# Date 2008-01-16 Time 02:57:15 PST -0800 (1200481035.33 s)
#phil __OFF__

Command line arguments: "../1040.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2012
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1040

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.1647, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.74, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.01038
Completeness in resolution range: 0.976618
Completeness with d_max=infinity: 0.973608

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1778
                             d_min =   2.0104

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.01038
Completeness in resolution range: 0.976618
Completeness with d_max=infinity: 0.973608

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1782 -  4.3015 [2099/2124]  1889   210  10.0%
  bin  2:  4.3015 -  3.4271 [2031/2051]  1828   203  10.0%
  bin  3:  3.4271 -  2.9977 [1997/2016]  1795   202  10.1%
  bin  4:  2.9977 -  2.7253 [1972/2002]  1778   194   9.8%
  bin  5:  2.7253 -  2.5310 [1977/1996]  1780   197  10.0%
  bin  6:  2.5310 -  2.3823 [1958/1983]  1763   195  10.0%
  bin  7:  2.3823 -  2.2634 [1945/1973]  1745   200  10.3%
  bin  8:  2.2634 -  2.1652 [1942/1978]  1749   193   9.9%
  bin  9:  2.1652 -  2.0821 [1930/1972]  1742   188   9.7%
  bin 10:  2.0821 -  2.0104 [1738/1963]  1561   177  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1040/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: 0.11 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:
        1.79 -     2.41: 7
        2.41 -     3.03: 2117
        3.03 -     3.66: 4556
        3.66 -     4.28: 8967
        4.28 -     4.90: 12285
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.791 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.404 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27927 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_1040/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1040/model_refine_001.geo

CPU time processing inputs: 8.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.16465 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4346   r_free= 0.4199   ksol= 0.00   Bsol= 0.00   scale= 0.813    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.230359                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7975 0.99   1372  152 0.3641 0.3411      6.5334      6.4169|
|  2:  4.7975 -  3.8280 0.99   1315  146 0.3272 0.3421      6.6562       6.702|
|  3:  3.8280 -  3.3501 0.99   1287  144 0.3746 0.3543      6.5658      6.5638|
|  4:  3.3501 -  3.0465 0.99   1279  144 0.4150 0.3561      6.4625      6.3597|
|  5:  3.0465 -  2.8296 0.99   1279  141 0.4472 0.4316      6.3141      6.3529|
|  6:  2.8296 -  2.6637 0.99   1269  139 0.4607 0.4903      6.2534      6.1877|
|  7:  2.6637 -  2.5310 0.99   1269  140 0.4864 0.4792      6.2025      6.2197|
|  8:  2.5310 -  2.4212 0.98   1256  143 0.4899 0.4421      6.1693       6.113|
|  9:  2.4212 -  2.3284 0.98   1242  134 0.4769 0.4932      6.0891      6.1192|
| 10:  2.3284 -  2.2483 1.00   1249  144 0.4873 0.4800      6.0948      6.0954|
| 11:  2.2483 -  2.1782 0.97   1261  136 0.4869 0.4398      6.0244      6.0018|
| 12:  2.1782 -  2.1161 0.98   1230  138 0.4965 0.4874      5.9811      5.9965|
| 13:  2.1161 -  2.0605 0.99   1243  142 0.5079 0.5010      5.9005      5.8944|
| 14:  2.0605 -  2.0104 0.84   1079  116 0.5015 0.4449      5.8525      5.6824|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7975  1372   152  0.75  29.93   0.80     0.77      54699.34|
|  2:  4.7975 -  3.8280  1315   146  0.78  27.74   0.91     0.81      71839.03|
|  3:  3.8280 -  3.3501  1287   144  0.72  34.07   0.86     0.79      76411.25|
|  4:  3.3501 -  3.0465  1279   144  0.64  40.24   0.83     0.71      70306.20|
|  5:  3.0465 -  2.8296  1279   141  0.55  47.78   0.76     0.63      62709.56|
|  6:  2.8296 -  2.6637  1269   139  0.52  50.50   0.76     0.57      57601.59|
|  7:  2.6637 -  2.5310  1269   140  0.48  53.43   0.73     0.54      54126.34|
|  8:  2.5310 -  2.4212  1256   143  0.46  54.98   0.76     0.53      50172.55|
|  9:  2.4212 -  2.3284  1242   134  0.48  53.84   0.74     0.53      44687.04|
| 10:  2.3284 -  2.2483  1249   144  0.49  53.04   0.77     0.55      40128.94|
| 11:  2.2483 -  2.1782  1261   136  0.47  54.38   0.76     0.54      37235.95|
| 12:  2.1782 -  2.1161  1230   138  0.46  55.58   0.77     0.54      35631.75|
| 13:  2.1161 -  2.0605  1243   142  0.47  54.71   0.74     0.54      29969.07|
| 14:  2.0605 -  2.0104  1079   116  0.56  47.47   0.72     0.59      20764.63|
|alpha:            min =        0.53 max =            0.81 mean =         0.62|
|beta:             min =    20764.63 max =        76411.25 mean =     50983.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.99 mean =        46.75|
|phase err.(test): min =        0.00 max =           89.99 mean =        46.75|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.160750              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.361   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.662109              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.238   (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:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      674 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1487 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2586 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3880 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4968 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6532 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7639 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.279 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.609 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.219)------------------------------------------|
|    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 = 12.219)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4418   r_free= 0.4241   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.234116                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4275   r_free= 0.4051   ksol= 0.30   Bsol= 20.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.54,8.02,8.30,0.00,0.00,0.00); trace/3= 8.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.224713                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.547733              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.967   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.621929              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.515   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4275      final r-factor (work) = 0.3164          |
| start r-factor (free) = 0.4051      final r-factor (free) = 0.3418          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.8390 = 7.55 * 0.50 * 6.2428 + 1.00 * 54.2794                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0106 = 7.55 * 0.50 * 6.0653 + 1.00 * 0.1209                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3164      final r-factor (work) = 0.2572          |
| start r-factor (free) = 0.3418      final r-factor (free) = 0.2920          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7870 = 0.62 * 1.00 * 6.0653 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6819 = 0.62 * 1.00 * 5.9017 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.219)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.89   10.08    None  None   None       |
|    all(noH): 2823   0      0.00    62.89   10.08    None  None   None       |
|    Sol.    : 438    0      0.00    62.89   25.99    None  None   None       |
|    Mac.    : 2385   0      0.00    52.60   7.16     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.289: 1359   |   5:    31.445 -  37.734:   86        |
|      1:     6.289 -  12.578:  756   |   6:    37.734 -  44.023:   55        |
|      2:    12.578 -  18.867:  255   |   7:    44.023 -  50.312:   24        |
|      3:    18.867 -  25.156:  157   |   8:    50.312 -  56.601:   11        |
