230 " =    1.082
peak=   -3.604 closest distance to " O   HOH Z 119 " =    2.212
peak=   -3.592 closest distance to " N   ASP A  27 " =    1.137
peak=   -3.591 closest distance to " O   HOH Z 390 " =    0.957
peak=   -3.569 closest distance to " O   HOH Z 250 " =    1.182
peak=   -3.563 closest distance to " CA  GLY A 241 " =    3.774
peak=   -3.550 closest distance to " N   GLY A  35 " =    1.441
peak=   -3.550 closest distance to " N   ASN A 215 " =    1.976
peak=   -3.522 closest distance to " O   HOH Z  54 " =    1.479
peak=   -3.518 closest distance to " O   HOH Z 144 " =    1.219
peak=   -3.510 closest distance to " OG BSER A 164 " =    1.751
peak=   -3.505 closest distance to " N   SER A 212 " =    1.649
peak=   -3.480 closest distance to " C   LEU A 101 " =    1.135
peak=   -3.480 closest distance to " C   GLN A  58 " =    0.850
peak=   -3.479 closest distance to " ND2 ASN A 285 " =    2.341
peak=   -3.477 closest distance to " O   VAL A 189 " =    2.321
peak=   -3.475 closest distance to " CG1BVAL A  72 " =    2.750
peak=   -3.466 closest distance to " O   ASN A 148 " =    1.868
peak=   -3.466 closest distance to " CD  LYS A 289 " =    2.486
peak=   -3.462 closest distance to " O   HOH Z   7 " =    1.669
peak=   -3.458 closest distance to " O   HOH Z  35 " =    2.833
peak=   -3.458 closest distance to " CZ  ARG A 138 " =    1.241
peak=   -3.457 closest distance to " C   ASN A  74 " =    1.020
peak=   -3.454 closest distance to " C   GLY A  17 " =    1.361
peak=   -3.448 closest distance to " O   HOH Z 279 " =    1.103
peak=   -3.448 closest distance to " O   HOH Z  40 " =    3.149
peak=   -3.448 closest distance to " O   HOH Z 417 " =    1.490
peak=   -3.445 closest distance to " CD1 LEU A 282 " =    2.507
peak=   -3.443 closest distance to " CB  TRP A 177 " =    1.695
peak=   -3.436 closest distance to " O   HOH Z 368 " =    1.570
peak=   -3.425 closest distance to " O   ILE A 106 " =    1.987
peak=   -3.422 closest distance to " CG  PRO A 243 " =    1.757
peak=   -3.414 closest distance to " CG  GLN A 103 " =    2.022
peak=   -3.412 closest distance to " N   SER A 134 " =    1.148
peak=   -3.410 closest distance to " OG  SER A 288 " =    1.187
peak=   -3.408 closest distance to " CG1 VAL A 296 " =    1.062
peak=   -3.404 closest distance to " O   HOH Z 394 " =    2.072
peak=   -3.403 closest distance to " O   HOH Z 269 " =    1.218
peak=   -3.399 closest distance to " O   HOH Z  65 " =    1.339
peak=   -3.399 closest distance to " O   HOH Z 273 " =    0.932
peak=   -3.398 closest distance to " O   HOH Z 151 " =    0.905
peak=   -3.392 closest distance to " CD2 TYR A  30 " =    2.593
peak=   -3.386 closest distance to " CA  GLY A 229 " =    2.420
peak=   -3.385 closest distance to " CB  SER A  26 " =    1.293
peak=   -3.384 closest distance to " NE2 HIS A  86 " =    0.776
peak=   -3.377 closest distance to " CD  GLN A  58 " =    0.727
peak=   -3.376 closest distance to " CA  ALA A 184 " =    1.145
peak=   -3.369 closest distance to " C   ILE A 120 " =    1.292
peak=   -3.367 closest distance to " O   HOH Z 244 " =    1.531
peak=   -3.365 closest distance to " O   HOH Z 255 " =    0.825
peak=   -3.365 closest distance to " O   MET A  47 " =    2.119
peak=   -3.363 closest distance to " O   HOH Z 257 " =    1.841
peak=   -3.359 closest distance to " O   THR A 220 " =    2.014