|      4:    25.156 -  31.445:  119   |   9:    56.601 -  62.890:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2572 r_free = 0.2920             target_work(ml) = 5.839         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2565 r_free = 0.2921             target_work(ml) = 5.838         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2565   r_free= 0.2921   ksol= 0.30   Bsol= 20.00   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.54,8.02,8.30,0.00,0.00,0.00); trace/3= 8.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.837676                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2528   r_free= 0.2886   ksol= 0.33   Bsol= 56.41   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.27,4.80,5.34,0.00,0.00,0.00); trace/3= 5.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.837446                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.220992              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.025   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.374912              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.905  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2528      final r-factor (work) = 0.1759          |
| start r-factor (free) = 0.2886      final r-factor (free) = 0.2163          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6325 = 3.22 * 0.50 * 5.9060 + 1.00 * 0.1209                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2053 = 3.22 * 0.50 * 5.6757 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1759      final r-factor (work) = 0.1677          |
| start r-factor (free) = 0.2163      final r-factor (free) = 0.2102          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1577 = 0.37 * 1.00 * 5.6757 + 1.00 * 0.0298                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1870 = 0.37 * 1.00 * 5.4866 + 1.00 * 0.1300                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.219)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.69   10.31    None  None   None       |
|    all(noH): 2823   0      0.00    78.69   10.31    None  None   None       |
|    Sol.    : 438    0      0.43    62.97   27.06    None  None   None       |
|    Mac.    : 2385   0      0.00    78.69   7.23     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.869: 1642   |   5:    39.344 -  47.213:   67        |
|      1:     7.869 -  15.738:  633   |   6:    47.213 -  55.082:   17        |
|      2:    15.738 -  23.606:  188   |   7:    55.082 -  62.950:    0        |
|      3:    23.606 -  31.475:  174   |   8:    62.950 -  70.819:    1        |
|      4:    31.475 -  39.344:  100   |   9:    70.819 -  78.688:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1677 r_free = 0.2102             target_work(ml) = 5.473         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1675 r_free = 0.2103             target_work(ml) = 5.472         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1675   r_free= 0.2103   ksol= 0.33   Bsol= 56.41   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.27,4.80,5.34,0.00,0.00,0.00); trace/3= 5.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.472324                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1667   r_free= 0.2094   ksol= 0.34   Bsol= 56.41   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,3.72,4.54,0.00,0.00,0.00); trace/3= 3.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.472916                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.955996              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.896  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.784317              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.482   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1667      final r-factor (work) = 0.1434          |
| start r-factor (free) = 0.2094      final r-factor (free) = 0.1879          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4356 = 1.96 * 0.50 * 5.4920 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3408 = 1.96 * 0.50 * 5.3997 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1434      final r-factor (work) = 0.1301          |
| start r-factor (free) = 0.1879      final r-factor (free) = 0.1761          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.0537 = 2.78 * 1.00 * 5.3997 + 1.00 * 0.0192                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.7711 = 2.78 * 1.00 * 5.2995 + 1.00 * 0.0158                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.219)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.64   12.04    None  None   None       |
|    all(noH): 2823   0      0.00    81.64   12.04    None  None   None       |
|    Sol.    : 438    0      0.00    81.64   36.13    None  None   None       |
|    Mac.    : 2385   0      0.00    78.37   7.61     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.164: 1678   |   5:    40.821 -  48.985:   81        |
|      1:     8.164 -  16.329:  561   |   6:    48.985 -  57.150:   82        |
|      2:    16.329 -  24.493:  166   |   7:    57.150 -  65.314:   38        |
|      3:    24.493 -  32.657:  108   |   8:    65.314 -  73.478:   16        |
|      4:    32.657 -  40.821:   85   |   9:    73.478 -  81.642:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1301 r_free = 0.1761             target_work(ml) = 5.271         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1301 r_free = 0.1761             target_work(ml) = 5.271         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1761   ksol= 0.34   Bsol= 56.41   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,3.72,4.54,0.00,0.00,0.00); trace/3= 3.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.270814                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1300   r_free= 0.1761   ksol= 0.33   Bsol= 61.07   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,3.41,4.35,0.00,0.00,0.00); trace/3= 3.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.270093                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.377358              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.817  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.246080              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.863  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1300      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1761      final r-factor (free) = 0.1664          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0079 = 3.38 * 0.50 * 5.2988 + 1.00 * 0.0600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8993 = 3.38 * 0.50 * 5.2232 + 1.00 * 0.0790                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1664      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3014 = 0.25 * 1.00 * 5.2232 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3039 = 0.25 * 1.00 * 5.1907 + 1.00 * 0.0265                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.219)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.47   11.40    None  None   None       |
|    all(noH): 2823   0      0.00    76.47   11.40    None  None   None       |
|    Sol.    : 438    0      0.99    76.47   33.46    None  None   None       |
|    Mac.    : 2385   0      0.00    76.21   7.35     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.647: 1662   |   5:    38.233 -  45.880:   80        |
|      1:     7.647 -  15.293:  579   |   6:    45.880 -  53.527:   74        |
|      2:    15.293 -  22.940:  158   |   7:    53.527 -  61.173:   29        |
|      3:    22.940 -  30.587:  103   |   8:    61.173 -  68.820:   16        |
|      4:    30.587 -  38.233:  116   |   9:    68.820 -  76.467:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1621             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1621             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1621   ksol= 0.33   Bsol= 61.07   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,3.41,4.35,0.00,0.00,0.00); trace/3= 3.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176730                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1618   ksol= 0.33   Bsol= 61.07   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,3.41,4.35,0.00,0.00,0.00); trace/3= 3.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176298                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.668723              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.520  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.677819              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.610   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1166      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0053 = 2.67 * 0.50 * 5.1907 + 1.00 * 0.0790                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9733 = 2.67 * 0.50 * 5.1686 + 1.00 * 0.0765                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1601      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5162 = 0.68 * 1.00 * 5.1686 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5267 = 0.68 * 1.00 * 5.1564 + 1.00 * 0.0316                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.219)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.51   11.53    None  None   None       |
|    all(noH): 2823   0      0.00    78.51   11.53    None  None   None       |
|    Sol.    : 438    0      0.78    77.21   34.16    None  None   None       |
|    Mac.    : 2385   0      0.00    78.51   7.37     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.851: 1683   |   5:    39.255 -  47.106:   78        |
|      1:     7.851 -  15.702:  551   |   6:    47.106 -  54.957:   77        |
|      2:    15.702 -  23.553:  164   |   7:    54.957 -  62.808:   27        |
|      3:    23.553 -  31.404:  109   |   8:    62.808 -  70.659:   15        |
|      4:    31.404 -  39.255:  112   |   9:    70.659 -  78.510:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1131 r_free = 0.1602             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1603             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1603   ksol= 0.33   Bsol= 61.07   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,3.41,4.35,0.00,0.00,0.00); trace/3= 3.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159157                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7975 0.99   1372  152 0.1018 0.1334      5.4014      5.5263|
|  2:  4.7975 -  3.8280 0.99   1315  146 0.0871 0.1122      5.4507      5.6405|
|  3:  3.8280 -  3.3501 0.99   1287  144 0.1060 0.1490      5.4865      5.8427|
|  4:  3.3501 -  3.0465 0.99   1279  144 0.1209 0.1560      5.4634      5.6244|
|  5:  3.0465 -  2.8296 0.99   1279  141 0.1335 0.1769      5.3431      5.5594|
|  6:  2.8296 -  2.6637 0.99   1269  139 0.1205 0.1884       5.229       5.458|
|  7:  2.6637 -  2.5310 0.99   1269  140 0.1304 0.1682      5.1931      5.4188|
|  8:  2.5310 -  2.4212 0.98   1256  143 0.1193 0.1718      5.0985      5.3636|
|  9:  2.4212 -  2.3284 0.98   1242  134 0.1179 0.1696      5.0626      5.2786|
| 10:  2.3284 -  2.2483 1.00   1249  144 0.1145 0.1862      4.9938      5.3139|
| 11:  2.2483 -  2.1782 0.97   1261  136 0.1176 0.1745      4.9711      5.2539|
| 12:  2.1782 -  2.1161 0.98   1230  138 0.1122 0.1843      4.8884      5.2633|
| 13:  2.1161 -  2.0605 0.99   1243  142 0.1144 0.1717      4.8178      5.0823|
| 14:  2.0605 -  2.0104 0.84   1079  116 0.1074 0.1803      4.6996      4.9514|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7975  1372   152  0.94   9.22   0.97     0.95       7308.45|
|  2:  4.7975 -  3.8280  1315   146  0.95   8.10   1.00     0.99       9159.16|
|  3:  3.8280 -  3.3501  1287   144  0.93  11.31   1.01     1.01      10620.08|
|  4:  3.3501 -  3.0465  1279   144  0.92  13.44   1.00     0.99      10382.12|
|  5:  3.0465 -  2.8296  1279   141  0.90  16.09   0.99     0.96       8563.43|
|  6:  2.8296 -  2.6637  1269   139  0.90  15.77   0.98     0.96       7369.14|
|  7:  2.6637 -  2.5310  1269   140  0.90  16.17   0.98     0.96       6529.97|
|  8:  2.5310 -  2.4212  1256   143  0.91  15.45   0.99     0.96       5576.54|
|  9:  2.4212 -  2.3284  1242   134  0.91  15.72   1.00     0.96       5351.49|
| 10:  2.3284 -  2.2483  1249   144  0.91  15.43   0.99     0.95       4560.21|
| 11:  2.2483 -  2.1782  1261   136  0.89  17.01   0.99     0.95       4651.89|
| 12:  2.1782 -  2.1161  1230   138  0.91  15.08   1.00     0.98       3990.44|
| 13:  2.1161 -  2.0605  1243   142  0.90  16.14   1.00     0.98       3556.75|
| 14:  2.0605 -  2.0104  1079   116  0.91  15.39   0.97     0.93       2761.97|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2761.97 max =        10620.08 mean =      6530.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.86 mean =        14.24|
|phase err.(test): min =        0.00 max =           89.46 mean =        13.69|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1603   ksol= 0.32   Bsol= 57.30   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.36,-0.29,0.65,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158962                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1603   ksol= 0.32   Bsol= 57.30   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.36,-0.29,0.65,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158962                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7975 0.99   1372  152 0.1012 0.1329      5.3951       5.521|
|  2:  4.7975 -  3.8280 0.99   1315  146 0.0867 0.1115       5.446      5.6346|
|  3:  3.8280 -  3.3501 0.99   1287  144 0.1058 0.1489      5.4845      5.8417|
|  4:  3.3501 -  3.0465 0.99   1279  144 0.1211 0.1560      5.4645      5.6256|
|  5:  3.0465 -  2.8296 0.99   1279  141 0.1338 0.1773      5.3453      5.5618|
|  6:  2.8296 -  2.6637 0.99   1269  139 0.1209 0.1886      5.2313      5.4601|
|  7:  2.6637 -  2.5310 0.99   1269  140 0.1305 0.1683      5.1947      5.4203|
|  8:  2.5310 -  2.4212 0.98   1256  143 0.1195 0.1720      5.0996      5.3648|
|  9:  2.4212 -  2.3284 0.98   1242  134 0.1179 0.1695      5.0629      5.2782|
| 10:  2.3284 -  2.2483 1.00   1249  144 0.1146 0.1865      4.9943      5.3147|
| 11:  2.2483 -  2.1782 0.97   1261  136 0.1177 0.1745      4.9715      5.2541|
| 12:  2.1782 -  2.1161 0.98   1230  138 0.1122 0.1845      4.8887      5.2639|
| 13:  2.1161 -  2.0605 0.99   1243  142 0.1144 0.1719      4.8183      5.0829|
| 14:  2.0605 -  2.0104 0.84   1079  116 0.1075 0.1804      4.7001      4.9521|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7975  1372   152  0.94   9.13   0.97     0.95       7201.07|
|  2:  4.7975 -  3.8280  1315   146  0.95   8.04   1.00     0.99       9066.02|
|  3:  3.8280 -  3.3501  1287   144  0.93  11.27   1.02     1.01      10569.16|
|  4:  3.3501 -  3.0465  1279   144  0.92  13.46   1.00     0.99      10402.01|
|  5:  3.0465 -  2.8296  1279   141  0.90  16.11   0.99     0.96       8599.41|
|  6:  2.8296 -  2.6637  1269   139  0.90  15.81   0.98     0.96       7403.04|
|  7:  2.6637 -  2.5310  1269   140  0.90  16.19   0.98     0.96       6553.13|
|  8:  2.5310 -  2.4212  1256   143  0.91  15.47   0.99     0.96       5588.04|
|  9:  2.4212 -  2.3284  1242   134  0.91  15.73   1.00     0.96       5356.57|
| 10:  2.3284 -  2.2483  1249   144  0.90  15.44   0.99     0.95       4563.76|
| 11:  2.2483 -  2.1782  1261   136  0.89  17.02   0.99     0.95       4656.83|
| 12:  2.1782 -  2.1161  1230   138  0.91  15.10   1.00     0.98       3995.34|
| 13:  2.1161 -  2.0605  1243   142  0.90  16.16   1.00     0.98       3562.30|
| 14:  2.0605 -  2.0104  1079   116  0.91  15.40   0.97     0.93       2765.80|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2765.80 max =        10569.16 mean =      6522.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.24|
|phase err.(test): min =        0.00 max =           89.40 mean =        13.69|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.219)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.70    82.21   15.22    None  None   None       |
|    all(noH): 2823   0      3.70    82.21   15.22    None  None   None       |
|    Sol.    : 438    0      4.48    80.91   37.86    None  None   None       |
|    Mac.    : 2385   0      3.70    82.21   11.07    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:     3.697 -  11.548: 1683   |   5:    42.952 -  50.803:   78        |
|      1:    11.548 -  19.399:  551   |   6:    50.803 -  58.654:   77        |
|      2:    19.399 -  27.250:  164   |   7:    58.654 -  66.505:   27        |
|      3:    27.250 -  35.101:  109   |   8:    66.505 -  74.356:   15        |
|      4:    35.101 -  42.952:  112   |   9:    74.356 -  82.207:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.304 - 4.794
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 320
   mapped sites are within: 0.708 - 4.794

peak=    9.526 closest distance to " CG2 VAL A 230 " =    1.289
peak=    6.468 closest distance to " CG2 VAL A 296 " =    1.085
peak=    6.233 closest distance to " CG  LEU A   5 " =    1.208
peak=    6.111 closest distance to " O   HOH Z 111 " =    2.253
peak=    5.747 closest distance to " CG  LEU A 228 " =    1.154
peak=    5.612 closest distance to " CB  GLN A 223 " =    1.436
peak=    5.390 closest distance to " CB  VAL A 230 " =    1.200
peak=    5.212 closest distance to " CD2 LEU A   5 " =    1.133
peak=    4.943 closest distance to " CB  VAL A 296 " =    1.081
peak=    4.901 closest distance to " CB  GLN A 183 " =    1.264
peak=    4.886 closest distance to " CB  SER A  63 " =    1.332
peak=    4.789 closest distance to " NE2 GLN A  11 " =    1.098
peak=    4.663 closest distance to " O   HOH Z 232 " =    2.349
peak=    4.522 closest distance to " O   HOH Z 369 " =    2.126