peak=   -3.355 closest distance to " O   HOH Z   6 " =    1.523
peak=   -3.351 closest distance to " ND2 ASN A  39 " =    1.658
peak=   -3.350 closest distance to " O   HOH Z 179 " =    2.145
peak=   -3.349 closest distance to " CD1 TRP A 274 " =    1.144
peak=   -3.341 closest distance to " O   HOH Z 176 " =    1.470
peak=   -3.341 closest distance to " O   HOH Z 185 " =    2.468
peak=   -3.341 closest distance to " O   HOH Z 197 " =    1.665
peak=   -3.339 closest distance to " OE1 GLN A 144 " =    2.435
peak=   -3.334 closest distance to " CB  ASN A  69 " =    1.436
peak=   -3.327 closest distance to " O   HOH Z 222 " =    1.102
peak=   -3.326 closest distance to " O   TRP A 274 " =    2.603
peak=   -3.324 closest distance to " O   ASN A 301 " =    1.462
peak=   -3.321 closest distance to " CA  GLU A 277 " =    0.929
peak=   -3.316 closest distance to " O   HOH Z 124 " =    1.756
peak=   -3.309 closest distance to " OG  SER A   3 " =    1.026
peak=   -3.309 closest distance to " CA  ALA A   8 " =    1.313
peak=   -3.306 closest distance to " CG  LEU A  83 " =    1.592
peak=   -3.306 closest distance to " CG2 THR A 251 " =    1.595
peak=   -3.306 closest distance to " CB  THR A  29 " =    1.072
peak=   -3.302 closest distance to " CA  VAL A 197 " =    1.009
peak=   -3.300 closest distance to " O   HOH Z 216 " =    0.879
peak=   -3.299 closest distance to " O   HOH Z  19 " =    2.294
peak=   -3.294 closest distance to " O   HOH Z 414 " =    1.921
peak=   -3.291 closest distance to " O   GLN A  73 " =    1.114
peak=   -3.291 closest distance to " CB  ASP A 286 " =    2.499
peak=   -3.289 closest distance to " CG1AVAL A 121 " =    1.106
peak=   -3.286 closest distance to " OD1 ASN A 249 " =    1.127
peak=   -3.284 closest distance to " CG2 VAL A 202 " =    2.422
peak=   -3.279 closest distance to " CB  SER A  12 " =    1.077
peak=   -3.278 closest distance to " CG2 ILE A  33 " =    2.596
peak=   -3.273 closest distance to " OG  SER A 276 " =    1.003
peak=   -3.273 closest distance to " CA  LEU A  25 " =    1.024
peak=   -3.265 closest distance to " O   ASN A 285 " =    2.228
peak=   -3.263 closest distance to " CD1 ILE A 109 " =    2.390
peak=   -3.263 closest distance to " CB  VAL A 265 " =    0.929
peak=   -3.261 closest distance to " O   HOH Z 431 " =    1.481
peak=   -3.261 closest distance to " CZ2 TRP A  70 " =    1.180
peak=   -3.259 closest distance to " OG  SER A 245 " =    0.872
peak=   -3.254 closest distance to " C   LEU A 228 " =    1.991
peak=   -3.249 closest distance to " CD2 TYR A 293 " =    1.602
peak=   -3.246 closest distance to " O   HOH Z 216 " =    5.957
peak=   -3.245 closest distance to " OE1 GLN A 122 " =    2.298
peak=   -3.239 closest distance to " O   HOH Z 428 " =    1.315
peak=   -3.235 closest distance to " OG  SER A  26 " =    2.696
peak=   -3.230 closest distance to " CG BMET A  47 " =    1.178
peak=   -3.229 closest distance to " O   LYS A 289 " =    2.914
peak=   -3.227 closest distance to " O   PRO A 198 " =    1.200
peak=   -3.227 closest distance to " O   HOH Z 150 " =    0.742
peak=   -3.226 closest distance to " CG1 VAL A 232 " =    2.358
peak=   -3.215 closest distance to " CD  ARG A 269 " =    2.387
peak=   -3.207 closest distance to " NH2AARG A 145 " =    1.549
peak=   -3.204 closest distance to " O   HOH Z   7 " =    2.338
peak=   -3.202 closest distance to " OD2 ASP A 286 " =    2.891
peak=   -3.202 closest distance to " O   HOH Z  53 " =    0.916
peak=   -3.200 closest distance to " O   HOH Z 352 " =    1.741
peak=   -3.192 closest distance to " O   THR A  82 " =    1.706
peak=   -3.188 closest distance to " O   HOH Z  55 " =    1.963
peak=   -3.187 closest distance to " O   LEU A 300 " =    2.445
peak=   -3.187 closest distance to " O   ASN A 110 " =    1.812
peak=   -3.187 closest distance to " O   ALA A 227 " =    2.002
peak=   -3.184 closest distance to " OE1 GLU A 236 " =    1.019
peak=   -3.183 closest distance to " OD1 ASP A 171 " =    1.751
peak=   -3.182 closest distance to " CA  GLY A  23 " =    2.427
peak=   -3.175 closest distance to " CG2 THR A 264 " =    1.866
peak=   -3.174 closest distance to " CG  GLU A 277 " =    3.090
peak=   -3.171 closest distance to " OD1 ASP A 231 " =    0.962
peak=   -3.171 closest distance to " O   HOH Z 122 " =    1.067
peak=   -3.171 closest distance to " N   GLN A  58 " =    1.231
peak=   -3.167 closest distance to " O   HOH Z  88 " =    3.146
peak=   -3.160 closest distance to " CH2 TRP A 179 " =    1.039
peak=   -3.159 closest distance to " N   LEU A  96 " =    0.828
peak=   -3.159 closest distance to " O   HOH Z 251 " =    4.403
peak=   -3.144 closest distance to " O   HOH Z 205 " =    1.477
peak=   -3.140 closest distance to " O   HOH Z 340 " =    0.800
peak=   -3.132 closest distance to " O   HOH Z 295 " =    2.389
peak=   -3.118 closest distance to " CD  ARG A  14 " =    3.136
peak=   -3.116 closest distance to " ND2 ASN A 249 " =    1.153
peak=   -3.115 closest distance to " N   SER A 216 " =    1.944
peak=   -3.113 closest distance to " OG BSER A 164 " =    4.526
peak=   -3.110 closest distance to " O   HOH Z  14 " =    0.905
peak=   -3.107 closest distance to " O   HOH Z 110 " =    1.261
peak=   -3.094 closest distance to " C   GLY A  35 " =    1.102
peak=   -3.090 closest distance to " CE2 PHE A 283 " =    2.690
peak=   -3.088 closest distance to " ND2 ASN A 110 " =    1.050
peak=   -3.086 closest distance to " OG  SER A  26 " =    1.262
peak=   -3.085 closest distance to " N   TYR A  68 " =    2.205
peak=   -3.081 closest distance to " CE1 TYR A  30 " =    1.882
peak=   -3.078 closest distance to " O   HOH Z 135 " =    0.703
peak=   -3.071 closest distance to " CG  ASN A  60 " =    0.961
peak=   -3.067 closest distance to " CD2 TYR A 169 " =    2.193
peak=   -3.060 closest distance to " C   PHE A  16 " =    1.645
peak=   -3.050 closest distance to " N   VAL A 230 " =    0.752
peak=   -3.043 closest distance to " O   HOH Z  90 " =    3.073
peak=   -3.041 closest distance to " CE3 TRP A 274 " =    2.919
peak=   -3.040 closest distance to " O   HOH Z 116 " =    4.802

================= 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    :  0.5345 0.5228   6.317332e+00   6.307230e+00
   1_bss:  0.5302 0.5193   5.524184e+00   5.521965e+00
   1_xyz:  0.4860 0.4938   6.279316e+00   6.283161e+00
   1_adp:  0.4416 0.4899   5.883306e+00   5.923962e+00
   1_occ:  0.4406 0.4924   5.883666e+00   5.924782e+00
   2_bss:  0.4394 0.4878   5.884993e+00   5.924424e+00
   2_xyz:  0.3941 0.4629   5.818356e+00   5.897348e+00
   2_adp:  0.3903 0.4540   6.169538e+00   6.242612e+00
   2_occ:  0.3903 0.4541   6.169499e+00   6.242634e+00
   3_bss:  0.3904 0.4518   6.169800e+00   6.241469e+00
   3_xyz:  0.3419 0.4090   6.078223e+00   6.179461e+00