peak=    4.519 closest distance to " CG  PRO A 213 " =    1.187
peak=    4.478 closest distance to " CZ  PHE A 218 " =    1.059
peak=    4.462 closest distance to " O   HOH Z 368 " =    2.270
peak=    4.383 closest distance to " O   HOH Z 126 " =    1.883
peak=    4.350 closest distance to " C   PRO A 198 " =    1.539
peak=    4.349 closest distance to " O   HOH Z 298 " =    1.864
peak=    4.340 closest distance to " O   HOH Z 265 " =    2.341
peak=    4.314 closest distance to " O   HOH Z 303 " =    2.082
peak=    4.304 closest distance to " OD1 ASN A  69 " =    2.626
peak=    4.294 closest distance to " CB  TRP A 266 " =    0.951
peak=    4.244 closest distance to " CG  PRO A 243 " =    1.130
peak=    4.214 closest distance to " O   HOH Z 427 " =    3.113
peak=    4.199 closest distance to " CB  ASN A 148 " =    1.365
peak=    4.196 closest distance to " CB  TYR A 169 " =    0.708
peak=    4.191 closest distance to " CB  ARG A 190 " =    1.588
peak=    4.191 closest distance to " O   HOH Z 142 " =    1.601
peak=    4.190 closest distance to " CB  ARG A 275 " =    0.872
peak=    4.161 closest distance to " CB  GLU A 128 " =    1.115
peak=    4.158 closest distance to " CA  TYR A  30 " =    0.974
peak=    4.142 closest distance to " CB  ASP A 140 " =    0.941
peak=    4.140 closest distance to " O   HOH Z  78 " =    1.712
peak=    4.136 closest distance to " CB  ARG A  79 " =    1.473
peak=    4.136 closest distance to " O   HOH Z 316 " =    3.125
peak=    4.094 closest distance to " O   HOH Z  44 " =    2.138
peak=    4.089 closest distance to " CG  PRO A 198 " =    1.261
peak=    4.089 closest distance to " CB  GLU A 152 " =    1.152
peak=    4.089 closest distance to " O   HOH Z 425 " =    1.420
peak=    4.080 closest distance to " O   HOH Z 403 " =    1.654
peak=    4.066 closest distance to " O   SER A  87 " =    2.303
peak=    4.060 closest distance to " CB  GLU A 277 " =    3.678
peak=    4.046 closest distance to " CD2 LEU A 228 " =    1.098
peak=    4.044 closest distance to " O   HOH Z  43 " =    1.994
peak=    4.038 closest distance to " O   HOH Z 423 " =    1.741
peak=    4.036 closest distance to " O   HOH Z  63 " =    2.001
peak=    4.026 closest distance to " NH1AARG A 145 " =    1.210
peak=    4.022 closest distance to " O   HOH Z 261 " =    2.061
peak=    4.019 closest distance to " O   HOH Z 236 " =    1.941
peak=    4.011 closest distance to " ND2 ASN A 249 " =    1.936
peak=    4.010 closest distance to " O   HOH Z 272 " =    1.910
peak=    3.991 closest distance to " O   HOH Z 346 " =    1.596
peak=    3.987 closest distance to " O   HOH Z  15 " =    2.146
peak=    3.986 closest distance to " CB  ASP A 124 " =    0.711
peak=    3.963 closest distance to " O   HOH Z  61 " =    1.677
peak=    3.925 closest distance to " CG  MET A 185 " =    1.245
peak=    3.919 closest distance to " O   HOH Z 234 " =    3.774
peak=    3.912 closest distance to " O   HOH Z 158 " =    3.111
peak=    3.909 closest distance to " O   HOH Z 411 " =    3.620
peak=    3.908 closest distance to " O   HOH Z 203 " =    1.727
peak=    3.894 closest distance to " ND2 ASN A 187 " =    1.476
peak=    3.891 closest distance to " CB  SER A   3 " =    1.302
peak=    3.870 closest distance to " CB  ASN A 187 " =    1.153
peak=    3.864 closest distance to " CD  ARG A 159 " =    0.768
peak=    3.861 closest distance to " CA  ALA A  51 " =    0.998
peak=    3.854 closest distance to " CD  ARG A  66 " =    2.518
peak=    3.850 closest distance to " O   MET A 105 " =    1.815
peak=    3.829 closest distance to " O   HOH Z  19 " =    2.407
peak=    3.828 closest distance to " CG  ARG A 138 " =    1.178
peak=    3.810 closest distance to " CB  LEU A 143 " =    1.209
peak=    3.802 closest distance to " O   HOH Z 280 " =    2.966
peak=    3.797 closest distance to " CD ALYS A 290 " =    1.029
peak=    3.769 closest distance to " CB  VAL A 265 " =    1.284
peak=    3.764 closest distance to " O   HOH Z 193 " =    1.703
peak=    3.760 closest distance to " O   HOH Z 126 " =    1.586
peak=    3.760 closest distance to " OG  SER A  97 " =    3.023
peak=    3.755 closest distance to " CZ  PHE A 192 " =    1.001
peak=    3.742 closest distance to " O   HOH Z  68 " =    2.092
peak=    3.741 closest distance to " NH2 ARG A 156 " =    1.114
peak=    3.739 closest distance to " CB  PRO A  54 " =    0.791
peak=    3.738 closest distance to " CB  ASN A  39 " =    0.871
peak=    3.731 closest distance to " CG2 THR A 221 " =    1.132
peak=    3.730 closest distance to " CB  ALA A   9 " =    1.621
peak=    3.718 closest distance to " O   HOH Z 193 " =    2.131
peak=    3.718 closest distance to " O   HOH Z 214 " =    2.130
peak=    3.714 closest distance to " O   HOH Z  88 " =    3.238
peak=    3.701 closest distance to " O   HOH Z 126 " =    1.787
peak=    3.695 closest distance to " CB  THR A  82 " =    1.395
peak=    3.692 closest distance to " O   HOH Z 112 " =    1.664
peak=    3.689 closest distance to " CG1 VAL A 153 " =    0.993
peak=    3.677 closest distance to " CG1 ILE A  33 " =    1.289
peak=    3.675 closest distance to " CD  ARG A 269 " =    0.929
peak=    3.673 closest distance to " CB AVAL A  41 " =    1.159
peak=    3.653 closest distance to " CB  VAL A 202 " =    1.598
peak=    3.648 closest distance to " CA  SER A  87 " =    0.991
peak=    3.643 closest distance to " CA  THR A 264 " =    0.744
peak=    3.643 closest distance to " CD  ARG A  66 " =    2.401
peak=    3.641 closest distance to " O   HOH Z  80 " =    1.714
peak=    3.637 closest distance to " CB  ALA A 291 " =    1.391
peak=    3.635 closest distance to " CA  ARG A 195 " =    1.188
peak=    3.634 closest distance to " N   ASN A  39 " =    1.264
peak=    3.629 closest distance to " CD1 LEU A 300 " =    1.142
peak=    3.628 closest distance to " N   VAL A 126 " =    1.425
peak=    3.621 closest distance to " O   HOH Z 197 " =    2.960
peak=    3.612 closest distance to " CB  GLU A  46 " =    0.993
peak=    3.608 closest distance to " O   HOH Z 248 " =    1.677
peak=    3.604 closest distance to " OG BSER A 164 " =    2.190
peak=    3.602 closest distance to " O   HOH Z 133 " =    1.746
peak=    3.601 closest distance to " CB  LEU A 228 " =    1.188
peak=    3.599 closest distance to " O   HOH Z 184 " =    1.343
peak=    3.599 closest distance to " CG2 VAL A 257 " =    0.869
peak=    3.597 closest distance to " CB  ASN A 142 " =    1.085
peak=    3.597 closest distance to " CG1 ILE A  49 " =    1.498
peak=    3.595 closest distance to " O   HOH Z 437 " =    1.772
peak=    3.591 closest distance to " O   HOH Z 402 " =    1.478
peak=    3.589 closest distance to " CA  GLY A 267 " =    0.790
peak=    3.585 closest distance to " CA  ASN A 215 " =    1.228
peak=    3.579 closest distance to " CD  LYS A 166 " =    1.296
peak=    3.578 closest distance to " O   HOH Z 147 " =    1.771
peak=    3.571 closest distance to " O   HOH Z 285 " =    2.918
peak=    3.569 closest distance to " ND1 HIS A  81 " =    1.661
peak=    3.569 closest distance to " CG1BVAL A  72 " =    1.688
peak=    3.568 closest distance to " O   HOH Z 245 " =    1.369
peak=    3.562 closest distance to " O   HOH Z  40 " =    1.793
peak=    3.562 closest distance to " CA  THR A 221 " =    0.910
peak=    3.560 closest distance to " CG1 VAL A 296 " =    1.211
peak=    3.559 closest distance to " O   HOH Z 128 " =    2.127
peak=    3.558 closest distance to " CA  TYR A  30 " =    1.053
peak=    3.554 closest distance to " CA  ALA A  21 " =    1.177
peak=    3.554 closest distance to " O   HOH Z 171 " =    3.905
peak=    3.553 closest distance to " CA  ALA A 295 " =    1.118
peak=    3.549 closest distance to " CG BARG A 275 " =    1.469
peak=    3.548 closest distance to " O   HOH Z 371 " =    3.173
peak=    3.541 closest distance to " O   HOH Z 422 " =    2.694
peak=    3.539 closest distance to " CA  LYS A 117 " =    1.230
peak=    3.538 closest distance to " CZ  PHE A  38 " =    1.202
peak=    3.537 closest distance to " O   HOH Z 227 " =    1.708
peak=    3.537 closest distance to " O   HOH Z  48 " =    1.717
peak=    3.532 closest distance to " O   HOH Z 193 " =    1.828
peak=    3.525 closest distance to " N   PHE A 130 " =    1.248
peak=    3.524 closest distance to " O   HOH Z 102 " =    1.324
peak=    3.519 closest distance to " CB  TRP A 179 " =    1.470
peak=    3.519 closest distance to " CE1 TYR A 186 " =    1.290
peak=    3.515 closest distance to " O   HOH Z 133 " =    2.370
peak=    3.515 closest distance to " O   HOH Z 163 " =    1.613
peak=    3.506 closest distance to " O   ASP A 124 " =    1.079
peak=    3.505 closest distance to " O   ALA A 158 " =    1.428
peak=    3.505 closest distance to " CG  LEU A 167 " =    1.197
peak=    3.502 closest distance to " NE2 HIS A 207 " =    1.314
peak=    3.497 closest distance to " O   HOH Z  97 " =    2.086
peak=    3.492 closest distance to " O   HOH Z 313 " =    1.795
peak=    3.490 closest distance to " O   HOH Z  21 " =    1.722
peak=    3.489 closest distance to " CA  ALA A 158 " =    1.211
peak=    3.483 closest distance to " O   HOH Z 128 " =    2.204
peak=    3.480 closest distance to " CG1 ILE A 151 " =    1.071
peak=    3.478 closest distance to " O   HOH Z 368 " =    3.549
peak=    3.466 closest distance to " CA  MET A  40 " =    1.179
peak=    3.466 closest distance to " CG2 THR A 220 " =    0.920
peak=    3.462 closest distance to " O   TRP A 274 " =    1.876
peak=    3.462 closest distance to " OG  SER A  97 " =    2.705
peak=    3.457 closest distance to " O   HOH Z 250 " =    1.357
peak=    3.453 closest distance to " CB  ASN A 110 " =    1.232
peak=    3.451 closest distance to " CD1 LEU A   5 " =    1.351
peak=    3.444 closest distance to " CA  ALA A 291 " =    0.913
peak=    3.443 closest distance to " CB  MET A  40 " =    0.796
peak=    3.440 closest distance to " CB  SER A 273 " =    0.862
peak=    3.439 closest distance to " O   HOH Z 263 " =    1.653
peak=    3.435 closest distance to " CG  GLN A  88 " =    1.058
peak=    3.434 closest distance to " O   HOH Z 247 " =    1.354
peak=    3.433 closest distance to " O   HOH Z 135 " =    1.925
peak=    3.429 closest distance to " CB  SER A 212 " =    1.213
peak=    3.428 closest distance to " CB  ILE A 120 " =    1.334
peak=    3.426 closest distance to " O   HOH Z 273 " =    2.759
peak=    3.417 closest distance to " CE  LYS A  76 " =    0.852
peak=    3.415 closest distance to " O   HOH Z 290 " =    1.111
peak=    3.415 closest distance to " O   HOH Z 141 " =    1.683
peak=    3.414 closest distance to " CD1 ILE A  33 " =    1.681
peak=    3.414 closest distance to " CB  ARG A  79 " =    0.921
peak=    3.411 closest distance to " CA  ARG A  36 " =    1.154
peak=    3.410 closest distance to " OD2 ASP A 286 " =    2.896
peak=    3.409 closest distance to " NH1 ARG A  56 " =    1.000
peak=    3.405 closest distance to " CB  THR A 157 " =    1.112
peak=    3.404 closest distance to " O   HOH Z 180 " =    2.093
peak=    3.402 closest distance to " NE2 GLN A  77 " =    3.378
peak=    3.401 closest distance to " N   SER A 135 " =    1.372
peak=    3.399 closest distance to " OG  SER A  22 " =    2.852
peak=    3.396 closest distance to " CA  ASP A 162 " =    1.042
peak=    3.387 closest distance to " CB  TRP A 150 " =    1.372
peak=    3.386 closest distance to " O   HOH Z 383 " =    2.116
peak=    3.381 closest distance to " CB  SER A 216 " =    0.829
peak=    3.378 closest distance to " CB  ALA A 242 " =    0.845
peak=    3.377 closest distance to " CB  ALA A 248 " =    1.114
peak=    3.376 closest distance to " CB  THR A  31 " =    1.650
peak=    3.373 closest distance to " O   HOH Z 350 " =    1.673
peak=    3.370 closest distance to " CB  ALA A 104 " =    0.758
peak=    3.369 closest distance to " CB  ARG A 138 " =    0.965
peak=    3.365 closest distance to " CB  HIS A 108 " =    0.784
peak=    3.362 closest distance to " CA  LEU A 282 " =    1.042
peak=    3.361 closest distance to " OE1 GLN A  11 " =    1.911
peak=    3.360 closest distance to " CD2 TRP A 179 " =    1.350
peak=    3.355 closest distance to " O   HOH Z  62 " =    2.210
peak=    3.350 closest distance to " O   HOH Z 172 " =    3.748
peak=    3.348 closest distance to " CA  LYS A 181 " =    1.077
peak=    3.348 closest distance to " O   HOH Z 305 " =    3.620
peak=    3.333 closest distance to " CB  ALA A 248 " =    1.440
peak=    3.333 closest distance to " CB  VAL A 268 " =    0.851
peak=    3.332 closest distance to " O   HOH Z 213 " =    1.772
peak=    3.331 closest distance to " O   ALA A 165 " =    1.455
peak=    3.329 closest distance to " O   HOH Z 353 " =    2.713
peak=    3.327 closest distance to " O   HOH Z  97 " =    2.529
peak=    3.324 closest distance to " CB  GLN A  88 " =    1.218
peak=    3.322 closest distance to " CA  GLY A 211 " =    1.334
peak=    3.322 closest distance to " NZ  LYS A 117 " =    3.336
peak=    3.321 closest distance to " O   HOH Z 295 " =    1.525
peak=    3.321 closest distance to " CB  ALA A  34 " =    0.865
peak=    3.321 closest distance to " CA  TYR A 116 " =    1.489
peak=    3.318 closest distance to " O   HOH Z 327 " =    2.351
peak=    3.313 closest distance to " CB  LYS A 117 " =    1.180
peak=    3.308 closest distance to " O   HOH Z 417 " =    3.249
peak=    3.307 closest distance to " O   HOH Z 134 " =    1.399
peak=    3.307 closest distance to " CA  VAL A  41 " =    0.845
peak=    3.302 closest distance to " O  BHOH Z 338 " =    2.374
peak=    3.300 closest distance to " CA  VAL A 125 " =    1.213
peak=    3.299 closest distance to " O   HOH Z 291 " =    1.637
peak=    3.293 closest distance to " O   HOH Z 365 " =    2.987
peak=    3.289 closest distance to " O   HOH Z 132 " =    2.739
peak=    3.288 closest distance to " OG1 THR A 294 " =    2.407
peak=    3.287 closest distance to " CB  GLN A  89 " =    1.172
peak=    3.287 closest distance to " CB  MET A  47 " =    1.040
peak=    3.286 closest distance to " O   HOH Z 327 " =    1.924
peak=    3.284 closest distance to " O   HOH Z 420 " =    1.879
peak=    3.282 closest distance to " NH1 ARG A  14 " =    0.945
peak=    3.279 closest distance to " O   HOH Z  20 " =    1.681
peak=    3.275 closest distance to " C   TYR A 214 " =    1.558
peak=    3.270 closest distance to " CB  ARG A 139 " =    0.845
peak=    3.269 closest distance to " O   HOH Z 299 " =    4.276
peak=    3.261 closest distance to " O   HOH Z 426 " =    1.552
peak=    3.252 closest distance to " O   HOH Z 148 " =    3.261
peak=    3.249 closest distance to " O   HOH Z 403 " =    1.404
peak=    3.248 closest distance to " ND1 HIS A  86 " =    1.769
peak=    3.248 closest distance to " O   HOH Z  10 " =    1.762
peak=    3.247 closest distance to " NH2 ARG A  79 " =    1.388
peak=    3.245 closest distance to " O   HOH Z 325 " =    2.255
peak=    3.244 closest distance to " CB  ALA A   1 " =    4.794
peak=    3.241 closest distance to " NE  ARG A  79 " =    1.216
peak=    3.237 closest distance to " CG  MET A 185 " =    1.052
peak=    3.229 closest distance to " O   HOH Z 109 " =    2.625
peak=    3.229 closest distance to " O   HOH Z 344 " =    3.084
peak=    3.225 closest distance to " CA  ASP A 191 " =    0.760
peak=    3.222 closest distance to " NZ  LYS A  48 " =    1.388
peak=    3.222 closest distance to " O   PRO A  90 " =    1.359
peak=    3.219 closest distance to " O   HOH Z 313 " =    1.744
peak=    3.219 closest distance to " CB  ALA A 137 " =    1.073
peak=    3.213 closest distance to " O   GLN A 278 " =    1.537
peak=    3.212 closest distance to " CZ3 TRP A  85 " =    0.980
peak=    3.210 closest distance to " O   HOH Z 359 " =    1.340
peak=    3.206 closest distance to " CG2 ILE A 234 " =    0.768
peak=    3.205 closest distance to " O   HOH Z 425 " =    2.021
peak=    3.195 closest distance to " CG  GLU A  37 " =    0.825
peak=    3.195 closest distance to " CB  TYR A 116 " =    0.876
peak=    3.195 closest distance to " N   ASN A 127 " =    1.234
peak=    3.194 closest distance to " OG BSER A 134 " =    2.895
peak=    3.193 closest distance to " CB  GLN A 103 " =    1.072
peak=    3.191 closest distance to " CD2 LEU A 255 " =    1.678
peak=    3.180 closest distance to " CB  ALA A 100 " =    1.258
peak=    3.180 closest distance to " O   HOH Z 271 " =    2.419
peak=    3.180 closest distance to " O   HOH Z 187 " =    2.321
peak=    3.178 closest distance to " CA  ALA A 233 " =    1.515
peak=    3.178 closest distance to " O   HOH Z 435 " =    1.998
peak=    3.177 closest distance to " N   SER A 146 " =    1.685
peak=    3.176 closest distance to " O   HOH Z 166 " =    3.545
peak=    3.173 closest distance to " O   HOH Z 145 " =    1.875
peak=    3.171 closest distance to " CZ3 TRP A 274 " =    4.638
peak=    3.169 closest distance to " O   HOH Z 406 " =    1.513
peak=    3.166 closest distance to " CD  LYS A 119 " =    1.921
peak=    3.165 closest distance to " OH  TYR A 214 " =    1.236
peak=    3.165 closest distance to " CA  ASP A 140 " =    1.257
peak=    3.164 closest distance to " O   HOH Z 261 " =    1.459
peak=    3.160 closest distance to " OG1 THR A 294 " =    1.739
peak=    3.143 closest distance to " O   GLU A   2 " =    1.558
peak=    3.142 closest distance to " O   ASN A 284 " =    1.807
peak=    3.142 closest distance to " O   HOH Z 329 " =    3.956