   3_adp:  0.3282 0.4005   6.055326e+00   6.168696e+00
   3_occ:  0.3280 0.4009   6.055005e+00   6.168882e+00
   4_bss:  0.3278 0.3996   6.054024e+00   6.168626e+00
   4_xyz:  0.2723 0.3427   5.911141e+00   6.065341e+00
   4_adp:  0.2409 0.3101   5.817730e+00   5.995590e+00
   4_occ:  0.2407 0.3107   5.817813e+00   5.995705e+00
   5_bss:  0.2405 0.3102   5.817139e+00   5.995177e+00
   5_xyz:  0.2056 0.2629   5.668819e+00   5.861014e+00
   5_adp:  0.1938 0.2469   5.617985e+00   5.811134e+00
   5_occ:  0.1935 0.2471   5.617254e+00   5.810506e+00
   5_bss:  0.1940 0.2472   5.617767e+00   5.810343e+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:  0.267  20.000   6.175   9.421   9.381   0.000   0.000   0.000
   1_xyz:  0.267  20.000   6.175   9.421   9.381   0.000   0.000   0.000
   1_adp:  0.267  20.000   6.175   9.421   9.381   0.000   0.000   0.000
   1_occ:  0.267  20.000   6.175   9.421   9.381   0.000   0.000   0.000
   2_bss:  0.325  80.000   3.428   5.305   5.980   0.000   0.000   0.000
   2_xyz:  0.325  80.000   3.428   5.305   5.980   0.000   0.000   0.000
   2_adp:  0.325  80.000   3.428   5.305   5.980   0.000   0.000   0.000
   2_occ:  0.325  80.000   3.428   5.305   5.980   0.000   0.000   0.000
   3_bss:  0.334  92.627   1.889   3.913   4.061   0.000   0.000   0.000
   3_xyz:  0.334  92.627   1.889   3.913   4.061   0.000   0.000   0.000
   3_adp:  0.334  92.627   1.889   3.913   4.061   0.000   0.000   0.000
   3_occ:  0.334  92.627   1.889   3.913   4.061   0.000   0.000   0.000
   4_bss:  0.328  80.000   1.489   3.296   3.084   0.000   0.000   0.000
   4_xyz:  0.328  80.000   1.489   3.296   3.084   0.000   0.000   0.000
   4_adp:  0.328  80.000   1.489   3.296   3.084   0.000   0.000   0.000
   4_occ:  0.328  80.000   1.489   3.296   3.084   0.000   0.000   0.000
   5_bss:  0.341  90.766   1.060   2.047   2.328   0.000   0.000   0.000
   5_xyz:  0.341  90.766   1.060   2.047   2.328   0.000   0.000   0.000
   5_adp:  0.341  90.766   1.060   2.047   2.328   0.000   0.000   0.000
   5_occ:  0.341  90.766   1.060   2.047   2.328   0.000   0.000   0.000
   5_bss:  0.337  86.255  -0.786   0.061   0.726   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  69.969 0.2634  0.3000    87388.894
   1_bss:  69.906 0.2636  0.3749    87137.247
   1_xyz:  62.347 0.3621  0.5122    75393.801
   1_adp:  62.614 0.3580  0.5836    74717.062
   1_occ:  63.049 0.3523  0.5726    75430.895
   2_bss:  62.636 0.3578  0.5278    75065.398
   2_xyz:  58.683 0.4074  0.6022    65625.246
   2_adp:  53.898 0.4706  0.6924    61330.282
   2_occ:  53.907 0.4705  0.6920    61353.986
   3_bss:  53.778 0.4720  0.6583    60963.629
   3_xyz:  46.371 0.5650  0.7849    48396.230
   3_adp:  45.038 0.5814  0.7922    46364.305
   3_occ:  45.139 0.5801  0.7899    46353.078
   4_bss:  45.082 0.5807  0.7740    46148.606
   4_xyz:  36.778 0.6805  0.8867    32906.644
   4_adp:  32.580 0.7293  0.9005    26515.359
   4_occ:  32.598 0.7291  0.8996    26527.374
   5_bss:  32.541 0.7296  0.8759    26436.892
   5_xyz:  26.868 0.7919  0.9240    18514.055
   5_adp:  24.622 0.8163  0.9212    16325.695
   5_occ:  24.602 0.8165  0.9213    16304.030
   5_bss:  24.587 0.8166  0.9169    16263.291
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.5087e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.5087e+01