peak=    3.141 closest distance to " CA  ILE A 106 " =    0.775
peak=    3.140 closest distance to " CA  MET A 105 " =    0.995
peak=    3.135 closest distance to " N   ARG A 156 " =    1.373
peak=    3.132 closest distance to " CG  ARG A 159 " =    1.026
peak=    3.130 closest distance to " O   HOH Z 293 " =    1.837
peak=    3.129 closest distance to " O   HOH Z 417 " =    2.580
peak=    3.124 closest distance to " CD1 ILE A 106 " =    0.987
peak=    3.120 closest distance to " N   TYR A  15 " =    0.825
peak=    3.118 closest distance to " CD1 LEU A 228 " =    1.922
peak=    3.118 closest distance to " CE2 TYR A  30 " =    0.819
peak=    3.116 closest distance to " CA  ALA A 154 " =    0.988
peak=    3.116 closest distance to " N   ASP A 162 " =    1.318
peak=    3.116 closest distance to " CD1 ILE A 199 " =    0.796
peak=    3.108 closest distance to " CA  ALA A 299 " =    0.973
peak=    3.106 closest distance to " O   HOH Z 345 " =    3.464
peak=    3.106 closest distance to " CB  PRO A 243 " =    1.546
peak=    3.101 closest distance to " OG  SER A  62 " =    2.956
peak=    3.096 closest distance to " O   THR A  31 " =    1.553
peak=    3.095 closest distance to " CG  GLN A  77 " =    2.118
peak=    3.094 closest distance to " OD1 ASN A 217 " =    1.622
peak=    3.081 closest distance to " O   HOH Z  59 " =    2.236
peak=    3.078 closest distance to " O   HOH Z 201 " =    3.082
peak=    3.073 closest distance to " O   HOH Z 294 " =    1.556
peak=    3.068 closest distance to " OE2 GLU A   2 " =    1.860
peak=    3.064 closest distance to " CA  LYS A 290 " =    1.243
peak=    3.063 closest distance to " CB  ALA A 114 " =    1.209
peak=    3.062 closest distance to " OE2 GLU A  53 " =    2.006
peak=    3.043 closest distance to " C   ASN A  39 " =    1.047
peak=    3.041 closest distance to " CB  ALA A 227 " =    0.980
peak=    3.028 closest distance to " CB  TYR A 169 " =    1.211

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.652 - 5.535
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.775 - 5.535

peak=   -5.318 closest distance to " CG2 VAL A 230 " =    0.904
peak=   -4.487 closest distance to " CD  ARG A 156 " =    2.024
peak=   -4.291 closest distance to " CB  PRO A 243 " =    2.652
peak=   -4.208 closest distance to " O   HOH Z 266 " =    5.306
peak=   -4.202 closest distance to " CB  ALA A 161 " =    2.583
peak=   -4.162 closest distance to " SG  CYS A 254 " =    3.381
peak=   -4.116 closest distance to " CD  GLN A  58 " =    0.993
peak=   -4.044 closest distance to " CG  GLN A 223 " =    2.176
peak=   -3.999 closest distance to " CG2BVAL A  41 " =    2.569
peak=   -3.990 closest distance to " O   HOH Z 196 " =    2.238
peak=   -3.968 closest distance to " OG  SER A  97 " =    2.278
peak=   -3.935 closest distance to " CG1 VAL A 112 " =    2.609
peak=   -3.890 closest distance to " O   HOH Z 231 " =    2.008
peak=   -3.867 closest distance to " O   HOH Z  52 " =    1.626
peak=   -3.856 closest distance to " CG1 VAL A 250 " =    2.765
peak=   -3.837 closest distance to " CZ3 TRP A 179 " =    1.163
peak=   -3.835 closest distance to " O   VAL A  67 " =    2.689
peak=   -3.806 closest distance to " N   ALA A  43 " =    2.561
peak=   -3.797 closest distance to " CE2 TYR A  30 " =    2.830
peak=   -3.791 closest distance to " O   HOH Z 114 " =    3.232
peak=   -3.774 closest distance to " CG1 VAL A 112 " =    2.908
peak=   -3.769 closest distance to " CZ2 TRP A  92 " =    2.853
peak=   -3.768 closest distance to " C   ALA A 158 " =    1.311
peak=   -3.764 closest distance to " O   HOH Z 166 " =    1.963
peak=   -3.737 closest distance to " OXT GLY A 302 " =    3.001
peak=   -3.736 closest distance to " O   HOH Z 426 " =    1.684
peak=   -3.735 closest distance to " CG2 VAL A 296 " =    1.272
peak=   -3.728 closest distance to " O   HOH Z 290 " =    1.255
peak=   -3.724 closest distance to " CG1 VAL A 296 " =    1.412
peak=   -3.722 closest distance to " O   HOH Z 351 " =    1.504
peak=   -3.716 closest distance to " CA  GLY A 241 " =    3.092
peak=   -3.715 closest distance to " CG  ASP A 231 " =    0.775
peak=   -3.710 closest distance to " C   HIS A 108 " =    1.151
peak=   -3.707 closest distance to " NH2AARG A 275 " =    5.357
peak=   -3.705 closest distance to " O   HOH Z 389 " =    2.011
peak=   -3.702 closest distance to " O   HOH Z  11 " =    1.905
peak=   -3.690 closest distance to " CD2 LEU A 300 " =    2.836
peak=   -3.687 closest distance to " O   HOH Z 241 " =    1.206
peak=   -3.682 closest distance to " N   ALA A 226 " =    2.161
peak=   -3.678 closest distance to " CD1 LEU A 101 " =    2.533
peak=   -3.674 closest distance to " O   HOH Z 211 " =    1.512
peak=   -3.673 closest distance to " CA  ASP A 298 " =    1.043
peak=   -3.670 closest distance to " O   HOH Z  73 " =    2.176
peak=   -3.665 closest distance to " O   HOH Z 435 " =    2.778
peak=   -3.658 closest distance to " CD1 LEU A 228 " =    2.363
peak=   -3.653 closest distance to " OG BSER A 134 " =    1.200
peak=   -3.644 closest distance to " O   HOH Z 394 " =    1.557
peak=   -3.624 closest distance to " OD1 ASN A 148 " =    1.481
peak=   -3.606 closest distance to " CB  PHE A 192 " =    1.897
peak=   -3.603 closest distance to " CE3 TRP A 150 " =    2.127
peak=   -3.602 closest distance to " O   HOH Z 103 " =    1.866
peak=   -3.599 closest distance to " CB  VAL A 230 " =    1.045
peak=   -3.587 closest distance to " O   PRO A 163 " =    2.135
peak=   -3.584 closest distance to " O   HOH Z  10 " =    1.537
peak=   -3.580 closest distance to " C   LEU A 143 " =    1.120
peak=   -3.578 closest distance to " NE2 GLN A  88 " =    2.124
peak=   -3.575 closest distance to " O   GLY A  80 " =    2.548
peak=   -3.573 closest distance to " CG1 VAL A 265 " =    2.414
peak=   -3.556 closest distance to " O   HOH Z 185 " =    2.354
peak=   -3.553 closest distance to " CB  ALA A  43 " =    2.584
peak=   -3.546 closest distance to " O   VAL A 189 " =    2.608
peak=   -3.546 closest distance to " ND2 ASN A  45 " =    1.874
peak=   -3.542 closest distance to " CG  HIS A  86 " =    1.026
peak=   -3.528 closest distance to " NE2 GLN A 194 " =    1.811
peak=   -3.519 closest distance to " CB  PRO A 163 " =    2.564
peak=   -3.515 closest distance to " CE  MET A 105 " =    2.194
peak=   -3.511 closest distance to " CD2 LEU A 167 " =    1.824
peak=   -3.511 closest distance to " O   HOH Z  44 " =    2.169
peak=   -3.503 closest distance to " O   HOH Z 377 " =    1.431
peak=   -3.496 closest distance to " O   HOH Z 353 " =    2.153
peak=   -3.496 closest distance to " CA  GLY A 241 " =    2.302
peak=   -3.495 closest distance to " ND2 ASN A  45 " =    1.145
peak=   -3.487 closest distance to " O   HOH Z  13 " =    1.468
peak=   -3.486 closest distance to " O   GLY A 203 " =    2.383
peak=   -3.481 closest distance to " CG  ARG A 269 " =    2.533
peak=   -3.465 closest distance to " CB  ASP A 132 " =    2.312
peak=   -3.460 closest distance to " O   HOH Z 407 " =    3.206
peak=   -3.459 closest distance to " O   HOH Z  38 " =    1.438
peak=   -3.458 closest distance to " CG  GLU A 277 " =    1.178
peak=   -3.454 closest distance to " O   HOH Z 377 " =    2.028
peak=   -3.448 closest distance to " CD1 PHE A  59 " =    1.938
peak=   -3.447 closest distance to " CD1 LEU A 101 " =    2.622
peak=   -3.445 closest distance to " OG  SER A  87 " =    1.576
peak=   -3.445 closest distance to " OE1 GLN A  88 " =    0.958
peak=   -3.437 closest distance to " NE2 GLN A 103 " =    1.781
peak=   -3.434 closest distance to " CB  ALA A 291 " =    2.189
peak=   -3.425 closest distance to " N   THR A 157 " =    1.511
peak=   -3.424 closest distance to " OD1 ASN A 187 " =    1.585
peak=   -3.422 closest distance to " CA  GLY A 203 " =    2.434
peak=   -3.418 closest distance to " CD2 TYR A 293 " =    2.010
peak=   -3.414 closest distance to " CB  ALA A 248 " =    2.117
peak=   -3.409 closest distance to " CG  LEU A 101 " =    2.464
peak=   -3.406 closest distance to " O   GLY A 211 " =    1.405
peak=   -3.404 closest distance to " CG  TRP A 266 " =    1.887
peak=   -3.404 closest distance to " O   HOH Z  60 " =    2.285
peak=   -3.380 closest distance to " CG1 VAL A 197 " =    2.280
peak=   -3.379 closest distance to " O   HOH Z 222 " =    1.564
peak=   -3.378 closest distance to " C   ASN A 285 " =    2.467
peak=   -3.374 closest distance to " O   HOH Z 350 " =    1.797
peak=   -3.370 closest distance to " O   SER A 271 " =    2.237
peak=   -3.369 closest distance to " NH2 ARG A  79 " =    2.035
peak=   -3.368 closest distance to " O   HOH Z 292 " =    4.645
peak=   -3.365 closest distance to " CG2 VAL A 112 " =    2.534
peak=   -3.365 closest distance to " O   HOH Z 123 " =    2.568
peak=   -3.364 closest distance to " O   HOH Z  17 " =    1.528
peak=   -3.357 closest distance to " N   VAL A 296 " =    2.614
peak=   -3.354 closest distance to " O   HOH Z  19 " =    2.347
peak=   -3.353 closest distance to " O   PRO A 198 " =    1.272
peak=   -3.353 closest distance to " CD  ARG A 139 " =    1.668
peak=   -3.352 closest distance to " N   THR A  18 " =    1.330
peak=   -3.348 closest distance to " CA  GLY A 133 " =    2.295
peak=   -3.347 closest distance to " O   HOH Z 102 " =    1.655
peak=   -3.344 closest distance to " CB  ALA A 248 " =    2.418
peak=   -3.340 closest distance to " CG2BVAL A  41 " =    1.749
peak=   -3.338 closest distance to " O   HOH Z 177 " =    1.697
peak=   -3.334 closest distance to " O   HOH Z 275 " =    1.551
peak=   -3.331 closest distance to " CD2 PHE A  61 " =    2.477
peak=   -3.321 closest distance to " O   HOH Z  43 " =    1.746
peak=   -3.316 closest distance to " O   HOH Z 396 " =    1.835
peak=   -3.315 closest distance to " OG ASER A 134 " =    1.279
peak=   -3.314 closest distance to " CE2 PHE A 218 " =    2.586
peak=   -3.313 closest distance to " OD2 ASP A  50 " =    2.385
peak=   -3.310 closest distance to " ND2 ASN A  60 " =    1.388
peak=   -3.307 closest distance to " C   ASN A 187 " =    1.814
peak=   -3.305 closest distance to " O   HOH Z 198 " =    1.497
peak=   -3.305 closest distance to " CD1 TYR A 247 " =    2.863
peak=   -3.302 closest distance to " O   HOH Z 359 " =    3.067
peak=   -3.295 closest distance to " O   ARG A  24 " =    2.136
peak=   -3.295 closest distance to " N   SER A   3 " =    2.065
peak=   -3.294 closest distance to " O   GLY A 196 " =    1.210
peak=   -3.294 closest distance to " O   HOH Z 184 " =    1.409
peak=   -3.291 closest distance to " CD1 ILE A 151 " =    2.401
peak=   -3.290 closest distance to " OG BSER A 134 " =    1.826
peak=   -3.290 closest distance to " CE BMET A  47 " =    1.850
peak=   -3.287 closest distance to " O   HOH Z 191 " =    5.535
peak=   -3.279 closest distance to " ND2 ASN A 187 " =    1.702
peak=   -3.277 closest distance to " CD  PRO A 213 " =    2.194
peak=   -3.273 closest distance to " O   HOH Z 311 " =    3.841
peak=   -3.265 closest distance to " O   HOH Z 234 " =    4.403
peak=   -3.255 closest distance to " O   HOH Z 295 " =    1.520
peak=   -3.251 closest distance to " CB  ALA A 291 " =    2.284
peak=   -3.248 closest distance to " OG  SER A 206 " =    1.773
peak=   -3.246 closest distance to " O   HOH Z 111 " =    2.192
peak=   -3.245 closest distance to " O   MET A  40 " =    2.798
peak=   -3.243 closest distance to " CG  PRO A 163 " =    2.474
peak=   -3.242 closest distance to " OG  SER A  62 " =    1.788
peak=   -3.242 closest distance to " N   SER A 212 " =    1.931
peak=   -3.236 closest distance to " O   HOH Z 231 " =    1.426
peak=   -3.235 closest distance to " O   HOH Z 431 " =    1.798
peak=   -3.232 closest distance to " CZ  TYR A 169 " =    1.674
peak=   -3.232 closest distance to " O   HOH Z 166 " =    1.630
peak=   -3.231 closest distance to " ND2 ASN A  60 " =    1.911
peak=   -3.228 closest distance to " N   SER A 276 " =    1.409
peak=   -3.226 closest distance to " C   MET A 188 " =    1.366
peak=   -3.222 closest distance to " O   HOH Z 136 " =    2.379
peak=   -3.220 closest distance to " C   LEU A 222 " =    0.862
peak=   -3.215 closest distance to " CG  MET A 105 " =    0.951
peak=   -3.209 closest distance to " O   HOH Z 113 " =    2.035
peak=   -3.204 closest distance to " N   ALA A 248 " =    1.838
peak=   -3.193 closest distance to " OD1 ASP A 171 " =    1.594
peak=   -3.189 closest distance to " O   HOH Z 128 " =    2.666
peak=   -3.188 closest distance to " OG  SER A  26 " =    1.375
peak=   -3.187 closest distance to " CA  ASN A 127 " =    1.105
peak=   -3.181 closest distance to " NH1 ARG A 195 " =    2.605
peak=   -3.180 closest distance to " O   HOH Z 174 " =    2.496
peak=   -3.174 closest distance to " CD1 TYR A 247 " =    2.379
peak=   -3.170 closest distance to " OH  TYR A 214 " =    1.201
peak=   -3.169 closest distance to " O   HOH Z 313 " =    1.130
peak=   -3.167 closest distance to " CD1 ILE A 199 " =    2.605
peak=   -3.164 closest distance to " CD  GLN A  88 " =    0.818
peak=   -3.164 closest distance to " CG  PHE A 283 " =    2.867
peak=   -3.163 closest distance to " CE3 TRP A  70 " =    1.776
peak=   -3.162 closest distance to " O   HOH Z   6 " =    1.658
peak=   -3.156 closest distance to " O   HOH Z  90 " =    1.616
peak=   -3.156 closest distance to " CG2 VAL A 189 " =    2.077
peak=   -3.152 closest distance to " CA  SER A 135 " =    1.324
peak=   -3.150 closest distance to " O   VAL A 125 " =    2.330
peak=   -3.146 closest distance to " CH2 TRP A 177 " =    2.168
peak=   -3.145 closest distance to " CG1 VAL A 125 " =    1.969
peak=   -3.144 closest distance to " N   GLN A  58 " =    1.622
peak=   -3.140 closest distance to " O   HOH Z  51 " =    1.356
peak=   -3.138 closest distance to " ND2 ASN A  69 " =    1.829
peak=   -3.137 closest distance to " O   ASP A 270 " =    1.629
peak=   -3.136 closest distance to " O   SER A 276 " =    1.730
peak=   -3.135 closest distance to " O   HOH Z 139 " =    3.033
peak=   -3.135 closest distance to " CG1 VAL A  67 " =    2.979
peak=   -3.132 closest distance to " NH2 ARG A  66 " =    1.933
peak=   -3.129 closest distance to " OD2 ASP A 171 " =    1.873
peak=   -3.127 closest distance to " O   HOH Z 326 " =    5.065
peak=   -3.125 closest distance to " NH2 ARG A  79 " =    1.619
peak=   -3.118 closest distance to " OD1 ASN A 249 " =    2.195
peak=   -3.116 closest distance to " O   HOH Z 262 " =    2.889
peak=   -3.114 closest distance to " O   HOH Z 165 " =    1.800
peak=   -3.113 closest distance to " OD1 ASN A 173 " =    1.374
peak=   -3.113 closest distance to " NE2 GLN A  88 " =    1.003
peak=   -3.110 closest distance to " O   HOH Z 176 " =    0.867
peak=   -3.110 closest distance to " N   ASN A  60 " =    1.298
peak=   -3.103 closest distance to " CB  ASP A 132 " =    2.338
peak=   -3.086 closest distance to " O   HOH Z 313 " =    1.692
peak=   -3.079 closest distance to " CB  TYR A  15 " =    2.246
peak=   -3.072 closest distance to " CB  TRP A  85 " =    2.534
peak=   -3.065 closest distance to " O   THR A  18 " =    1.548
peak=   -3.064 closest distance to " O   PRO A 198 " =    1.348
peak=   -3.059 closest distance to " O   HOH Z 106 " =    1.889
peak=   -3.057 closest distance to " CG2 THR A 178 " =    2.245

================= 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    :  0.4346 0.4199   6.230359e+00   6.203794e+00
   1_bss:  0.4275 0.4051   6.224713e+00   6.190439e+00
   1_xyz:  0.3164 0.3418   6.013354e+00   6.066028e+00
   1_adp:  0.2572 0.2920   5.838981e+00   5.951705e+00
   1_occ:  0.2565 0.2921   5.837676e+00   5.953035e+00
   2_bss:  0.2528 0.2886   5.837446e+00   5.949717e+00
   2_xyz:  0.1759 0.2163   5.515157e+00   5.682454e+00
   2_adp:  0.1677 0.2102   5.472664e+00   5.651938e+00
   2_occ:  0.1675 0.2103   5.472324e+00   5.652252e+00
   3_bss:  0.1667 0.2094   5.472916e+00   5.651936e+00
   3_xyz:  0.1434 0.1879   5.344830e+00   5.551244e+00
   3_adp:  0.1301 0.1761   5.270778e+00   5.498394e+00
   3_occ:  0.1301 0.1761   5.270814e+00   5.498709e+00
   4_bss:  0.1300 0.1761   5.270093e+00   5.498327e+00
   4_xyz:  0.1167 0.1664   5.187858e+00   5.440954e+00
   4_adp:  0.1165 0.1621   5.177297e+00   5.418900e+00
   4_occ:  0.1164 0.1621   5.176730e+00   5.418561e+00
   5_bss:  0.1166 0.1618   5.176298e+00   5.416453e+00
   5_xyz:  0.1142 0.1601   5.161857e+00   5.404634e+00
   5_adp:  0.1131 0.1602   5.159495e+00   5.407231e+00
   5_occ:  0.1130 0.1603   5.159157e+00   5.407030e+00
   5_bss:  0.1130 0.1603   5.158962e+00   5.406887e+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:  0.300  20.000   8.539   8.019   8.297   0.000   0.000   0.000
   1_xyz:  0.300  20.000   8.539   8.019   8.297   0.000   0.000   0.000
   1_adp:  0.300  20.000   8.539   8.019   8.297   0.000   0.000   0.000
   1_occ:  0.300  20.000   8.539   8.019   8.297   0.000   0.000   0.000
   2_bss:  0.328  56.413   5.266   4.800   5.337   0.000   0.000   0.000
   2_xyz:  0.328  56.413   5.266   4.800   5.337   0.000   0.000   0.000
   2_adp:  0.328  56.413   5.266   4.800   5.337   0.000   0.000   0.000
   2_occ:  0.328  56.413   5.266   4.800   5.337   0.000   0.000   0.000
   3_bss:  0.339  56.413   3.633   3.724   4.536   0.000   0.000   0.000
   3_xyz:  0.339  56.413   3.633   3.724   4.536   0.000   0.000   0.000
   3_adp:  0.339  56.413   3.633   3.724   4.536   0.000   0.000   0.000