   1_xyz:   1.829  0.015  0.114 18.544  0.008  4.125   1.6605e-01
   1_adp:   1.829  0.015  0.114 18.544  0.008  4.125   1.6605e-01
   1_occ:   1.829  0.015  0.114 18.544  0.008  4.125   1.6605e-01
   2_bss:   1.829  0.015  0.114 18.544  0.008  4.125   1.6605e-01
   2_xyz:   1.401  0.010  0.094 17.608  0.005  4.109   1.1888e-01
   2_adp:   1.401  0.010  0.094 17.608  0.005  4.109   1.1888e-01
   2_occ:   1.401  0.010  0.094 17.608  0.005  4.109   1.1888e-01
   3_bss:   1.401  0.010  0.094 17.608  0.005  4.109   1.1888e-01
   3_xyz:   1.382  0.010  0.102 17.022  0.004  4.111   1.1074e-01
   3_adp:   1.382  0.010  0.102 17.022  0.004  4.111   1.1074e-01
   3_occ:   1.382  0.010  0.102 17.022  0.004  4.111   1.1074e-01
   4_bss:   1.382  0.010  0.102 17.022  0.004  4.111   1.1074e-01
   4_xyz:   1.374  0.012  0.098 16.346  0.005  4.111   1.1599e-01
   4_adp:   1.374  0.012  0.098 16.346  0.005  4.111   1.1599e-01
   4_occ:   1.374  0.012  0.098 16.346  0.005  4.111   1.1599e-01
   5_bss:   1.374  0.012  0.098 16.346  0.005  4.111   1.1599e-01
   5_xyz:   1.111  0.009  0.080 15.588  0.004  4.133   7.6629e-02
   5_adp:   1.111  0.009  0.080 15.588  0.004  4.133   7.6629e-02
   5_occ:   1.111  0.009  0.080 15.588  0.004  4.133   7.6629e-02
   5_bss:   1.111  0.009  0.080 15.588  0.004  4.133   7.6629e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.1421e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.1421e+00
   1_xyz:  14.963  0.123  0.466 87.448  0.057  2.119   1.1234e-01
   1_adp:  14.963  0.123  0.466 87.448  0.057  2.119   1.1234e-01
   1_occ:  14.963  0.123  0.466 87.448  0.057  2.119   1.1234e-01
   2_bss:  14.963  0.123  0.466 87.448  0.057  2.119   1.1234e-01
   2_xyz:   8.068  0.073  0.285 87.570  0.043  1.921   6.7045e-02
   2_adp:   8.068  0.073  0.285 87.570  0.043  1.921   6.7045e-02
   2_occ:   8.068  0.073  0.285 87.570  0.043  1.921   6.7045e-02
   3_bss:   8.068  0.073  0.285 87.570  0.043  1.921   6.7045e-02
   3_xyz:  11.420  0.096  0.421 82.587  0.017  2.041   1.1197e-01
   3_adp:  11.420  0.096  0.421 82.587  0.017  2.041   1.1197e-01
   3_occ:  11.420  0.096  0.421 82.587  0.017  2.041   1.1197e-01
   4_bss:  11.420  0.096  0.421 82.587  0.017  2.041   1.1197e-01
   4_xyz:   8.016  0.073  0.283 79.021  0.039  2.018   9.2779e-02
   4_adp:   8.016  0.073  0.283 79.021  0.039  2.018   9.2779e-02
   4_occ:   8.016  0.073  0.283 79.021  0.039  2.018   9.2779e-02
   5_bss:   8.016  0.073  0.283 79.021  0.039  2.018   9.2779e-02
   5_xyz:   7.782  0.056  0.276 78.330  0.041  2.244   6.6049e-02
   5_adp:   7.782  0.056  0.276 78.330  0.041  2.244   6.6049e-02
   5_occ:   7.782  0.056  0.276 78.330  0.041  2.244   6.6049e-02
   5_bss:   7.782  0.056  0.276 78.330  0.041  2.244   6.6049e-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: 149.37   0.00  22.07 103.79   0.00  20.46 149.37   0.00  30.86
   1_occ: 149.37   0.00  22.07 103.79   0.00  20.46 149.37   0.00  30.86
   2_bss: 149.37   0.00  22.07 103.79   0.00  20.46 149.37   0.00  30.86
   2_xyz: 149.37   0.00  22.07 103.79   0.00  20.46 149.37   0.00  30.86
   2_adp: 151.64   0.00  18.14  91.03   0.00  16.52 151.64   0.00  26.93
   2_occ: 151.64   0.00  18.14  91.03   0.00  16.52 151.64   0.00  26.93
   3_bss: 151.64   0.00  18.14  91.03   0.00  16.52 151.64   0.00  26.93
   3_xyz: 151.64   0.00  18.14  91.03   0.00  16.52 151.64   0.00  26.93