   3_occ:  0.339  56.413   3.633   3.724   4.536   0.000   0.000   0.000
   4_bss:  0.329  61.072   3.338   3.407   4.346   0.000   0.000   0.000
   4_xyz:  0.329  61.072   3.338   3.407   4.346   0.000   0.000   0.000
   4_adp:  0.329  61.072   3.338   3.407   4.346   0.000   0.000   0.000
   4_occ:  0.329  61.072   3.338   3.407   4.346   0.000   0.000   0.000
   5_bss:  0.333  61.072   3.338   3.407   4.346   0.000   0.000   0.000
   5_xyz:  0.333  61.072   3.338   3.407   4.346   0.000   0.000   0.000
   5_adp:  0.333  61.072   3.338   3.407   4.346   0.000   0.000   0.000
   5_occ:  0.333  61.072   3.338   3.407   4.346   0.000   0.000   0.000
   5_bss:  0.322  57.298  -0.359  -0.290   0.649   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.749 0.5624  0.6182    50987.166
   1_bss:  46.239 0.5673  0.7991    48715.657
   1_xyz:  37.405 0.6724  0.9205    32640.542
   1_adp:  30.103 0.7572  1.0059    22945.608
   1_occ:  30.158 0.7565  1.0047    22998.927
   2_bss:  29.993 0.7584  0.9005    22824.991
   2_xyz:  20.813 0.8540  0.9840    11881.071
   2_adp:  19.889 0.8633  1.0013    11167.738
   2_occ:  19.899 0.8632  1.0011    11181.971
   3_bss:  19.880 0.8634  0.9589    11191.084
   3_xyz:  17.373 0.8867  0.9710     8971.432
   3_adp:  16.153 0.8975  0.9734     7942.324
   3_occ:  16.160 0.8974  0.9732     7943.553
   4_bss:  16.152 0.8975  0.9638     7936.488
   4_xyz:  14.947 0.9074  0.9696     7017.032
   4_adp:  14.428 0.9119  0.9708     6758.242
   4_occ:  14.422 0.9119  0.9707     6752.003
   5_bss:  14.407 0.9119  0.9700     6697.623
   5_xyz:  14.121 0.9144  0.9703     6512.747
   5_adp:  14.185 0.9139  0.9663     6531.681
   5_occ:  14.183 0.9139  0.9662     6530.659
   5_bss:  14.184 0.9139  0.9660     6522.547
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4279e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4279e+01
   1_xyz:   1.539  0.012  0.102 17.979  0.006  4.127   1.2095e-01
   1_adp:   1.539  0.012  0.102 17.979  0.006  4.127   1.2095e-01
   1_occ:   1.539  0.012  0.102 17.979  0.006  4.127   1.2095e-01
   2_bss:   1.539  0.012  0.102 17.979  0.006  4.127   1.2095e-01
   2_xyz:   1.001  0.007  0.071 16.414  0.004  4.129   6.4520e-02
   2_adp:   1.001  0.007  0.071 16.414  0.004  4.129   6.4520e-02
   2_occ:   1.001  0.007  0.071 16.414  0.004  4.129   6.4520e-02
   3_bss:   1.001  0.007  0.071 16.414  0.004  4.129   6.4520e-02
   3_xyz:   0.980  0.007  0.076 16.009  0.003  4.138   5.9956e-02
   3_adp:   0.980  0.007  0.076 16.009  0.003  4.138   5.9956e-02
   3_occ:   0.980  0.007  0.076 16.009  0.003  4.138   5.9956e-02
   4_bss:   0.980  0.007  0.076 16.009  0.003  4.138   5.9956e-02
   4_xyz:   1.129  0.011  0.092 15.997  0.004  4.147   7.9032e-02
   4_adp:   1.129  0.011  0.092 15.997  0.004  4.147   7.9032e-02
   4_occ:   1.129  0.011  0.092 15.997  0.004  4.147   7.9032e-02
   5_bss:   1.129  0.011  0.092 15.997  0.004  4.147   7.9032e-02
   5_xyz:   1.097  0.010  0.090 15.847  0.004  4.116   7.6525e-02
   5_adp:   1.097  0.010  0.090 15.847  0.004  4.116   7.6525e-02
   5_occ:   1.097  0.010  0.090 15.847  0.004  4.116   7.6525e-02
   5_bss:   1.097  0.010  0.090 15.847  0.004  4.116   7.6525e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0383e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0383e+00
   1_xyz:  12.312  0.144  0.398 85.364  0.038  2.278   9.2284e-02
   1_adp:  12.312  0.144  0.398 85.364  0.038  2.278   9.2284e-02
   1_occ:  12.312  0.144  0.398 85.364  0.038  2.278   9.2284e-02
   2_bss:  12.312  0.144  0.398 85.364  0.038  2.278   9.2284e-02
   2_xyz:   6.863  0.068  0.231 85.910  0.036  2.340   5.4343e-02
   2_adp:   6.863  0.068  0.231 85.910  0.036  2.340   5.4343e-02
   2_occ:   6.863  0.068  0.231 85.910  0.036  2.340   5.4343e-02
   3_bss:   6.863  0.068  0.231 85.910  0.036  2.340   5.4343e-02
   3_xyz:   7.455  0.053  0.402 82.691  0.036  2.420   3.6094e-02
   3_adp:   7.455  0.053  0.402 82.691  0.036  2.420   3.6094e-02
   3_occ:   7.455  0.053  0.402 82.691  0.036  2.420   3.6094e-02
   4_bss:   7.455  0.053  0.402 82.691  0.036  2.420   3.6094e-02
   4_xyz:   7.500  0.045  0.626 82.830  0.041  2.307   5.7803e-02
   4_adp:   7.500  0.045  0.626 82.830  0.041  2.307   5.7803e-02
   4_occ:   7.500  0.045  0.626 82.830  0.041  2.307   5.7803e-02
   5_bss:   7.500  0.045  0.626 82.830  0.041  2.307   5.7803e-02
   5_xyz:   7.557  0.050  0.611 82.774  0.040  2.357   5.3957e-02
   5_adp:   7.557  0.050  0.611 82.774  0.040  2.357   5.3957e-02
   5_occ:   7.557  0.050  0.611 82.774  0.040  2.357   5.3957e-02
   5_bss:   7.557  0.050  0.611 82.774  0.040  2.357   5.3957e-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:  62.89   0.00  10.08  52.60   0.00   7.16  62.89   0.00  25.99
   1_occ:  62.89   0.00  10.08  52.60   0.00   7.16  62.89   0.00  25.99
   2_bss:  62.89   0.00  10.08  52.60   0.00   7.16  62.89   0.00  25.99
   2_xyz:  62.89   0.00  10.08  52.60   0.00   7.16  62.89   0.00  25.99
   2_adp:  78.69   0.00  10.31  78.69   0.00   7.23  62.97   0.43  27.06
   2_occ:  78.69   0.00  10.31  78.69   0.00   7.23  62.97   0.43  27.06
   3_bss:  78.69   0.00  10.31  78.69   0.00   7.23  62.97   0.43  27.06
   3_xyz:  78.69   0.00  10.31  78.69   0.00   7.23  62.97   0.43  27.06
   3_adp:  81.64   0.00  12.04  78.37   0.00   7.61  81.64   0.00  36.13
   3_occ:  81.64   0.00  12.04  78.37   0.00   7.61  81.64   0.00  36.13
   4_bss:  81.64   0.00  12.04  78.37   0.00   7.61  81.64   0.00  36.13
   4_xyz:  81.64   0.00  12.04  78.37   0.00   7.61  81.64   0.00  36.13
   4_adp:  76.47   0.00  11.40  76.21   0.00   7.35  76.47   0.99  33.46
   4_occ:  76.47   0.00  11.40  76.21   0.00   7.35  76.47   0.99  33.46
   5_bss:  76.47   0.00  11.40  76.21   0.00   7.35  76.47   0.99  33.46
   5_xyz:  76.47   0.00  11.40  76.21   0.00   7.35  76.47   0.99  33.46
   5_adp:  78.51   0.00  11.53  78.51   0.00   7.37  77.21   0.78  34.16
   5_occ:  78.51   0.00  11.53  78.51   0.00   7.37  77.21   0.78  34.16
   5_bss:  82.21   3.70  15.22  82.21   3.70  11.07  80.91   4.48  37.86
------------------------------------------------------------------------
 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:    1.202    0.010    0.404
   1_adp:    1.202    0.010    0.404
   1_occ:    1.202    0.010    0.404
   2_bss:    1.202    0.010    0.404
   2_xyz:    1.533    0.054    0.510
   2_adp:    1.533    0.054    0.510
   2_occ:    1.533    0.054    0.510
   3_bss:    1.533    0.054    0.510
   3_xyz:    1.468    0.040    0.533
   3_adp:    1.468    0.040    0.533
   3_occ:    1.468    0.040    0.533
   4_bss:    1.468    0.040    0.533
   4_xyz:    1.402    0.022    0.560
   4_adp:    1.402    0.022    0.560
   4_occ:    1.402    0.022    0.560
   5_bss:    1.402    0.022    0.560
   5_xyz:    1.455    0.038    0.569
   5_adp:    1.455    0.038    0.569
   5_occ:    1.455    0.038    0.569
   5_bss:    1.455    0.038    0.569
------------------------------------------------------------------------

CPU time actual refinement: 271.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1040/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_1040/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1040/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1040/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1040/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 271.51 
  Macro-tasks:
    bulk solvent and scale       = 33.42  
    individual site refinement   = 113.24 
    weights calculation          = 26.83  
    collect and process          = 5.51   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 179.11 
  Micro-tasks:
    mask                            = 1.46   
    f_calc                          = 81.73  
    alpha_beta                      = 7.23   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 92.30  
    fmodel                         = 6.01   
    r_factors                      = 0.16   
    phase_errors                   = 9.03   
    foms                           = 0.19   
    TOTAL for micro-tasks          = 199.11 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.814 micro seconds
Total CPU time: 4.72 minutes
from_scatterers_fft:    647 calls, 81.37 s
gradients_fft:          593 calls, 80.67 s

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

# Date 2008-01-16 Time 03:01:58 PST -0800 (1200481318.48 s)
Start R-work = 0.4346, R-free = 0.4199 (no bulk solvent and anisotropic scale)
Final R-work = 0.1295, R-free = 0.1757 (no bulk solvent and anisotropic scale)

Start R-work = 0.4275, R-free = 0.4051
Final R-work = 0.1130, R-free = 0.1603