   3_adp: 174.35   0.00  17.69 174.35   0.00  15.57 151.05   0.00  29.20
   3_occ: 174.35   0.00  17.69 174.35   0.00  15.57 151.05   0.00  29.20
   4_bss: 174.35   0.00  17.69 174.35   0.00  15.57 151.05   0.00  29.20
   4_xyz: 174.35   0.00  17.69 174.35   0.00  15.57 151.05   0.00  29.20
   4_adp: 147.25   0.00  17.13 113.16   0.00  12.93 147.25   0.00  39.99
   4_occ: 147.25   0.00  17.13 113.16   0.00  12.93 147.25   0.00  39.99
   5_bss: 147.25   0.00  17.13 113.16   0.00  12.93 147.25   0.00  39.99
   5_xyz: 147.25   0.00  17.13 113.16   0.00  12.93 147.25   0.00  39.99
   5_adp: 132.78   0.00  15.92 101.76   0.00  11.18 132.78   0.72  41.69
   5_occ: 132.78   0.00  15.92 101.76   0.00  11.18 132.78   0.72  41.69
   5_bss: 134.47   1.69  17.61 103.45   1.69  12.88 134.47   2.41  43.38
------------------------------------------------------------------------
 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:    1.200    0.026    0.413
   1_adp:    1.200    0.026    0.413
   1_occ:    1.200    0.026    0.413
   2_bss:    1.200    0.026    0.413
   2_xyz:    1.703    0.046    0.584
   2_adp:    1.703    0.046    0.584
   2_occ:    1.703    0.046    0.584
   3_bss:    1.703    0.046    0.584
   3_xyz:    1.830    0.040    0.733
   3_adp:    1.830    0.040    0.733
   3_occ:    1.830    0.040    0.733
   4_bss:    1.830    0.040    0.733
   4_xyz:    2.267    0.075    0.899
   4_adp:    2.267    0.075    0.899
   4_occ:    2.267    0.075    0.899
   5_bss:    2.267    0.075    0.899
   5_xyz:    2.204    0.083    0.979
   5_adp:    2.204    0.083    0.979
   5_occ:    2.204    0.083    0.979
   5_bss:    2.204    0.083    0.979
------------------------------------------------------------------------

CPU time actual refinement: 347.56


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1209/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_1209/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1209/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1209/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1209/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.40 
  Macro-tasks:
    bulk solvent and scale       = 62.73  
    individual site refinement   = 140.40 
    weights calculation          = 31.38  
    collect and process          = 6.10   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 240.72 
  Micro-tasks:
    mask                            = 2.86   
    f_calc                          = 100.71 
    alpha_beta                      = 8.25   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 111.28 
    fmodel                         = 9.78   
    r_factors                      = 0.37   
    phase_errors                   = 9.21   
    foms                           = 0.28   
    TOTAL for micro-tasks          = 243.88 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.897 micro seconds
Total CPU time: 6.01 minutes
from_scatterers_fft:    597 calls, 100.43 s
gradients_fft:          541 calls,  98.66 s

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

# Date 2008-01-16 Time 03:27:44 PST -0800 (1200482864.57 s)
Start R-work = 0.5345, R-free = 0.5228 (no bulk solvent and anisotropic scale)
Final R-work = 0.2074, R-free = 0.2623 (no bulk solvent and anisotropic scale)

Start R-work = 0.5302, R-free = 0.5193
Final R-work = 0.1940, R-free = 0.2472